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Nyawo G, Naidoo C, Wu BG, Kwok B, Clemente JC, Li Y, Minnies S, Reeve B, Moodley S, John TJ, Karamchand S, Singh S, Pecararo A, Doubell A, Kyriakakis C, Warren R, Segal LN, Theron G. Bad company? The pericardium microbiome in people investigated for tuberculosis pericarditis in an HIV-prevalent setting. medRxiv 2024:2024.04.26.24306431. [PMID: 38712063 PMCID: PMC11071582 DOI: 10.1101/2024.04.26.24306431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Background The microbiome likely plays a role in tuberculosis (TB) pathogenesis. We evaluated the site-of-disease microbiome and predicted metagenome in people with presumptive tuberculous pericarditis, a major cause of mortality, and explored for the first time, the interaction between its association with C-reactive protein (CRP), a potential diagnostic biomarker and the site-of-disease microbiome in extrapulmonary TB. Methods People with effusions requiring diagnostic pericardiocentesis (n=139) provided background sampling controls and pericardial fluid (PF) for 16S rRNA gene sequencing analysed using QIIME2 and PICRUSt2. Blood was collected to measure CRP. Results PF from people with definite (dTB, n=91), probable (pTB, n=25), and non- (nTB, n=23) tuberculous pericarditis differed in β-diversity. dTBs were, vs. nTBs, Mycobacterium-, Lacticigenium-, and Kocuria- enriched. Within dTBs, HIV-positives were Mycobacterium-, Bifidobacterium- , Methylobacterium- , and Leptothrix -enriched vs. HIV-negatives and HIV-positive dTBs on ART were Mycobacterium - and Bifidobacterium -depleted vs. those not on ART. Compared to nTBs, dTBs exhibited short-chain fatty acid (SCFA) and mycobacterial metabolism microbial pathway enrichment. People with additional non-pericardial involvement had differentially PF taxa (e.g., Mycobacterium -enrichment and Streptococcus -depletion associated with pulmonary infiltrates). Mycobacterium reads were in 34% (31/91), 8% (2/25) and 17% (4/23) of dTBs, pTBs, and nTBs, respectively. β-diversity differed between patients with CRP above vs. below the median value ( Pseudomonas -depleted). There was no correlation between enriched taxa in dTBs and CRP. Conclusions PF is compositionally distinct based on TB status, HIV (and ART) status and dTBs are enriched in SCFA-associated taxa. The clinical significance of these findings, including mycobacterial reads in nTBs and pTBs, requires evaluation.
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Chiyaka TL, Nyawo GR, Naidoo C, Moodley S, Clemente JC, Malherbe ST, Warren R, Ku D, Segal LN, Theron G. A novel aerosol collection method shows the cough aeromicrobiome of people with tuberculosis is phylogenetically distinct from respiratory tract specimens. Res Sq 2024:rs.3.rs-4106141. [PMID: 38659922 PMCID: PMC11042404 DOI: 10.21203/rs.3.rs-4106141/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Background Tuberculosis (TB), a major cause of disease and antimicrobial resistance, is spread via aerosols. Aerosols have diagnostic potential and airborne-microbes other than Mycobacterium tuberculosis complex (MTBC) may influence transmission. We evaluated whether PneumoniaCheck (PMC), a commercial aerosol collection device, captures MTBC and the aeromicrobiome of people with TB. Methods PMC was done in sputum culture-positive people (≥30 forced coughs each, n=16) pre-treatment and PMC air reservoir (bag, corresponding to upper airways) and filter (lower airways) washes underwent Xpert MTB/RIF Ultra (Ultra) and 16S rRNA gene sequencing (sequencing also done on sputum). In a subset (n=6), PMC microbiota (bag, filter) was compared to oral washes and bronchoalveolar lavage fluid (BALF). Findings 54% (7/13) bags and 46% (6/14) filters were Ultra-positive. Sequencing read counts and microbial diversity did not differ across bags, filters, and sputum. However, microbial composition in bags (Sphingobium-, Corynebacterium-, Novosphingobium-enriched) and filters (Mycobacterium-, Sphingobium-, Corynebacterium-enriched) each differed vs. sputum. Furthermore, sequencing only detected Mycobacterium in bags and filters but not sputum. In the subset, bag and filter microbial diversity did not differ vs. oral washes or BALF but microbial composition differed. Bags vs. BALF were Sphingobium-enriched and Mycobacterium-, Streptococcus-, and Anaerosinus-depleted (Anaerosinus also depleted in filters vs. BALF). Compared to BALF, none of the aerosol-enriched taxa were enriched in oral washes or sputum. Interpretation PMC captures aerosols with Ultra-detectable MTBC and MTBC is more detectable in aerosols than sputum by sequencing. The aeromicrobiome is distinct from sputum, oral washes and BALF and contains differentially-enriched lower respiratory tract microbes.
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3
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Bianchimano P, Iwanowski K, Smith EM, Cantor A, Leone P, Bongers G, Gonzalez CG, Hongsup Y, Elias J, Weiner HL, Clemente JC, Tankou SK. Oral vancomycin treatment suppresses gut trypsin activity and preserves intestinal barrier function during EAE. iScience 2023; 26:108143. [PMID: 37915599 PMCID: PMC10616394 DOI: 10.1016/j.isci.2023.108143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/30/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
Studies have reported increased intestinal permeability in multiple sclerosis (MS) patients and its mouse model experimental autoimmune encephalomyelitis (EAE). However, the mechanisms driving increased intestinal permeability that in turn exacerbate neuroinflammation during EAE remain unclear. Here we showed that vancomycin preserved the integrity of the intestinal barrier, while also suppressing gut trypsin activity, enhancing the relative abundance of specific Lactobacilli and ameliorating disease during EAE. Furthermore, Lactobacilli enriched in the gut of vancomycin-treated EAE mice at day 3 post immunization negatively correlated with gut trypsin activity and EAE severity. In untreated EAE mice, we observed increased intestinal permeability and increased intestinal protease activated receptor 2 (PAR2) expression at day 3 post immunization. Prior studies have shown that trypsin increases intestinal permeability by activating PAR2. Our results suggest that the interaction between intestinal PAR2 and trypsin may be a key modulator of intestinal permeability and disease severity during EAE.
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Affiliation(s)
- Paola Bianchimano
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kacper Iwanowski
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma M. Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Cantor
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paola Leone
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerold Bongers
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos G. Gonzalez
- Department of Pharmacology, University of California San Diego, San Diego, CA 92093, USA
| | - Yoon Hongsup
- Institute of Clinical Neuroimmunology, Hospital and Biomedical Center of the Ludwig-Maximilian-University, Martinsried, Germany
- Hertie Senior Professor Group, Max-Plank-Institute of Neurobiology, Martinsried, Germany
| | - Joshua Elias
- Mass Spectrometry Platform, Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Howard L. Weiner
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jose C. Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephanie K. Tankou
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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4
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Sulaiman I, Wu BG, Chung M, Isaacs B, Tsay JCJ, Holub M, Barnett CR, Kwok B, Kugler MC, Natalini JG, Singh S, Li Y, Schluger R, Carpenito J, Collazo D, Perez L, Kyeremateng Y, Chang M, Campbell CD, Hansbro PM, Oppenheimer BW, Berger KI, Goldring RM, Koralov SB, Weiden MD, Xiao R, D’Armiento J, Clemente JC, Ghedin E, Segal LN. Lower Airway Dysbiosis Augments Lung Inflammatory Injury in Mild-to-Moderate Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2023; 208:1101-1114. [PMID: 37677136 PMCID: PMC10867925 DOI: 10.1164/rccm.202210-1865oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 09/07/2023] [Indexed: 09/09/2023] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) is associated with high morbidity, mortality, and healthcare costs. Cigarette smoke is a causative factor; however, not all heavy smokers develop COPD. Microbial colonization and infections are contributing factors to disease progression in advanced stages. Objectives: We investigated whether lower airway dysbiosis occurs in mild-to-moderate COPD and analyzed possible mechanistic contributions to COPD pathogenesis. Methods: We recruited 57 patients with a >10 pack-year smoking history: 26 had physiological evidence of COPD, and 31 had normal lung function (smoker control subjects). Bronchoscopy sampled the upper airways, lower airways, and environmental background. Samples were analyzed by 16S rRNA gene sequencing, whole genome, RNA metatranscriptome, and host RNA transcriptome. A preclinical mouse model was used to evaluate the contributions of cigarette smoke and dysbiosis on lower airway inflammatory injury. Measurements and Main Results: Compared with smoker control subjects, microbiome analyses showed that the lower airways of subjects with COPD were enriched with common oral commensals. The lower airway host transcriptomics demonstrated differences in markers of inflammation and tumorigenesis, such as upregulation of IL-17, IL-6, ERK/MAPK, PI3K, MUC1, and MUC4 in mild-to-moderate COPD. Finally, in a preclinical murine model exposed to cigarette smoke, lower airway dysbiosis with common oral commensals augments the inflammatory injury, revealing transcriptomic signatures similar to those observed in human subjects with COPD. Conclusions: Lower airway dysbiosis in the setting of smoke exposure contributes to inflammatory injury early in COPD. Targeting the lower airway microbiome in combination with smoking cessation may be of potential therapeutic relevance.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Benjamin G. Wu
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs (VA) New York Harbor Healthcare System, New York, New York
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Bradley Isaacs
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Jun-Chieh J. Tsay
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Veterans Affairs (VA) New York Harbor Healthcare System, New York, New York
| | - Meredith Holub
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Hartford Health Care, Hartford, Connecticut
| | - Clea R. Barnett
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Benjamin Kwok
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | | | - Jake G. Natalini
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Shivani Singh
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Rosemary Schluger
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Joseph Carpenito
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Destiny Collazo
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Luisanny Perez
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Yaa Kyeremateng
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Miao Chang
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Christina D. Campbell
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Sydney, New South Wales, Australia
| | | | - Kenneth I. Berger
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | | | | | - Michael D. Weiden
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
| | - Rui Xiao
- Department of Physiology and Cellular Biophysics, Columbia University School of Medicine, New York, New York; and
| | - Jeanine D’Armiento
- Department of Physiology and Cellular Biophysics, Columbia University School of Medicine, New York, New York; and
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Leopoldo N. Segal
- Division of Pulmonary and Critical Care Medicine
- Department of Medicine
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York University (NYU) Langone Health, New York, New York
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5
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Lee JJ, Piras E, Tamburini S, Bu K, Wallach DS, Remsen B, Cantor A, Kong J, Goetz D, Hoffman KW, Bonner M, Joe P, Mueller BR, Robinson-Papp J, Lotan E, Gonen O, Malaspina D, Clemente JC. Gut and oral microbiome modulate molecular and clinical markers of schizophrenia-related symptoms: A transdiagnostic, multilevel pilot study. Psychiatry Res 2023; 326:115279. [PMID: 37331068 PMCID: PMC10595250 DOI: 10.1016/j.psychres.2023.115279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/09/2023] [Accepted: 05/30/2023] [Indexed: 06/20/2023]
Abstract
Although increasing evidence links microbial dysbiosis with the risk for psychiatric symptoms through the microbiome-gut-brain axis (MGBA), the specific mechanisms remain poorly characterized. In a diagnostically heterogeneous group of treated psychiatric cases and nonpsychiatric controls, we characterized the gut and oral microbiome, plasma cytokines, and hippocampal inflammatory processes via proton magnetic resonance spectroscopic imaging (1H-MRSI). Using a transdiagnostic approach, these data were examined in association with schizophrenia-related symptoms measured by the Positive and Negative Syndrome Scale (PANSS). Psychiatric cases had significantly greater heterogeneity of gut alpha diversity and an enrichment of pathogenic taxa, like Veillonella and Prevotella, in the oral microbiome, which was an accurate classifier of phenotype. Cases exhibited significantly greater positive, negative, and general PANSS scores that uniquely correlated with bacterial taxa. Strong, positive correlations of bacterial taxa were also found with cytokines and hippocampal gliosis, dysmyelination, and excitatory neurotransmission. This pilot study supports the hypothesis that the MGBA influences psychiatric symptomatology in a transdiagnostic manner. The relative importance of the oral microbiome in peripheral and hippocampal inflammatory pathways was highlighted, suggesting opportunities for probiotics and oral health to diagnose and treat psychiatric conditions.
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Affiliation(s)
- Jakleen J Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Enrica Piras
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sabrina Tamburini
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David S Wallach
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Brooke Remsen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Adam Cantor
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jennifer Kong
- Academy for the Advancement of Science and Technology, Bergen County Academies, Hackensack, NJ, United States
| | - Deborah Goetz
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Kevin W Hoffman
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mharisi Bonner
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Peter Joe
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bridget R Mueller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jessica Robinson-Papp
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eyal Lotan
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Oded Gonen
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Dolores Malaspina
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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6
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Zhou L, Qiu W, Wang J, Zhao A, Zhou C, Sun T, Xiong Z, Cao P, Shen W, Chen J, Lai X, Zhao LH, Wu Y, Li M, Qiu F, Yu Y, Xu ZZ, Zhou H, Jia W, Liao Y, Retnakaran R, Krewski D, Wen SW, Clemente JC, Chen T, Xie RH, He Y. Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: A blinded randomized controlled trial. Cell Host Microbe 2023; 31:1232-1247.e5. [PMID: 37327780 DOI: 10.1016/j.chom.2023.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/22/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
The microbiomes of cesarean-born infants differ from vaginally delivered infants and are associated with increased disease risks. Vaginal microbiota transfer (VMT) to newborns may reverse C-section-related microbiome disturbances. Here, we evaluated the effect of VMT by exposing newborns to maternal vaginal fluids and assessing neurodevelopment, as well as the fecal microbiota and metabolome. Sixty-eight cesarean-delivered infants were randomly assigned a VMT or saline gauze intervention immediately after delivery in a triple-blind manner (ChiCTR2000031326). Adverse events were not significantly different between the two groups. Infant neurodevelopment, as measured by the Ages and Stages Questionnaire (ASQ-3) score at 6 months, was significantly higher with VMT than saline. VMT significantly accelerated gut microbiota maturation and regulated levels of certain fecal metabolites and metabolic functions, including carbohydrate, energy, and amino acid metabolisms, within 42 days after birth. Overall, VMT is likely safe and may partially normalize neurodevelopment and the fecal microbiome in cesarean-delivered infants.
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Affiliation(s)
- Lepeng Zhou
- School of Nursing, Affiliated Foshan Maternity & Child Healthcare Hospital, Department of Laboratory Medicine in Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China; School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China; Department of Nursing, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Wen Qiu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China
| | - Jie Wang
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Aihua Zhao
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Chuhui Zhou
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Tao Sun
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Ziyu Xiong
- Department of Nursing, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Peihua Cao
- Clinical Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wei Shen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; Department of Neonatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jingfen Chen
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Xiaolu Lai
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Liu-Hong Zhao
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Yue Wu
- Department of Cardiology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Meng Li
- Department of Obstetrics, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Feng Qiu
- Department of Laboratory Medicine, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Yanhong Yu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Zhenjiang Zech Xu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; State Key Laboratory of Food Science and Technology, Institute of Nutrition and College of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wei Jia
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yan Liao
- Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
| | - Ravi Retnakaran
- Leadership Sinai Centre for Diabetes, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Division of Endocrinology, University of Toronto, Toronto, ON M5S 2E8, Canada
| | - Daniel Krewski
- McLaughlin Centre for Population Health Risk Assessment, Faculty of Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Risk Science International, Ottawa, ON K1P 5J6, Canada; School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Shi Wu Wen
- Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Department of Obstetrics and Gynecology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Jose C Clemente
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Tianlu Chen
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China.
| | - Ri-Hua Xie
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China.
| | - Yan He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Clinical Research Center for Laboratory Medicine, Guangzhou, Guangdong 510033, China.
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7
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Luu HN, Tran CTD, Wang R, Nguyen MVT, Tran MT, Tuong TTV, Tran QH, Le LC, Pham HTT, Vu HH, Bui NC, Ha HTT, Trinh DT, Thomas CE, Adams-Haduch J, Velikokhatnaya L, Schoen RE, Xie G, Jia W, Boffetta P, Clemente JC, Yuan JM. Associations between Ileal Juice Bile Acids and Colorectal Advanced Adenoma. Nutrients 2023; 15:2930. [PMID: 37447256 DOI: 10.3390/nu15132930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND There is an urgent need to identify biomarkers for advanced adenoma, an important precursor of colorectal cancer (CRC). We aimed to determine alterations in ileal juice bile acids associated with colorectal advanced adenoma. METHODS We quantified a comprehensive panel of primary and secondary bile acids and their conjugates using an ultraperformance liquid chromatography triple-quadrupole mass spectrometric assay in ileal juice collected at colonoscopy from 46 study subjects (i.e., 14 biopsy-confirmed advanced adenomas and 32 controls free of adenoma or cancer). Using analysis of covariance (ANCOVA), we examined the differences in bile acid concentrations by disease status, adjusting for age, sex, body mass index, smoking status and type 2 diabetes. RESULTS The concentrations of hyodeoxycholic acid (HCA) species in ileal juice of the advanced adenoma patients (geometric mean = 4501.9 nM) were significantly higher than those of controls (geometric mean = 1292.3 nM, p = 0.001). The relative abundance of ursodeoxycholic acid (UDCA) in total bile acids was significantly reduced in cases than controls (0.73% in cases vs. 1.33% in controls; p = 0.046). No significant difference between cases and controls was observed for concentrations of total or specific primary bile acids (i.e., cholic acid (CA), chenodeoxycholic acid (CDCA) and their glycine- and taurine-conjugates) and total and specific major secondary bile acids (i.e., deoxycholic acid and lithocholic acid). CONCLUSIONS Colorectal advanced adenoma was associated with altered bile acids in ileal juice. The HCA species may promote the development of colorectal advanced adenoma, whereas gut microbiota responsible for the conversion of CDCA to UDCA may protect against it. Our findings have important implications for the use of bile acids as biomarkers in early detection of colorectal cancer.
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Affiliation(s)
- Hung N Luu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Chi Thi-Du Tran
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
- College of Health Sciences, VinUniversity (VinUni), Hanoi 10000, Vietnam
- Center of Applied Sciences, Regenerative Medicine and Advanced Technologies, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Renwei Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Mai Vu-Tuyet Nguyen
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Mo Thi Tran
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Thuy Thi-Van Tuong
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Quang Hong Tran
- Vietnam Colorectal Cancer and Polyps Research, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Linh Cu Le
- College of Health Sciences, VinUniversity (VinUni), Hanoi 10000, Vietnam
| | - Huong Thi-Thu Pham
- Department of Gastroenterology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Hien Huy Vu
- Department of Gastroenterology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Nam Chi Bui
- Department of Gastroenterology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Hien Thi-Thu Ha
- Department of Cytopathology, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Dung Tuan Trinh
- Department of Cytopathology, Vinmec Healthcare System, Hanoi 10000, Vietnam
- Department of Cytopathology, Tam Anh General Hospital, Hanoi 10000, Vietnam
| | - Claire E Thomas
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | | | | | - Robert E Schoen
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Guoxiang Xie
- University of Hawai'i Cancer Center, University of Hawaii, Honolulu, HI 96813, USA
| | - Wei Jia
- University of Hawai'i Cancer Center, University of Hawaii, Honolulu, HI 96813, USA
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Jose C Clemente
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian-Min Yuan
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
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8
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Boix-Amorós A, Badri MH, Manasson J, Blank RB, Haberman RH, Neimann AL, Girija PV, Jimenez Hernandez A, Heguy A, Koralov SB, Bonneau R, Clemente JC, Scher JU. Alterations in the cutaneous microbiome of patients with psoriasis and psoriatic arthritis reveal similarities between non-lesional and lesional skin. Ann Rheum Dis 2023; 82:507-514. [PMID: 36600182 DOI: 10.1136/ard-2022-223389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To investigate the cutaneous microbiome spanning the entire psoriatic disease spectrum, and to evaluate distinguishing features of psoriasis (PsO) and psoriatic arthritis (PsA). METHODS Skin swabs were collected from upper and lower extremities of healthy individuals and patients with PsO and PsA. Psoriatic patients contributed both lesional (L) and contralateral non-lesional (NL) samples. Microbiota were analysed using 16S rRNA sequencing. RESULTS Compared with healthy skin, alpha diversity in psoriatic NL and L skin was significantly reduced (p<0.05) and samples clustered separately in plots of beta diversity (p<0.05). Kocuria and Cutibacterium were enriched in healthy subjects, while Staphylococcus was enriched in psoriatic disease. Microbe-microbe association networks revealed a higher degree of similarity between psoriatic NL and L skin compared with healthy skin despite the absence of clinically evident inflammation. Moreover, the relative abundance of Corynebacterium was higher in NL PsA samples compared with NL PsO samples (p<0.05), potentially serving as a biomarker for disease progression. CONCLUSIONS These findings show differences in diversity, bacterial composition and microbe-microbe interactions between healthy and psoriatic skin, both L and NL. We further identified bacterial biomarkers that differentiate disease phenotypes, which could potentially aid in predicting the transition from PsO to PsA.
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Affiliation(s)
- Alba Boix-Amorós
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michelle H Badri
- Department of Biology, New York University, New York, New York, USA
| | - Julia Manasson
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Rebecca B Blank
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Rebecca H Haberman
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Andrea L Neimann
- Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, New York, USA
| | - Parvathy V Girija
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Anthony Jimenez Hernandez
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
| | - Adriana Heguy
- NYU Langone Health Genome Technology Center, Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
| | - Sergei B Koralov
- Department of Pathology, New York University Grossman School of Medicine, New York, New York, USA
| | - Richard Bonneau
- Department of Biology, New York University, New York, New York, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Jose C Clemente
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jose U Scher
- Division of Rheumatology, Department of Medicine and Psoriatic Arthritis Center, New York University Grossman School of Medicine, New York, New York, USA
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9
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Nyawo GR, Naidoo CC, Wu B, Sulaiman I, Clemente JC, Li Y, Minnies S, Reeve BWP, Moodley S, Rautenbach C, Wright C, Singh S, Whitelaw A, Schubert P, Warren R, Segal L, Theron G. More than Mycobacterium tuberculosis: site-of-disease microbial communities, and their functional and clinical profiles in tuberculous lymphadenitis. Thorax 2023; 78:297-308. [PMID: 36598079 PMCID: PMC9957952 DOI: 10.1136/thorax-2022-219103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/31/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Lymphadenitis is the most common extrapulmonary tuberculosis (EPTB) manifestation. The microbiome is important to human health but uninvestigated in EPTB. We profiled the site-of-disease lymph node microbiome in tuberculosis lymphadenitis (TBL). METHODS Fine-needle aspiration biopsies were collected from 158 pretreatment presumptive TBL patients in Cape Town, South Africa. 16S Illumina MiSeq rRNA gene sequencing was done. RESULTS We analysed 89 definite TBLs (dTBLs) and 61 non-TBLs (nTBLs), which had similar α- but different β-diversities (p=0.001). Clustering identified five lymphotypes prior to TB status stratification: Mycobacterium-dominant, Prevotella-dominant and Streptococcus-dominant lymphotypes were more frequent in dTBLs whereas a Corynebacterium-dominant lymphotype and a fifth lymphotype (no dominant taxon) were more frequent in nTBLs. When restricted to dTBLs, clustering identified a Mycobacterium-dominant lymphotype with low α-diversity and non-Mycobacterium-dominated lymphotypes (termed Prevotella-Corynebacterium, Prevotella-Streptococcus). The Mycobacterium dTBL lymphotype was associated with HIV-positivity and features characteristic of severe lymphadenitis (eg, larger nodes). dTBL microbial communities were enriched with potentially proinflammatory microbial short-chain fatty acid metabolic pathways (propanoate, butanoate) vs nTBLs. 11% (7/61) of nTBLs had Mycobacterium reads BLAST-confirmed as Mycobacterium tuberculosis complex. CONCLUSIONS TBL at the site-of-disease is not microbially homogeneous. Distinct microbial community clusters exist that, in our setting, are associated with different clinical characteristics, and immunomodulatory potentials. Non-Mycobacterium-dominated dTBL lymphotypes, which contain taxa potentially targeted by TB treatment, were associated with milder, potentially earlier stage disease. These investigations lay foundations for studying the microbiome's role in lymphatic TB. The long-term clinical significance of these lymphotypes requires prospective validation.
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Affiliation(s)
- Georgina R Nyawo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Charissa C Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Benjamin Wu
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Imran Sulaiman
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Stephanie Minnies
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Byron W P Reeve
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Suventha Moodley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Cornelia Rautenbach
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Colleen Wright
- Division Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Shivani Singh
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Andrew Whitelaw
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Pawel Schubert
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
- Division Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Robin Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Leopoldo Segal
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
- African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, Western Cape, South Africa
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10
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Bianchimano P, Britton GJ, Wallach DS, Smith EM, Cox LM, Liu S, Iwanowski K, Weiner HL, Faith JJ, Clemente JC, Tankou SK. Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis. Microbiome 2022; 10:174. [PMID: 36253847 PMCID: PMC9575236 DOI: 10.1186/s40168-022-01364-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The gut microbiome plays an important role in autoimmunity including multiple sclerosis and its mouse model called experimental autoimmune encephalomyelitis (EAE). Prior studies have demonstrated that the multiple sclerosis gut microbiota can contribute to disease, hence making it a potential therapeutic target. In addition, antibiotic treatment has been shown to ameliorate disease in the EAE mouse model of multiple sclerosis. Yet, to this date, the mechanisms mediating these antibiotic effects are not understood. Furthermore, there is no consensus on the gut-derived bacterial strains that drive neuroinflammation in multiple sclerosis. RESULTS Here, we characterized the gut microbiome of untreated and vancomycin-treated EAE mice over time to identify bacteria with neuroimmunomodulatory potential. We observed alterations in the gut microbiota composition following EAE induction. We found that vancomycin treatment ameliorates EAE, and that this protective effect is mediated via the microbiota. Notably, we observed increased abundance of bacteria known to be strong inducers of regulatory T cells, including members of Clostridium clusters XIVa and XVIII in vancomycin-treated mice during the presymptomatic phase of EAE, as well as at disease peak. We identified 50 bacterial taxa that correlate with EAE severity. Interestingly, several of these taxa exist in the human gut, and some of them have been implicated in multiple sclerosis including Anaerotruncus colihominis, a butyrate producer, which had a positive correlation with disease severity. We found that Anaerotruncus colihominis ameliorates EAE, and this is associated with induction of RORγt+ regulatory T cells in the mesenteric lymph nodes. CONCLUSIONS We identified vancomycin as a potent modulator of the gut-brain axis by promoting the proliferation of bacterial species that induce regulatory T cells. In addition, our findings reveal 50 gut commensals as regulator of the gut-brain axis that can be used to further characterize pathogenic and beneficial host-microbiota interactions in multiple sclerosis patients. Our findings suggest that elevated Anaerotruncus colihominis in multiple sclerosis patients may represent a protective mechanism associated with recovery from the disease. Video Abstract.
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Affiliation(s)
- Paola Bianchimano
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David S Wallach
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma M Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
| | - Laura M Cox
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Shirong Liu
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Present address: Department of Medical Oncology, Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Kacper Iwanowski
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose C Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephanie K Tankou
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA.
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11
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Boix-Amorós A, Monaco H, Sambataro E, Clemente JC. Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease. Gut Microbes 2022; 14:2107866. [PMID: 36104776 PMCID: PMC9481095 DOI: 10.1080/19490976.2022.2107866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.
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Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Hilary Monaco
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Elisa Sambataro
- Department of Biological Sciences, CUNY Hunter College, New York, NY, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA,CONTACT Jose C. Clemente Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY10029USA
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12
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Joe P, Clemente JC, Piras E, Wallach DS, Robinson-Papp J, Boka E, Remsen B, Bonner M, Kimhy D, Goetz D, Hoffman K, Lee J, Ruby E, Fendrich S, Gonen O, Malaspina D. An integrative study of the microbiome gut-brain-axis and hippocampal inflammation in psychosis: Persistent effects from mode of birth. Schizophr Res 2022; 247:101-115. [PMID: 34625336 PMCID: PMC8980116 DOI: 10.1016/j.schres.2021.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
The mechanism producing psychosis appears to include hippocampal inflammation, which could be associated with the microbiome-gut-brain-axis (MGBS). To test this hypothesis we are conducting a multidisciplinary study, herein described. The procedures are illustrated with testing of a single subject and group level information on the impact of C-section birth are presented. METHOD Study subjects undergo research diagnostic interviews and symptom assessments to be categorized into one of 3 study groups: psychosis, nonpsychotic affective disorder or healthy control. Hippocampal volume and metabolite concentrations are assessed using 3-dimensional, multi-voxel H1 Magnetic Resonance Imaging (MRSI) encompassing all gray matter in the entire hippocampal volume. Rich self-report information is obtained with the PROMIS interview, which was developed by the NIH Commons for research in chronic conditions. Early trauma is assessed and cognition is quantitated using the MATRICS. The method also includes the most comprehensive autonomic nervous system (ANS) battery used to date in psychiatric research. Stool and oral samples are obtained for microbiome assessments and cytokines and other substances are measured in blood samples. RESULTS Group level preliminary data shows that C-section birth is associated with higher concentrations of GLX, a glutamate related hippocampal neurotransmitter in psychotic cases, worse symptoms in affective disorder cases and smaller hippocampal volume in controls. CONCLUSION Mode of birth appears to have persistent influences through adulthood. The methodology described for this study will define pathways through which the MGBA may influence the risk for psychiatric disorders.
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Affiliation(s)
- Peter Joe
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA.
| | - Jose C Clemente
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Enrica Piras
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - David S Wallach
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | | | - Emeka Boka
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
| | - Brooke Remsen
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA; Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Mharisi Bonner
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
| | - David Kimhy
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
| | - Deborah Goetz
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
| | - Kevin Hoffman
- Perelman School of Medicine, University of Pennsylvania, Department of Psychiatry, Philadelphia, PA, USA
| | - Jakleen Lee
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Eugene Ruby
- University of California, Los Angeles, Department of Psychology, Los Angeles, CA, USA
| | - Sarah Fendrich
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA; Perelman School of Medicine, University of Pennsylvania, Center for Health Care Incentives & Behavioral Economics, Philadelphia, PA, USA
| | - Oded Gonen
- NYU Langone Medical Center, Department of Radiology, New York, NY, USA
| | - Dolores Malaspina
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
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13
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Puthota J, Alatorre A, Walsh S, Clemente JC, Malaspina D, Spicer J. Prenatal ambient temperature and risk for schizophrenia. Schizophr Res 2022; 247:67-83. [PMID: 34620533 PMCID: PMC8977400 DOI: 10.1016/j.schres.2021.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/21/2022]
Abstract
OBJECTIVE We conducted a systematic review of the published literature to test the hypothesis that maternal exposure to extremes of ambient temperatures during pregnancy is associated with the risk for psychiatric disorders or congenital malformations in offspring, both of which are indicative of perturbations of fetal neurodevelopment. METHOD This study was conducted in accordance with the recommendations outlined in the Meta-analysis of Observational Studies in Epidemiology (MOOSE) reporting proposal. Electronic databases (Ovid MEDLINE, Ovid Embase, Ovid PsycINFO, Ovid Global Health, Web of Science, and Cochrane Library) were searched. Four independent reviewers selected studies with the following criteria: (1) prenatal maternal ambient temperature exposure; (2) outcome of offspring psychiatric disorder or congenital defects; (3) empirical study; (4) full-length article, no conference presentations or abstracts. RESULTS Twenty-two studies met criteria and one was added from a reference list (n = 23). Of these, schizophrenia (n = 5), anorexia nervosa (n = 3) and congenital cardiovascular malformations (n = 6) studies were the most common. Each of these categories showed some evidence of association with an early pregnancy maternal ambient heat exposure effect, with other evidence for a late pregnancy cold effect. CONCLUSION Some evidence supports a role for early pregnancy maternal exposure to extreme ambient heat in the development of psychiatric disorders, but large-scale, prospective cohort data on individual births is essential. Optimal studies will be conducted in seasonally variable climates, accounting for actual maternal residence over the pregnancy and at parturition, local environmental temperature records, and appropriate covariates, similar to studies identified by this systematic review for congenital malformations.
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Affiliation(s)
| | - Andrea Alatorre
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, United States of America
| | - Samantha Walsh
- Levy Library, Icahn School of Medicine at Mount Sinai, United States of America
| | - Jose C Clemente
- Department of Genetics & Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, United States of America
| | - Dolores Malaspina
- Departments of Psychiatry, Neuroscience, Genetics & Genomics, Icahn School of Medicine at Mount Sinai, United States of America
| | - Julie Spicer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, United States of America.
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14
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Fendrich SJ, Koralnik LR, Bonner M, Goetz D, Joe P, Lee J, Mueller B, Robinson-Papp J, Gonen O, Clemente JC, Malaspina D. Patient-reported exposures and outcomes link the gut-brain axis and inflammatory pathways to specific symptoms of severe mental illness. Psychiatry Res 2022; 312:114526. [PMID: 35462090 DOI: 10.1016/j.psychres.2022.114526] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/16/2022] [Accepted: 03/20/2022] [Indexed: 02/08/2023]
Abstract
UNLABELLED We developed a "gut-brain-axis questionnaire" (GBAQ) to obtain standardized person-specific "review of systems" data for microbiome-gut-brain-axis studies. Individual items were compared to PANSS symptom measures using dimensional, transdiagnostic and traditional categorical approaches. METHOD Forty psychotic participants, independent of diagnoses, and 42 without psychosis (18 nonpsychotic affective disorders, 24 healthy controls) completed the GBAQ and underwent research diagnostic and symptom assessments. The PANSS scales and its dysphoric mood, autistic preoccupation and activation factors were computed. RESULTS Transdiagnostic analyses robustly linked psychosis severity to constipation (p<.001), and Negative (p=.045) and General Psychopathology scores (p=.016) with bowel hypomotility. Activation factor scores predicted numbers of psychiatric (p=.009) and medical conditions (p=.003), BMI (p=.003), skin (p<.001) and other conditions. Categorical analyses comparing psychotic, nonpsychotic and control groups revealed behavioral differences: cigarette smoking (p=.013), alcohol use (p=.007), diet (p's <.05), exercise (p<.001). All subjects accurately self-reported their diagnosis. CONCLUSIONS The GBAQ is a promising tool. Transdiagnostic analyses associated psychotic symptoms to gut hypomotility, indicative of low gut vagal tone, consistent with reduced cardiovagal activity in psychosis. Activation, similar to delirium symptoms, predicted medical comorbidity and systemic inflammatory conditions. Group level comparisons only showed behavioral differences. Underpinnings of psychiatric disorders may include reduced gut vagal function, producing psychosis, and systemic inflammation, impacting risks for psychotic and nonpsychotic conditions.
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Affiliation(s)
- Sarah J Fendrich
- Departments of Psychiatry, Neuroscience, and Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Medical Ethics and Health Policy, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lauren R Koralnik
- Department of Psychology, Barnard College of Columbia University, New York, New York, USA
| | - Mharisi Bonner
- Departments of Psychiatry, Neuroscience, and Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Deborah Goetz
- Departments of Psychiatry, Neuroscience, and Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Peter Joe
- Departments of Psychiatry, Neuroscience, and Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jakleen Lee
- Departments of Psychiatry, Neuroscience, and Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bridget Mueller
- Departments of Psychiatry, Neuroscience, and Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessica Robinson-Papp
- Departments of Psychiatry, Neuroscience, and Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Oded Gonen
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dolores Malaspina
- Departments of Psychiatry, Neuroscience, and Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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15
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Aggarwala V, Mogno I, Li Z, Yang C, Britton GJ, Chen-Liaw A, Mitcham J, Bongers G, Gevers D, Clemente JC, Colombel JF, Grinspan A, Faith J. Author Correction: Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes. Nat Microbiol 2022; 7:736. [PMID: 35388189 PMCID: PMC9064791 DOI: 10.1038/s41564-022-01118-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Varun Aggarwala
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhihua Li
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chao Yang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Josephine Mitcham
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerold Bongers
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Jose C Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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16
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Centa M, Weinstein EG, Clemente JC, Faith JJ, Fiel MI, Lyallpuri R, Herbin O, Alexandropoulos K. Impaired central tolerance induces changes in the gut microbiota that exacerbate autoimmune hepatitis. J Autoimmun 2022; 128:102808. [PMID: 35276587 PMCID: PMC8963681 DOI: 10.1016/j.jaut.2022.102808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/10/2022] [Accepted: 02/19/2022] [Indexed: 12/18/2022]
Abstract
Medullary thymic epithelial cells (mTECs) induce T cell tolerance in the thymus through the elimination of self-reactive thymocytes. Commensal bacteria are also critical for shaping T cell responses in the gut and distal organs. We previously showed that mice depleted of mTECs (Traf6ΔTEC) generated autoreactive T cells and developed autoimmune hepatitis (AIH). In this report, we found that Toll-like receptor (TLR)-mediated microbial sensing on liver hematopoietic cells and the gut microbiota contributed to AIH development in Traf6ΔTEC mice. While adoptive transfer of thymic Traf6ΔTEC T cells in immune-deficient mice was sufficient for AIH development, colonization of germ-free mice with Traf6ΔTEC microbiota failed to induce AIH, suggesting that the gut microbiota contributes to but is not sufficient for AIH development. Microbiota-mediated exacerbation of AIH associated with increased numbers of hepatic Foxp3+ T cells and their increase was proportional to the degree of inflammation. The contribution of the gut microbiota to AIH development associated with an altered microbial signature whose composition was influenced by the qualitative nature of the thymic T cell compartment. These results suggest that aberrant selection of T cells in the thymus can induce changes in the gut microbiota that lead to exacerbation of organ-specific autoimmunity and AIH. Our results add to our understanding of the mechanisms of AIH development and create a platform towards developing novel therapeutic approaches for treating this disease.
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Affiliation(s)
- Monica Centa
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jose C Clemente
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robby Lyallpuri
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Konstantina Alexandropoulos
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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17
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Bu K, Wallach DS, Wilson Z, Shen N, Segal LN, Bagiella E, Clemente JC. Identifying correlations driven by influential observations in large datasets. Brief Bioinform 2021; 23:6447676. [PMID: 34864851 DOI: 10.1093/bib/bbab482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/28/2021] [Accepted: 10/23/2021] [Indexed: 12/16/2022] Open
Abstract
Although high-throughput data allow researchers to interrogate thousands of variables simultaneously, it can also introduce a significant number of spurious results. Here we demonstrate that correlation analysis of large datasets can yield numerous false positives due to the presence of outliers that canonical methods fail to identify. We present Correlations Under The InfluencE (CUTIE), an open-source jackknifing-based method to detect such cases with both parametric and non-parametric correlation measures, and which can also uniquely rescue correlations not originally deemed significant or with incorrect sign. Our approach can additionally be used to identify variables or samples that induce these false correlations in high proportion. A meta-analysis of various omics datasets using CUTIE reveals that this issue is pervasive across different domains, although microbiome data are particularly susceptible to it. Although the significance of a correlation eventually depends on the thresholds used, our approach provides an efficient way to automatically identify those that warrant closer examination in very large datasets.
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Affiliation(s)
- Kevin Bu
- Department of Genetics and Data Science, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - David S Wallach
- Department of Genetics and Data Science, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Zach Wilson
- Department of Genetics and Data Science, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Nan Shen
- Department of Genetics and Data Science, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Emilia Bagiella
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose C Clemente
- Department of Genetics and Data Science, Icahn School of Medicine at Mount Sinai. New York, NY, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
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18
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Seppo AE, Bu K, Jumabaeva M, Thakar J, Choudhury RA, Yonemitsu C, Bode L, Martina CA, Allen M, Tamburini S, Piras E, Wallach DS, Looney RJ, Clemente JC, Järvinen KM. Infant gut microbiome is enriched with Bifidobacterium longum ssp. infantis in Old Order Mennonites with traditional farming lifestyle. Allergy 2021; 76:3489-3503. [PMID: 33905556 DOI: 10.1111/all.14877] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/16/2021] [Accepted: 03/24/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Growing up on traditional, single-family farms is associated with protection against asthma in school age, but the mechanisms against early manifestations of atopic disease are largely unknown. We sought determine the gut microbiome and metabolome composition in rural Old Order Mennonite (OOM) infants at low risk and Rochester, NY urban/suburban infants at high risk for atopic diseases. METHODS In a cohort of 65 OOM and 39 Rochester mother-infant pairs, 101 infant stool and 61 human milk samples were assessed by 16S rRNA gene sequencing for microbiome composition and qPCR to quantify Bifidobacterium spp. and B. longum ssp. infantis (B. infantis), a consumer of human milk oligosaccharides (HMOs). Fatty acids (FAs) were analyzed in 34 stool and human 24 milk samples. Diagnoses and symptoms of atopic diseases by 3 years of age were assessed by telephone. RESULTS At a median age of 2 months, stool was enriched with Bifidobacteriaceae, Clostridiaceae, and Aerococcaceae in the OOM compared with Rochester infants. B. infantis was more abundant (p < .001) and prevalent, detected in 70% of OOM compared with 21% of Rochester infants (p < .001). Stool colonized with B. infantis had higher levels of lactate and several medium- to long/odd-chain FAs. In contrast, paired human milk was enriched with a distinct set of FAs including butyrate. Atopic diseases were reported in 6.5% of OOM and 35% of Rochester children (p < .001). CONCLUSION A high rate of B. infantis colonization, similar to that seen in developing countries, is found in the OOM at low risk for atopic diseases.
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Affiliation(s)
- Antti E. Seppo
- Division of Allergy and Immunology Center for Food Allergy Department of Pediatrics University of Rochester School of Medicine and Dentistry Golisano Children's Hospital Rochester New York USA
| | - Kevin Bu
- Department of Genetics and Genomic Sciences Icahn Institute for Data Science and Genomic Technology Precision Immunology Institute Icahn School of Medicine at Mount Sinai New York City NY USA
| | - Madina Jumabaeva
- Division of Allergy and Immunology Center for Food Allergy Department of Pediatrics University of Rochester School of Medicine and Dentistry Golisano Children's Hospital Rochester New York USA
| | - Juilee Thakar
- Department of Microbiology and Immunology and Department of Biostatistics University of Rochester School of Medicine and Dentistry Rochester New York USA
| | - Rakin A. Choudhury
- Department of Microbiology and Immunology and Department of Biostatistics University of Rochester School of Medicine and Dentistry Rochester New York USA
| | - Chloe Yonemitsu
- Division of Neonatology and Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of California San Diego La Jolla California USA
| | - Lars Bode
- Division of Neonatology and Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of California San Diego La Jolla California USA
- Mother‐Milk‐Infant Center of Research Excellence (MOMI CORE) University of California, San Diego La Jolla California USA
| | - Camille A. Martina
- Department of Public Health & Environmental Medicine University of Rochester School of Medicine and Dentistry Rochester New York USA
| | - Maria Allen
- Division of Allergy, Immunology, and Rheumatology Department of Medicine University of Rochester School of Medicine and Dentistry Rochester New York USA
| | - Sabrina Tamburini
- Department of Genetics and Genomic Sciences Icahn Institute for Data Science and Genomic Technology Precision Immunology Institute Icahn School of Medicine at Mount Sinai New York City NY USA
| | - Enrica Piras
- Department of Genetics and Genomic Sciences Icahn Institute for Data Science and Genomic Technology Precision Immunology Institute Icahn School of Medicine at Mount Sinai New York City NY USA
| | - David S. Wallach
- Department of Genetics and Genomic Sciences Icahn Institute for Data Science and Genomic Technology Precision Immunology Institute Icahn School of Medicine at Mount Sinai New York City NY USA
| | - R. John Looney
- Division of Allergy, Immunology, and Rheumatology Department of Medicine University of Rochester School of Medicine and Dentistry Rochester New York USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences Icahn Institute for Data Science and Genomic Technology Precision Immunology Institute Icahn School of Medicine at Mount Sinai New York City NY USA
| | - Kirsi M. Järvinen
- Division of Allergy and Immunology Center for Food Allergy Department of Pediatrics University of Rochester School of Medicine and Dentistry Golisano Children's Hospital Rochester New York USA
- Department of Microbiology and Immunology University of Rochester School of Medicine and Dentistry Rochester New York USA
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19
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Boix-Amorós A, Piras E, Bu K, Wallach D, Stapylton M, Fernández-Sesma A, Malaspina D, Clemente JC. Viral Inactivation Impacts Microbiome Estimates in a Tissue-Specific Manner. mSystems 2021; 6:e0067421. [PMID: 34609165 PMCID: PMC8547476 DOI: 10.1128/msystems.00674-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/08/2021] [Indexed: 11/20/2022] Open
Abstract
The global emergence of novel pathogenic viruses presents an important challenge for research, as high biosafety levels are required to process samples. While inactivation of infectious agents facilitates the use of less stringent safety conditions, its effect on other biological entities of interest present in the sample is generally unknown. Here, we analyzed the effect of five inactivation methods (heat, ethanol, formaldehyde, psoralen, and TRIzol) on microbiome composition and diversity in samples collected from four different body sites (gut, nasal, oral, and skin) and compared them against untreated samples from the same tissues. We performed 16S rRNA gene sequencing and estimated abundance and diversity of bacterial taxa present in all samples. Nasal and skin samples were the most affected by inactivation, with ethanol and TRIzol inducing the largest changes in composition, and heat, formaldehyde, TRIzol, and psoralen inducing the largest changes in diversity. Oral and stool microbiomes were more robust to inactivation, with no significant changes in diversity and only moderate changes in composition. Firmicutes was the taxonomic group least affected by inactivation, while Bacteroidetes had a notable enrichment in nasal samples and moderate enrichment in fecal and oral samples. Actinobacteria were more notably depleted in fecal and skin samples, and Proteobacteria exhibited a more variable behavior depending on sample type and inactivation method. Overall, our results demonstrate that inactivation methods can alter the microbiome in a tissue-specific manner and that careful consideration should be given to the choice of method based on the sample type under study. IMPORTANCE Understanding how viral infections impact and are modulated by the microbiome is an important problem in basic research but is also of high clinical relevance under the current pandemic. To facilitate the study of interactions between microbial communities and pathogenic viruses under safe conditions, the infectious agent is generally inactivated prior to processing samples. The effect of this inactivation process in the microbiome is, however, unknown. Further, it is unclear whether biases introduced by inactivation methods are dependent on the sample type under study. Estimating the magnitude and nature of the changes induced by different methods in samples collected from various body sites thus provides important information for current and future studies that require inactivation of pathogenic agents.
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Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Enrica Piras
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Wallach
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matthew Stapylton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Fernández-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai. New York, New York, USA
| | - Dolores Malaspina
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai. New York, New York, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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20
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Seppo AE, Choudhury R, Pizzarello C, Palli R, Fridy S, Rajani PS, Stern J, Martina C, Yonemitsu C, Bode L, Bu K, Tamburini S, Piras E, Wallach DS, Allen M, Looney RJ, Clemente JC, Thakar J, Järvinen KM. Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition. Front Immunol 2021; 12:741513. [PMID: 34707611 PMCID: PMC8545059 DOI: 10.3389/fimmu.2021.741513] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/01/2021] [Indexed: 01/11/2023] Open
Abstract
Background In addition to farming exposures in childhood, maternal farming exposures provide strong protection against allergic disease in their children; however, the effect of farming lifestyle on human milk (HM) composition is unknown. Objective This study aims to characterize the maternal immune effects of Old Order Mennonite (OOM) traditional farming lifestyle when compared with Rochester (ROC) families at higher risk for asthma and allergic diseases using HM as a proxy. Methods HM samples collected at median 2 months of lactation from 52 OOM and 29 ROC mothers were assayed for IgA1 and IgA2 antibodies, cytokines, endotoxin, HM oligosaccharides (HMOs), and targeted fatty acid (FA) metabolites. Development of early childhood atopic diseases in children by 3 years of age was assessed. In addition to group comparisons, systems level network analysis was performed to identify communities of multiple HM factors in ROC and OOM lifestyle. Results HM contains IgA1 and IgA2 antibodies broadly recognizing food, inhalant, and bacterial antigens. OOM HM has significantly higher levels of IgA to peanut, ovalbumin, dust mites, and Streptococcus equii as well TGF-β2, and IFN-λ3. A strong correlation occurred between maternal antibiotic use and levels of several HMOs. Path-based analysis of HMOs shows lower activity in the path involving lactoneohexaose (LNH) in the OOM as well as higher levels of lacto-N-neotetraose (LNnT) and two long-chain FAs C-18OH (stearic acid) and C-23OH (tricosanoic acid) compared with Rochester HM. OOM and Rochester milk formed five different clusters, e.g., butyrate production was associated with Prevotellaceae, Veillonellaceae, and Micrococcaceae cluster. Development of atopic disease in early childhood was more common in Rochester and associated with lower levels of total IgA, IgA2 to dust mite, as well as of TSLP. Conclusion Traditional, agrarian lifestyle, and antibiotic use are strong regulators of maternally derived immune and metabolic factors, which may have downstream implications for postnatal developmental programming of infant's gut microbiome and immune system.
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Affiliation(s)
- Antti E. Seppo
- Division of Allergy and Immunology and Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry and Golisano Children’s Hospital, Rochester, NY, United States
| | - Rakin Choudhury
- Department of Microbiology and Immunology and Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Catherine Pizzarello
- Division of Allergy and Immunology and Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry and Golisano Children’s Hospital, Rochester, NY, United States
| | - Rohith Palli
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Sade Fridy
- Division of Allergy and Immunology and Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry and Golisano Children’s Hospital, Rochester, NY, United States
| | - Puja Sood Rajani
- Division of Allergy and Immunology and Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry and Golisano Children’s Hospital, Rochester, NY, United States
| | - Jessica Stern
- Division of Allergy and Immunology and Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry and Golisano Children’s Hospital, Rochester, NY, United States
| | - Camille Martina
- Department of Public Health Sciences & Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Chloe Yonemitsu
- Division of Neonatology and Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Lars Bode
- Division of Neonatology and Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States,Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA, United States
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Precision Immunology Institue, Icahn School of Medicine at Mount Sinai, New York, New York, NY, United States
| | - Sabrina Tamburini
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Precision Immunology Institue, Icahn School of Medicine at Mount Sinai, New York, New York, NY, United States
| | - Enrica Piras
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Precision Immunology Institue, Icahn School of Medicine at Mount Sinai, New York, New York, NY, United States
| | - David S. Wallach
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Precision Immunology Institue, Icahn School of Medicine at Mount Sinai, New York, New York, NY, United States
| | - Maria Allen
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - R. John Looney
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Precision Immunology Institue, Icahn School of Medicine at Mount Sinai, New York, New York, NY, United States
| | - Juilee Thakar
- Department of Microbiology and Immunology and Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Kirsi M. Järvinen
- Division of Allergy and Immunology and Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry and Golisano Children’s Hospital, Rochester, NY, United States,Division of Allergy, Immunology, and Rheumatology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States,*Correspondence: Kirsi M. Järvinen,
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21
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Sulaiman I, Chung M, Angel L, Tsay JCJ, Wu BG, Yeung ST, Krolikowski K, Li Y, Duerr R, Schluger R, Thannickal SA, Koide A, Rafeq S, Barnett C, Postelnicu R, Wang C, Banakis S, Pérez-Pérez L, Shen G, Jour G, Meyn P, Carpenito J, Liu X, Ji K, Collazo D, Labarbiera A, Amoroso N, Brosnahan S, Mukherjee V, Kaufman D, Bakker J, Lubinsky A, Pradhan D, Sterman DH, Weiden M, Heguy A, Evans L, Uyeki TM, Clemente JC, de Wit E, Schmidt AM, Shopsin B, Desvignes L, Wang C, Li H, Zhang B, Forst CV, Koide S, Stapleford KA, Khanna KM, Ghedin E, Segal LN. Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome. Nat Microbiol 2021; 6:1245-1258. [PMID: 34465900 PMCID: PMC8484067 DOI: 10.1038/s41564-021-00961-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Respiratory failure is associated with increased mortality in COVID-19 patients. There are no validated lower airway biomarkers to predict clinical outcome. We investigated whether bacterial respiratory infections were associated with poor clinical outcome of COVID-19 in a prospective, observational cohort of 589 critically ill adults, all of whom required mechanical ventilation. For a subset of 142 patients who underwent bronchoscopy, we quantified SARS-CoV-2 viral load, analysed the lower respiratory tract microbiome using metagenomics and metatranscriptomics and profiled the host immune response. Acquisition of a hospital-acquired respiratory pathogen was not associated with fatal outcome. Poor clinical outcome was associated with lower airway enrichment with an oral commensal (Mycoplasma salivarium). Increased SARS-CoV-2 abundance, low anti-SARS-CoV-2 antibody response and a distinct host transcriptome profile of the lower airways were most predictive of mortality. Our data provide evidence that secondary respiratory infections do not drive mortality in COVID-19 and clinical management strategies should prioritize reducing viral replication and maximizing host responses to SARS-CoV-2.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Matthew Chung
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luis Angel
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Jun-Chieh J Tsay
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, NY, USA
| | - Stephen T Yeung
- Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Kelsey Krolikowski
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Ralf Duerr
- Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Rosemary Schluger
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Sara A Thannickal
- Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Akiko Koide
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA
| | - Samaan Rafeq
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Clea Barnett
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Radu Postelnicu
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Chang Wang
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Stephanie Banakis
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lizzette Pérez-Pérez
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Guomiao Shen
- Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - George Jour
- Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Peter Meyn
- Division of Pediatrics, Longhua Hospital affiliated to Shanghai University of Chinese Medicine, Shanghai, China
| | - Joseph Carpenito
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Xiuxiu Liu
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Division of Pediatrics, Longhua Hospital affiliated to Shanghai University of Chinese Medicine, Shanghai, China
| | - Kun Ji
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Dongfang Hospital affiliated to Beijing University of Traditional Chinese Medicine, Beijing, China
| | - Destiny Collazo
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Anthony Labarbiera
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Nancy Amoroso
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Shari Brosnahan
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Vikramjit Mukherjee
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - David Kaufman
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Jan Bakker
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Anthony Lubinsky
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Deepak Pradhan
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Daniel H Sterman
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Michael Weiden
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Adriana Heguy
- Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- NYU Langone Genome Technology Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Laura Evans
- Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Bo Shopsin
- Division of Infectious Diseases, Department of Medicine, New York University School of Medicine, NYU Langone Health, New York, NY, USA
| | - Ludovic Desvignes
- Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Chan Wang
- Department of Population Health, New York University School of Medicine, NYU Langone Health, New York, NY, USA
| | - Huilin Li
- Department of Population Health, New York University School of Medicine, NYU Langone Health, New York, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Kenneth A Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Kamal M Khanna
- Department of Microbiology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, USA.
| | - Leopoldo N Segal
- Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY, USA.
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22
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Aggarwala V, Mogno I, Li Z, Yang C, Britton GJ, Chen-Liaw A, Mitcham J, Bongers G, Gevers D, Clemente JC, Colombel JF, Grinspan A, Faith J. Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes. Nat Microbiol 2021; 6:1309-1318. [PMID: 34580445 PMCID: PMC8993687 DOI: 10.1038/s41564-021-00966-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023]
Abstract
Fecal microbiota transplantation (FMT) has been successfully applied to treat recurrent Clostridium difficile infection in humans, but a precise method to measure which bacterial strains stably engraft in recipients and evaluate their association with clinical outcomes is lacking. We assembled a collection of >1,000 different bacterial strains that were cultured from the fecal samples of 22 FMT donors and recipients. Using our strain collection combined with metagenomic sequencing data from the same samples, we developed a statistical approach named Strainer for the detection and tracking of bacterial strains from metagenomic sequencing data. We applied Strainer to evaluate a cohort of 13 FMT longitudinal clinical interventions and detected stable engraftment of 71% of donor microbiota strains in recipients up to 5 years post-FMT. We found that 80% of recipient gut bacterial strains pre-FMT were eliminated by FMT and that post-FMT the strains present persisted up to 5 years later, together with environmentally acquired strains. Quantification of donor bacterial strain engraftment in recipients independently explained (precision 100%, recall 95%) the clinical outcomes (relapse or success) after initial and repeat FMT. We report a compendium of bacterial species and strains that consistently engraft in recipients over time that could be used in defined live biotherapeutic products as an alternative to FMT. Our analytical framework and Strainer can be applied to systematically evaluate either FMT or defined live bacterial therapeutic studies by quantification of strain engraftment in recipients.
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Affiliation(s)
- Varun Aggarwala
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhihua Li
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chao Yang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Josephine Mitcham
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerold Bongers
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Jose C Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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23
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Sulaiman I, Wu BG, Li Y, Tsay JC, Sauthoff M, Scott AS, Ji K, Koralov SB, Weiden M, Clemente JC, Jones D, Huang YJ, Stringer KA, Zhang L, Geber A, Banakis S, Tipton L, Ghedin E, Segal LN. Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism. Eur Respir J 2021; 58:13993003.03434-2020. [PMID: 33446604 DOI: 10.1183/13993003.03434-2020] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/19/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Microbiome studies of the lower airways based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short-chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary. METHODS Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model. We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole-genome shotgun (WGS) and RNA metatranscriptome sequencing. SCFAs were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed. RESULTS Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome data were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFA levels were compared with WGS and metatranscriptome data. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing. CONCLUSIONS Functional characterisation of the lower airway microbiota through metatranscriptome data identifies metabolically active organisms capable of producing metabolites with immunomodulatory capacity, such as SCFAs.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jun-Chieh Tsay
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Maya Sauthoff
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Adrienne S Scott
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Kun Ji
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sergei B Koralov
- Dept of Pathology, New York University School of Medicine, New York, NY, USA
| | - Michael Weiden
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose C Clemente
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Drew Jones
- Dept of Biochemistry and Molecular Pharmacology and Dept of Radiation Oncology, New York University School of Medicine, New York, NY, USA
| | - Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kathleen A Stringer
- Dept of Clinical Pharmacy, College of Pharmacy, and Division of Pulmonary and Critical Care Medicine, Dept of Medicine, School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Lingdi Zhang
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Adam Geber
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Stephanie Banakis
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Laura Tipton
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA.,Dept of Epidemiology, School of Global Public Health, New York University, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
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24
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Wu BG, Sulaiman I, Tsay JCJ, Perez L, Franca B, Li Y, Wang J, Gonzalez AN, El-Ashmawy M, Carpenito J, Olsen E, Sauthoff M, Yie K, Liu X, Shen N, Clemente JC, Kapoor B, Zangari T, Mezzano V, Loomis C, Weiden MD, Koralov SB, D'Armiento J, Ahuja SK, Wu XR, Weiser JN, Segal LN. Episodic Aspiration with Oral Commensals Induces a MyD88-dependent, Pulmonary T-Helper Cell Type 17 Response that Mitigates Susceptibility to Streptococcus pneumoniae. Am J Respir Crit Care Med 2021; 203:1099-1111. [PMID: 33166473 DOI: 10.1164/rccm.202005-1596oc] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Rationale: Cross-sectional human data suggest that enrichment of oral anaerobic bacteria in the lung is associated with an increased T-helper cell type 17 (Th17) inflammatory phenotype.Objectives: In this study, we evaluated the microbial and host immune-response dynamics after aspiration with oral commensals using a preclinical mouse model.Methods: Aspiration with a mixture of human oral commensals (MOC; Prevotella melaninogenica, Veillonella parvula, and Streptococcus mitis) was modeled in mice followed by variable time of killing. The genetic backgrounds of mice included wild-type, MyD88-knockout, and STAT3C backgrounds.Measurements and Main Results: 16S-rRNA gene sequencing characterized changes in microbiota. Flow cytometry, cytokine measurement via Luminex and RNA host-transcriptome sequencing was used to characterize the host immune phenotype. Although MOC aspiration correlated with lower-airway dysbiosis that resolved within 5 days, it induced an extended inflammatory response associated with IL-17-producing T cells lasting at least 14 days. MyD88 expression was required for the IL-17 response to MOC aspiration, but not for T-cell activation or IFN-γ expression. MOC aspiration before a respiratory challenge with S. pneumoniae led to a decrease in hosts' susceptibility to this pathogen.Conclusions: Thus, in otherwise healthy mice, a single aspiration event with oral commensals is rapidly cleared from the lower airways but induces a prolonged Th17 response that secondarily decreases susceptibility to S. pneumoniae. Translationally, these data implicate an immunoprotective role of episodic microaspiration of oral microbes in the regulation of the lung immune phenotype and mitigation of host susceptibility to infection with lower-airway pathogens.
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Affiliation(s)
- Benjamin G Wu
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine.,Division of Pulmonary and Critical Care, New York Harbor Veterans Affairs, New York, New York
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | - Jun-Chieh J Tsay
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine.,Division of Pulmonary and Critical Care, New York Harbor Veterans Affairs, New York, New York
| | - Luisanny Perez
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | - Brendan Franca
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | - Yonghua Li
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | - Jing Wang
- Division of Pulmonary, Critical Care and Sleep Medicine.,Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Amber N Gonzalez
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | | | - Joseph Carpenito
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | - Evan Olsen
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | - Maya Sauthoff
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | - Kevin Yie
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | - Xiuxiu Liu
- Division of Pediatrics, Longhua Hospital, Shanghai University of Chinese Medicine, Shanghai, China
| | - Nan Shen
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Valeria Mezzano
- Division of Cardiology, Department of Medicine and.,Experimental Pathology Research Laboratory, Division of Advanced Research Technologies, and
| | - Cynthia Loomis
- Division of Cardiology, Department of Medicine and.,Department of Pathology, NYU Langone Health, New York, New York
| | - Michael D Weiden
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
| | | | - Jeanine D'Armiento
- Department of Anesthesiology, School of Medicine, Columbia University, New York, New York; and
| | - Sunil K Ahuja
- University of Texas Health Science Center, San Antonio, Texas
| | - Xue-Ru Wu
- Department of Pathology, NYU Langone Health, New York, New York.,Department of Urology, School of Medicine, New York University, New York, New York
| | | | - Leopoldo N Segal
- Division of Pulmonary, Critical Care and Sleep Medicine.,Department of Medicine
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25
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Naidoo CC, Nyawo GR, Sulaiman I, Wu BG, Turner CT, Bu K, Palmer Z, Li Y, Reeve BWP, Moodley S, Jackson JG, Limberis J, Diacon AH, van Helden PD, Clemente JC, Warren RM, Noursadeghi M, Segal LN, Theron G. Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis. EBioMedicine 2021; 67:103374. [PMID: 33975252 PMCID: PMC8122180 DOI: 10.1016/j.ebiom.2021.103374] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/07/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The relationship between tuberculosis (TB), one of the leading infectious causes of death worldwide, and the microbiome, which is critical for health, is poorly understood. METHODS To identify potential microbiome-host interactions, profiling of the oral, sputum and stool microbiota [n = 58 cases, n = 47 culture-negative symptomatic controls (SCs)] and whole blood transcriptome were done in pre-treatment presumptive pulmonary TB patients. This was a cross-sectional study. Microbiota were also characterised in close contacts of cases (CCCs, n = 73) and close contacts of SCs (CCSCs, n = 82) without active TB. FINDINGS Cases and SCs each had similar α- and β-diversities in oral washes and sputum, however, β-diversity differed in stool (PERMANOVA p = 0•035). Cases were enriched with anaerobes in oral washes, sputum (Paludibacter, Lautropia in both) and stool (Erysipelotrichaceae, Blautia, Anaerostipes) and their stools enriched in microbial genes annotated as amino acid and carbohydrate metabolic pathways. In pairwise comparisons with their CCCs, cases had Megasphaera-enriched oral and sputum microbiota and Bifidobacterium-, Roseburia-, and Dorea-depleted stools. Compared to their CCSCs, SCs had reduced α-diversities and many differential taxa per specimen type. Cases differed transcriptionally from SCs in peripheral blood (PERMANOVA p = 0•001). A co-occurrence network analysis showed stool taxa, Erysipelotrichaceae and Blautia, to negatively co-correlate with enriched "death receptor" and "EIF2 signalling" pathways whereas Anaerostipes positively correlated with enriched "interferon signalling", "Nur77 signalling" and "inflammasome" pathways; all of which are host pathways associated with disease severity. In contrast, none of the taxa enriched in SCs correlated with host pathways. INTERPRETATION TB-specific microbial relationships were identified in oral washes, induced sputum, and stool from cases before the confounding effects of antibiotics. Specific anaerobes in cases' stool predict upregulation of pro-inflammatory immunological pathways, supporting the gut microbiota's role in TB. FUNDING European & Developing Countries Clinical Trials Partnership, South African-Medical Research Council, National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Charissa C Naidoo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Georgina R Nyawo
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, United States
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, United States
| | - Carolin T Turner
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zaida Palmer
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, United States
| | - Byron W P Reeve
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Suventha Moodley
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Jennifer G Jackson
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Jason Limberis
- Division of Experimental Medicine, University of California, San Francisco, United States
| | - Andreas H Diacon
- Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Paul D van Helden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, United States
| | - Grant Theron
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa.
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26
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Sulaiman I, Chung M, Angel L, Tsay JCJ, Wu BG, Yeung ST, Krolikowski K, Li Y, Duerr R, Schluger R, Thannickal SA, Koide A, Rafeq S, Barnett C, Postelnicu R, Wang C, Banakis S, Perez-Perez L, Jour G, Shen G, Meyn P, Carpenito J, Liu X, Ji K, Collazo D, Labarbiera A, Amoroso N, Brosnahan S, Mukherjee V, Kaufman D, Bakker J, Lubinsky A, Pradhan D, Sterman DH, Weiden M, Hegu A, Evans L, Uyeki TM, Clemente JC, De Wit E, Schmidt AM, Shopsin B, Desvignes L, Wang C, Li H, Zhang B, Forst CV, Koide S, Stapleford KA, Khanna KM, Ghedin E, Segal LN. Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome. medRxiv 2021:2021.02.23.21252221. [PMID: 33655261 PMCID: PMC7924286 DOI: 10.1101/2021.02.23.21252221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal ( Mycoplasma salivarium ), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.
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27
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Wu BG, Kapoor B, Cummings KJ, Stanton ML, Nett RJ, Kreiss K, Abraham JL, Colby TV, Franko AD, Green FHY, Sanyal S, Clemente JC, Gao Z, Coffre M, Meyn P, Heguy A, Li Y, Sulaiman I, Borbet TC, Koralov SB, Tallaksen RJ, Wendland D, Bachelder VD, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Crawford JA, Edwards NT, Veillette M, Duchaine C, Warren K, Lundeen S, Blaser MJ, Segal LN. Evidence for Environmental-Human Microbiota Transfer at a Manufacturing Facility with Novel Work-related Respiratory Disease. Am J Respir Crit Care Med 2021; 202:1678-1688. [PMID: 32673495 DOI: 10.1164/rccm.202001-0197oc] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Rationale: Workers' exposure to metalworking fluid (MWF) has been associated with respiratory disease.Objectives: As part of a public health investigation of a manufacturing facility, we performed a cross-sectional study using paired environmental and human sampling to evaluate the cross-pollination of microbes between the environment and the host and possible effects on lung pathology present among workers.Methods: Workplace environmental microbiota were evaluated in air and MWF samples. Human microbiota were evaluated in lung tissue samples from workers with respiratory symptoms found to have lymphocytic bronchiolitis and alveolar ductitis with B-cell follicles and emphysema, in lung tissue samples from control subjects, and in skin, nasal, and oral samples from 302 workers from different areas of the facility. In vitro effects of MWF exposure on murine B cells were assessed.Measurements and Main Results: An increased similarity of microbial composition was found between MWF samples and lung tissue samples of case workers compared with control subjects. Among workers in different locations within the facility, those that worked in the machine shop area had skin, nasal, and oral microbiota more closely related to the microbiota present in the MWF samples. Lung samples from four index cases and skin and nasal samples from workers in the machine shop area were enriched with Pseudomonas, the dominant taxa in MWF. Exposure to used MWF stimulated murine B-cell proliferation in vitro, a hallmark cell subtype found in the pathology of index cases.Conclusions: Evaluation of a manufacturing facility with a cluster of workers with respiratory disease supports cross-pollination of microbes from MWF to humans and suggests the potential for exposure to these microbes to be a health hazard.
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Affiliation(s)
| | | | - Kristin J Cummings
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | - Marcia L Stanton
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | - Randall J Nett
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | - Kathleen Kreiss
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | - Jerrold L Abraham
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, New York
| | - Thomas V Colby
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, Arizona
| | - Angela D Franko
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Francis H Y Green
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Soma Sanyal
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, New York
| | - Jose C Clemente
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zhan Gao
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey
| | - Maryaline Coffre
- Department of Pathology, New York University School of Medicine, New York, New York
| | - Peter Meyn
- Department of Pathology, New York University School of Medicine, New York, New York
| | - Adriana Heguy
- Department of Pathology, New York University School of Medicine, New York, New York
| | | | | | | | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, New York
| | - Robert J Tallaksen
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | | | | | - Randy J Boylstein
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | - Ju-Hyeong Park
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | - Jean M Cox-Ganser
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | - M Abbas Virji
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | - Judith A Crawford
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, New York
| | - Nicole T Edwards
- Respiratory Health Division, National Institute for Occupational Safety and Health, CDC, Morgantown, West Virginia
| | - Marc Veillette
- Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Quebec, Canada
| | - Caroline Duchaine
- Department of Biochemistry, Microbiology and Bioinformatics, Laval University, Quebec, Canada
| | - Krista Warren
- St. Luke's Department of Pathology, St. Luke's Hospital, Duluth, Minnesota; and
| | - Sarah Lundeen
- St. Luke's Department of Pathology, St. Luke's Hospital, Duluth, Minnesota; and
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, New Jersey
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28
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Shapiro JM, de Zoete MR, Palm NW, Laenen Y, Bright R, Mallette M, Bu K, Bielecka AA, Xu F, Hurtado-Lorenzo A, Shah SA, Cho JH, LeLeiko NS, Sands BE, Flavell RA, Clemente JC. Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease. Cell Host Microbe 2021; 29:83-93.e3. [PMID: 33385335 PMCID: PMC10477929 DOI: 10.1016/j.chom.2020.12.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/18/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022]
Abstract
The immunopathogenesis of inflammatory bowel disease (IBD) has been attributed to a combination of host genetics and intestinal dysbiosis. Previous work in a small cohort of IBD patients suggested that pro-inflammatory bacterial taxa are highly coated with secretory immunoglobulin IgA. Using bacterial fluorescence-activated cell sorting coupled with 16S rRNA gene sequencing (IgA-SEQ), we profiled IgA coating of intestinal microbiota in a large cohort of IBD patients and identified bacteria associated with disease and treatment. Forty-three bacterial taxa displayed significantly higher IgA coating in IBD compared with controls, including 8 taxa exhibiting differential IgA coating but similar relative abundance. Patients treated with anti-TNF-α therapies exhibited dramatically altered microbiota-specific IgA responses compared with controls. Furthermore, increased IgA coating of Oscillospira was associated with a delay in time to surgery. These results demonstrate that investigating IgA responses to microbiota can uncover potential disease-modifying taxa and reveal improved biomarkers of clinical course in IBD.
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Affiliation(s)
- Jason M Shapiro
- Division of Pediatric Gastroenterology, Nutrition and Liver Diseases, Hasbro Children's Hospital, Providence, RI 02903, USA; Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Marcel R de Zoete
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Noah W Palm
- Human and Translational Immunobiology Program, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Yaro Laenen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rene Bright
- Division of Gastroenterology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Meaghan Mallette
- Division of Gastroenterology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Kevin Bu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Agata A Bielecka
- Human and Translational Immunobiology Program, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Fang Xu
- Division of Population Health, National Center for Chronic Disease Prevention and Health Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30341, USA
| | | | - Samir A Shah
- Alpert Medical School of Brown University, Providence, RI 02903, USA; Division of Gastroenterology, Rhode Island Hospital, Providence, RI 02903, USA
| | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Neal S LeLeiko
- Division of Pediatric Gastroenterology, Nutrition and Liver Diseases, Hasbro Children's Hospital, Providence, RI 02903, USA; Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Bruce E Sands
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard A Flavell
- Human and Translational Immunobiology Program, Yale University School of Medicine, New Haven, CT 06519, USA
| | - J C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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29
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Clemente JC, Iliev ID. Editorial overview: Microbiota united-bacteria, fungi and host responses come into focus. Curr Opin Microbiol 2020; 56:vi-viii. [PMID: 33323167 DOI: 10.1016/j.mib.2020.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Precision Immunology Institute, Icahn School of Medicine at New York, New York, NY 10029, USA.
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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30
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Luu HN, Behari J, Goh GBB, Wang R, Jin A, Thomas CE, Clemente JC, Odegaard AO, Koh WP, Yuan JM. Composite Score of Healthy Lifestyle Factors and Risk of Hepatocellular Carcinoma: Findings from a Prospective Cohort Study. Cancer Epidemiol Biomarkers Prev 2020; 30:380-387. [PMID: 33187965 DOI: 10.1158/1055-9965.epi-20-1201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/25/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND While the associations between individual lifestyle factors and risk of hepatocellular carcinoma (HCC) have been described previously, their combined impact on HCC risk is unknown. METHODS The association of a composite score of healthy lifestyle factors, including body mass index, alcohol consumption, cigarette smoking, alternative Mediterranean diet, and sleep duration, and HCC risk was examined in the Singapore Chinese Health Study, an ongoing prospective cohort study of 63,257 Chinese men and women. Cox proportional hazard regression method was used to estimate HR and its 95% confidence interval (CI). Conditional logistic regression method was used to evaluate this composite lifestyle score-HCC risk association among a subset of individuals who tested negative for hepatitis B surface antigen (HBsAg) and anti-hepatitis C antibody. RESULTS After a mean follow-up of 17.7 years, 561 participants developed HCC. Individuals with higher composite scores representing healthier lifestyles (range 0-8) were at significantly lower risk of HCC. Compared with the lowest composite score category (0-4), the HRs (95% CIs) for the composite scores of 5, 6, 7, and 8 were 0.67 (0.62-0.85), 0.61 (0.48-0.77), 0.49 (0.37-0.65), and 0.13 (0.06-0.30), respectively (P trend < 0.0001). A similar inverse association was observed in participants with negative HBsAg and anti-hepatitis C virus (HCV)-negative serology (HR, 0.38; 95% CI, 0.19-0.79; for the highest vs. the lowest category of the composite scores; P trend = 0.001). CONCLUSIONS Healthy lifestyles protect against HCC development, especially for individuals without hepatitis B virus and HCV infections. IMPACT This study highlights the importance of a comprehensive lifestyle modification strategy for HCC primary prevention.
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Affiliation(s)
- Hung N Luu
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania. .,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jaideep Behari
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - George Boon-Bee Goh
- Health Services and Systems Research, Duke-NUS Medical School Singapore, Singapore.,Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Aizhen Jin
- Health Services and Systems Research, Duke-NUS Medical School Singapore, Singapore
| | - Claire E Thomas
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrew O Odegaard
- Department of Epidemiology, School of Medicine, University of California-Irvine, Irvine, California
| | - Woon-Puay Koh
- Health Services and Systems Research, Duke-NUS Medical School Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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31
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Tsay JCJ, Wu BG, Sulaiman I, Gershner K, Schluger R, Li Y, Yie TA, Meyn P, Olsen E, Perez L, Franca B, Carpenito J, Iizumi T, El-Ashmawy M, Badri M, Morton JT, Shen N, He L, Michaud G, Rafeq S, Bessich JL, Smith RL, Sauthoff H, Felner K, Pillai R, Zavitsanou AM, Koralov SB, Mezzano V, Loomis CA, Moreira AL, Moore W, Tsirigos A, Heguy A, Rom WN, Sterman DH, Pass HI, Clemente JC, Li H, Bonneau R, Wong KK, Papagiannakopoulos T, Segal LN. Lower Airway Dysbiosis Affects Lung Cancer Progression. Cancer Discov 2020; 11:293-307. [PMID: 33177060 DOI: 10.1158/2159-8290.cd-20-0263] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 09/15/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022]
Abstract
In lung cancer, enrichment of the lower airway microbiota with oral commensals commonly occurs, and ex vivo models support that some of these bacteria can trigger host transcriptomic signatures associated with carcinogenesis. Here, we show that this lower airway dysbiotic signature was more prevalent in the stage IIIB-IV tumor-node-metastasis lung cancer group and is associated with poor prognosis, as shown by decreased survival among subjects with early-stage disease (I-IIIA) and worse tumor progression as measured by RECIST scores among subjects with stage IIIB-IV disease. In addition, this lower airway microbiota signature was associated with upregulation of the IL17, PI3K, MAPK, and ERK pathways in airway transcriptome, and we identified Veillonella parvula as the most abundant taxon driving this association. In a KP lung cancer model, lower airway dysbiosis with V. parvula led to decreased survival, increased tumor burden, IL17 inflammatory phenotype, and activation of checkpoint inhibitor markers. SIGNIFICANCE: Multiple lines of investigation have shown that the gut microbiota affects host immune response to immunotherapy in cancer. Here, we support that the local airway microbiota modulates the host immune tone in lung cancer, affecting tumor progression and prognosis.See related commentary by Zitvogel and Kroemer, p. 224.This article is highlighted in the In This Issue feature, p. 211.
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Affiliation(s)
- Jun-Chieh J Tsay
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York.,Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, New York
| | - Benjamin G Wu
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York.,Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, New York
| | - Imran Sulaiman
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Katherine Gershner
- Section of Pulmonary, Critical Care, Allergy and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Rosemary Schluger
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Ting-An Yie
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Peter Meyn
- NYU Langone Genomic Technology Center, New York University School of Medicine, New York, New York
| | - Evan Olsen
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Luisannay Perez
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Brendan Franca
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Joseph Carpenito
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Tadasu Iizumi
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Mariam El-Ashmawy
- Department of Medicine, New York University School of Medicine, New York, New York
| | - Michelle Badri
- Department of Biology, New York University, New York, New York
| | - James T Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York
| | - Nan Shen
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Linchen He
- Department of Population Health, New York University School of Medicine, New York, New York
| | - Gaetane Michaud
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Samaan Rafeq
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Jamie L Bessich
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Robert L Smith
- Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, New York
| | - Harald Sauthoff
- Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, New York
| | - Kevin Felner
- Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, New York
| | - Ray Pillai
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | | | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, New York
| | - Valeria Mezzano
- Department of Pathology, New York University School of Medicine, New York, New York
| | - Cynthia A Loomis
- Department of Pathology, New York University School of Medicine, New York, New York
| | - Andre L Moreira
- Department of Pathology, New York University School of Medicine, New York, New York
| | - William Moore
- Department of Radiology, New York University School of Medicine, New York, New York
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, New York
| | - Adriana Heguy
- NYU Langone Genomic Technology Center, New York University School of Medicine, New York, New York.,Department of Pathology, New York University School of Medicine, New York, New York
| | - William N Rom
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Daniel H Sterman
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University School of Medicine, New York, New York
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huilin Li
- Department of Population Health, New York University School of Medicine, New York, New York
| | - Richard Bonneau
- Department of Biology, New York University, New York, New York.,Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York.,Center for Data Science, New York University School of Medicine, New York, New York
| | - Kwok-Kin Wong
- Division of Hematology and Oncology, New York University School of Medicine, New York, New York
| | | | - Leopoldo N Segal
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, New York.
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Luu HN, Neelakantan N, Geng TT, Wang R, Goh GBB, Clemente JC, Jin A, van Dam RM, Jia W, Behari J, Koh WP, Yuan JM. Quality diet indexes and risk of hepatocellular carcinoma: Findings from the Singapore Chinese Health Study. Int J Cancer 2020; 148:2102-2114. [PMID: 33129230 DOI: 10.1002/ijc.33367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/15/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023]
Abstract
There is limited research on the effect of dietary quality on hepatocellular carcinoma (HCC) risk in populations with relatively high risk of HCC. Using data from Singapore Chinese Health Study, a prospective cohort study, of 63 257 Chinese aged 45 to 74, we assessed four diet-quality index (DQI) scores: the Alternative Health Eating Index-2010 (AHEI-2010), Alternate Mediterranean Diet (aMED), Dietary Approaches to Stop Hypertension (DASH) and Heathy Diet Indicator (HDI). We identified 561 incident HCC cases among the cohort participants after a mean of 17.6 years of follow-up. Cox proportional hazard regression model was used to estimate hazard ratio (HR) and 95% confidence interval (CI) for HCC in relation to these DQI scores. Unconditional logistic regression method was used to evaluate the associations between DQIs and HCC risk among a subset of individuals who tested negative for hepatitis B surface antigen (HBsAg). High scores of AHEI-2010, aMED and DASH, representing higher dietary quality, were associated with lower risk of HCC (all Ptrend < .05). Compared with the lowest quartile, HRs (95% CIs) of HCC for the highest quartile of AHEI-2010, aMED and DASH were 0.69 (0.53-0.89), 0.70 (0.52-0.95) and 0.67 (0.51-0.87), respectively. No significant association between HDI and HCC risk was observed. Among HBsAg-negative individuals, similar inverse associations were observed, and the strongest inverse association was for aMED (HRQ4vsQ1 = 0.46, 95% CI: 0.23-0.94, Ptrend = .10). These findings support the notion that adherence to a healthier diet may lower the risk of HCC, suggesting that dietary modification may be an effective approach for primary prevention of HCC.
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Affiliation(s)
- Hung N Luu
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, UPMC Cancer Pavilion, Pittsburgh, Pennsylvania, USA.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nithya Neelakantan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Ting-Ting Geng
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, UPMC Cancer Pavilion, Pittsburgh, Pennsylvania, USA
| | - George Boon-Bee Goh
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore.,Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore, Singapore
| | - Jose C Clemente
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Aizhen Jin
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore.,Department of Nutrition, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Wei Jia
- University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Jaideep Behari
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, UPMC Cancer Pavilion, Pittsburgh, Pennsylvania, USA.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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33
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Britton GJ, Contijoch EJ, Spindler MP, Aggarwala V, Dogan B, Bongers G, San Mateo L, Baltus A, Das A, Gevers D, Borody TJ, Kaakoush NO, Kamm MA, Mitchell H, Paramsothy S, Clemente JC, Colombel JF, Simpson KW, Dubinsky MC, Grinspan A, Faith JJ. Defined microbiota transplant restores Th17/RORγt + regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas. Proc Natl Acad Sci U S A 2020; 117:21536-21545. [PMID: 32817490 PMCID: PMC7474624 DOI: 10.1073/pnas.1922189117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The building evidence for the contribution of microbiota to human disease has spurred an effort to develop therapies that target the gut microbiota. This is particularly evident in inflammatory bowel diseases (IBDs), where clinical trials of fecal microbiota transplantation have shown some efficacy. To aid the development of novel microbiota-targeted therapies and to better understand the biology underpinning such treatments, we have used gnotobiotic mice to model microbiota manipulations in the context of microbiotas from humans with inflammatory bowel disease. Mice colonized with IBD donor-derived microbiotas exhibit a stereotypical set of phenotypes, characterized by abundant mucosal Th17 cells, a deficit in the tolerogenic RORγt+ regulatory T (Treg) cell subset, and susceptibility to disease in colitis models. Transplanting healthy donor-derived microbiotas into mice colonized with human IBD microbiotas led to induction of RORγt+ Treg cells, which was associated with an increase in the density of the microbiotas following transplant. Microbiota transplant reduced gut Th17 cells in mice colonized with a microbiota from a donor with Crohn's disease. By culturing strains from this microbiota and screening them in vivo, we identified a specific strain that potently induces Th17 cells. Microbiota transplants reduced the relative abundance of this strain in the gut microbiota, which was correlated with a reduction in Th17 cells and protection from colitis.
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Affiliation(s)
- Graham J Britton
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Eduardo J Contijoch
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Matthew P Spindler
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Varun Aggarwala
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - Gerold Bongers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | - Andrew Baltus
- Janssen Human Microbiome Institute, Janssen Research and Development, Cambridge, MA 02142
| | - Anuk Das
- Janssen Human Microbiome Institute, Janssen Research and Development, Cambridge, MA 02142
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research and Development, Cambridge, MA 02142
| | | | - Nadeem O Kaakoush
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael A Kamm
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, VIC 3065, Australia
- Department of Medicine, St Vincent's Hospital, Melbourne, VIC 3065, Australia
- Department of Gastroenterology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hazel Mitchell
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sudarshan Paramsothy
- Concord Clinical School, University of Sydney, Sydney, NSW 2050, Australia
- Department of Gastroenterology & Hepatology, Macquarie University Hospital, Sydney, NSW 2109, Australia
| | - Jose C Clemente
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kenneth W Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - Marla C Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ari Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jeremiah J Faith
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029;
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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34
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Leonardi I, Paramsothy S, Doron I, Semon A, Kaakoush NO, Clemente JC, Faith JJ, Borody TJ, Mitchell HM, Colombel JF, Kamm MA, Iliev ID. Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis. Cell Host Microbe 2020; 27:823-829.e3. [PMID: 32298656 DOI: 10.1016/j.chom.2020.03.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/10/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
Fecal microbiota transplantation (FMT) targeting gut microbiota has recently been successfully applied to ulcerative colitis. However, only a subset of patients responds to FMT, and there is a pressing need for biomarkers of responsiveness. Fungi (the mycobiota) represent a highly immunologically reactive component of the gut microbiota. We analyzed samples from a large randomized controlled trial of FMT for ulcerative colitis (UC). High Candida abundance pre-FMT was associated with a clinical response, whereas decreased Candida abundance post-FMT was indicative of ameliorated disease severity. High pre-FMT Candida was associated with increased bacterial diversity post-FMT, and the presence of genera was linked to FMT responsiveness. Although we detected elevated anti-Candida antibodies in placebo recipients, this increase was abrogated in FMT recipients. Our data suggest that FMT might reduce Candida to contain pro-inflammatory immunity during intestinal disease and highlight the utility of mycobiota-focused approaches to identify FMT responders prior to therapy initiation.
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Affiliation(s)
- Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Sudarshan Paramsothy
- University of New South Wales, Sydney NSW 2052, Australia; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Alexa Semon
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | | | - Jose C Clemente
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeremiah J Faith
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | - Michael A Kamm
- St. Vincent's Hospital and University of Melbourne, Melbourne, VIC 3065, Australia
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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35
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Manasson J, Wallach DS, Guggino G, Stapylton M, Badri MH, Solomon G, Reddy SM, Coras R, Aksenov AA, Jones DR, Girija PV, Neimann AL, Heguy A, Segal LN, Dorrestein PC, Bonneau R, Guma M, Ciccia F, Ubeda C, Clemente JC, Scher JU. Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25-Driven Intestinal Inflammation. Arthritis Rheumatol 2020; 72:645-657. [PMID: 31729183 DOI: 10.1002/art.41169] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To characterize the ecological effects of biologic therapies on the gut bacterial and fungal microbiome in psoriatic arthritis (PsA)/spondyloarthritis (SpA) patients. METHODS Fecal samples from PsA/SpA patients pre- and posttreatment with tumor necrosis factor inhibitors (TNFi; n = 15) or an anti-interleukin-17A monoclonal antibody inhibitor (IL-17i; n = 14) underwent sequencing (16S ribosomal RNA, internal transcribed spacer and shotgun metagenomics) and computational microbiome analysis. Fecal levels of fatty acid metabolites and cytokines/proteins implicated in PsA/SpA pathogenesis or intestinal inflammation were correlated with sequence data. Additionally, ileal biopsies obtained from SpA patients who developed clinically overt Crohn's disease (CD) after treatment with IL-17i (n = 5) were analyzed for expression of IL-23/Th17-related cytokines, IL-25/IL-17E-producing cells, and type 2 innate lymphoid cells (ILC2s). RESULTS There were significant shifts in abundance of specific taxa after treatment with IL-17i compared to TNFi, particularly Clostridiales (P = 0.016) and Candida albicans (P = 0.041). These subclinical alterations correlated with changes in bacterial community co-occurrence, metabolic pathways, IL-23/Th17-related cytokines, and various fatty acids. Ileal biopsies showed that clinically overt CD was associated with expansion of IL-25/IL-17E-producing tuft cells and ILC2s (P < 0.05), compared to pre-IL-17i treatment levels. CONCLUSION In a subgroup of SpA patients, the initiation of IL-17A blockade correlated with features of subclinical gut inflammation and intestinal dysbiosis of certain bacterial and fungal taxa, most notably C albicans. Further, IL-17i-related CD was associated with overexpression of IL-25/IL-17E-producing tuft cells and ILC2s. These results may help to explain the potential link between inhibition of a specific IL-17 pathway and the (sub)clinical gut inflammation observed in SpA.
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Affiliation(s)
- Julia Manasson
- New York University School of Medicine, New York, New York
| | | | | | | | | | - Gary Solomon
- New York University School of Medicine, New York, New York
| | - Soumya M Reddy
- New York University School of Medicine, New York, New York
| | | | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego
| | - Drew R Jones
- New York University School of Medicine, New York, New York
| | | | | | - Adriana Heguy
- New York University School of Medicine, New York, New York
| | | | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego
| | - Richard Bonneau
- Simons Foundation, New York University, and Courant Institute of Mathematical Sciences, New York, New York
| | | | | | - Carles Ubeda
- La Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain, and CIBERESP, Madrid, Spain
| | | | - Jose U Scher
- New York University School of Medicine, New York, New York
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36
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Carney SM, Clemente JC, Cox MJ, Dickson RP, Huang YJ, Kitsios GD, Kloepfer KM, Leung JM, LeVan TD, Molyneaux PL, Moore BB, O'Dwyer DN, Segal LN, Garantziotis S. Methods in Lung Microbiome Research. Am J Respir Cell Mol Biol 2020; 62:283-299. [PMID: 31661299 PMCID: PMC7055701 DOI: 10.1165/rcmb.2019-0273tr] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/29/2019] [Indexed: 12/13/2022] Open
Abstract
The lung microbiome is associated with host immune response and health outcomes in experimental models and patient cohorts. Lung microbiome research is increasing in volume and scope; however, there are no established guidelines for study design, conduct, and reporting of lung microbiome studies. Standardized approaches to yield reliable and reproducible data that can be synthesized across studies will ultimately improve the scientific rigor and impact of published work and greatly benefit microbiome research. In this review, we identify and address several key elements of microbiome research: conceptual modeling and hypothesis framing; study design; experimental methodology and pitfalls; data analysis; and reporting considerations. Finally, we explore possible future directions and research opportunities. Our goal is to aid investigators who are interested in this burgeoning research area and hopefully provide the foundation for formulating consensus approaches in lung microbiome research.
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Affiliation(s)
| | | | | | | | - Yvonne J Huang
- University of Michigan Medical School, Ann Arbor, Michigan
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Kirsten M Kloepfer
- Division of Pulmonary, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Janice M Leung
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Philip L Molyneaux
- Fibrosis Research Group, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Foundation National Health Service Trust, London, United Kingdom
| | | | | | - Leopoldo N Segal
- Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, New York; and
| | - Stavros Garantziotis
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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37
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Torres J, Hu J, Seki A, Eisele C, Nair N, Huang R, Tarassishin L, Jharap B, Cote-Daigneault J, Mao Q, Mogno I, Britton GJ, Uzzan M, Chen CL, Kornbluth A, George J, Legnani P, Maser E, Loudon H, Stone J, Dubinsky M, Faith JJ, Clemente JC, Mehandru S, Colombel JF, Peter I. Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. Gut 2020; 69:42-51. [PMID: 31036757 DOI: 10.1136/gutjnl-2018-317855] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/19/2019] [Accepted: 04/09/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Prenatal and early life bacterial colonisation is thought to play a major role in shaping the immune system. Furthermore, accumulating evidence links early life exposures to the risk of developing IBD later in life. We aimed to assess the effect of maternal IBD on the composition of the microbiome during pregnancy and on the offspring's microbiome. METHODS We prospectively examined the diversity and taxonomy of the microbiome of pregnant women with and without IBD and their babies at multiple time points. We evaluated the role of maternal IBD diagnosis, the mode of delivery, antibiotic use and feeding behaviour on the microbiome composition during early life. To assess the effects of IBD-associated maternal and infant microbiota on the enteric immune system, we inoculated germ-free mice (GFM) with the respective stool and profiled adaptive and innate immune cell populations in the murine intestines. RESULTS Pregnant women with IBD and their offspring presented with lower bacterial diversity and altered bacterial composition compared with control women and their babies. Maternal IBD was the main predictor of the microbiota diversity in the infant gut at 7, 14, 30, 60 and 90 days of life. Babies born to mothers with IBD demonstrated enrichment in Gammaproteobacteria and depletion in Bifidobacteria. Finally, GFM inoculated with third trimester IBD mother and 90-day infant stools showed significantly reduced microbial diversity and fewer class-switched memory B cells and regulatory T cells in the colon. CONCLUSION Aberrant gut microbiota composition persists during pregnancy with IBD and alters the bacterial diversity and abundance in the infant stool. The dysbiotic microbiota triggered abnormal imprinting of the intestinal immune system in GFM.
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Affiliation(s)
- Joana Torres
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Department of Gastroenterology, Hospital Beatriz Angelo, Loures, Portugal
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Akihiro Seki
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Caroline Eisele
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Nilendra Nair
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Ruiqi Huang
- Department of Health Evidence and Policy, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Leonid Tarassishin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Bindia Jharap
- Department of Gastroenterology and Hepatology, Meander Medical Center, Amersfoort, The Netherlands
| | - Justin Cote-Daigneault
- Department of Gastroenterology, Centre Hospitalier de L'Universite de Montreal, Montreal, Quebec, Canada
| | - Qixing Mao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Naijing, China
| | - Ilaria Mogno
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Graham J Britton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Mathieu Uzzan
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Ching-Lynn Chen
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Asher Kornbluth
- Department of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - James George
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Peter Legnani
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Elana Maser
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Holly Loudon
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Joanne Stone
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Marla Dubinsky
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Jeremiah J Faith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Saurabh Mehandru
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Jean-Frederic Colombel
- Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
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Wu BG, Sulaiman I, Wang J, Shen N, Clemente JC, Li Y, Laumbach RJ, Lu SE, Udasin I, Le-Hoang O, Perez A, Alimokhtari S, Black K, Plietz M, Twumasi A, Sanders H, Malecha P, Kapoor B, Scaglione BD, Wang A, Blazoski C, Weiden MD, Rapoport DM, Harrison D, Chitkara N, Vicente E, Marin JM, Sunderram J, Ayappa I, Segal LN. Severe Obstructive Sleep Apnea Is Associated with Alterations in the Nasal Microbiome and an Increase in Inflammation. Am J Respir Crit Care Med 2019; 199:99-109. [PMID: 29969291 DOI: 10.1164/rccm.201801-0119oc] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Obstructive sleep apnea (OSA) is associated with recurrent obstruction, subepithelial edema, and airway inflammation. The resultant inflammation may influence or be influenced by the nasal microbiome. OBJECTIVES To evaluate whether the composition of the nasal microbiota is associated with obstructive sleep apnea and inflammatory biomarkers. METHODS Two large cohorts were used: 1) a discovery cohort of 472 subjects from the WTCSNORE (Seated, Supine and Post-Decongestion Nasal Resistance in World Trade Center Rescue and Recovery Workers) cohort, and 2) a validation cohort of 93 subjects rom the Zaragoza Sleep cohort. Sleep apnea was diagnosed using home sleep tests. Nasal lavages were obtained from cohort subjects to measure: 1) microbiome composition (based on 16S rRNA gene sequencing), and 2) biomarkers for inflammation (inflammatory cells, IL-8, and IL-6). Longitudinal 3-month samples were obtained in the validation cohort, including after continuous positive airway pressure treatment when indicated. MEASUREMENTS AND MAIN RESULTS In both cohorts, we identified that: 1) severity of OSA correlated with differences in microbiome diversity and composition; 2) the nasal microbiome of subjects with severe OSA were enriched with Streptococcus, Prevotella, and Veillonella; and 3) the nasal microbiome differences were associated with inflammatory biomarkers. Network analysis identified clusters of cooccurring microbes that defined communities. Several common oral commensals (e.g., Streptococcus, Rothia, Veillonella, and Fusobacterium) correlated with apnea-hypopnea index. Three months of treatment with continuous positive airway pressure did not change the composition of the nasal microbiota. CONCLUSIONS We demonstrate that the presence of an altered microbiome in severe OSA is associated with inflammatory markers. Further experimental approaches to explore causal links are needed.
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Affiliation(s)
- Benjamin G Wu
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Imran Sulaiman
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Jing Wang
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York.,2 Beijing Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, The Capital University of Medicine, Beijing, China
| | - Nan Shen
- 3 Department of Genetics and Genomic Sciences.,4 Precision Immunology Institute, and
| | - Jose C Clemente
- 3 Department of Genetics and Genomic Sciences.,4 Precision Immunology Institute, and
| | - Yonghua Li
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Robert J Laumbach
- 5 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey.,6 Environment and Occupational Health Sciences Institute, Rutgers Biomedical Health Sciences, Piscataway, New Jersey
| | - Shou-En Lu
- 7 Rutgers School of Public Health, Piscataway, New Jersey
| | - Iris Udasin
- 7 Rutgers School of Public Health, Piscataway, New Jersey
| | - Oanh Le-Hoang
- 5 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Alan Perez
- 6 Environment and Occupational Health Sciences Institute, Rutgers Biomedical Health Sciences, Piscataway, New Jersey
| | - Shahnaz Alimokhtari
- 6 Environment and Occupational Health Sciences Institute, Rutgers Biomedical Health Sciences, Piscataway, New Jersey
| | - Kathleen Black
- 6 Environment and Occupational Health Sciences Institute, Rutgers Biomedical Health Sciences, Piscataway, New Jersey
| | - Michael Plietz
- 5 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Akosua Twumasi
- 8 Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Haley Sanders
- 8 Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Patrick Malecha
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Bianca Kapoor
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Benjamin D Scaglione
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Anbang Wang
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Cameron Blazoski
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Michael D Weiden
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - David M Rapoport
- 8 Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Denise Harrison
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Nishay Chitkara
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
| | - Eugenio Vicente
- 9 Instituto de Investigación Sanitaria Aragón, Hospital Universitario Miguel Servet, Zaragoza, Spain; and.,10 Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Madrid, Spain
| | - José M Marin
- 9 Instituto de Investigación Sanitaria Aragón, Hospital Universitario Miguel Servet, Zaragoza, Spain; and.,10 Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Madrid, Spain
| | - Jag Sunderram
- 5 Division of Pulmonary and Critical Care Medicine, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Indu Ayappa
- 8 Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Leopoldo N Segal
- 1 Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, New York
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Mittal P, Wang L, Akimova T, Leach CA, Clemente JC, Sender M, Chen Y, Turenen B, Hancock WW. Abstract 1965: Inhibiting the CCR2/MCP-1 chemokine pathway blocks MDSC recruitment and promotes anti-tumor immunity. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Host anti-tumor immunity, including the actions of cytotoxic T cells, plays a key role in curtailing the growth of “hot” tumors but can be hindered by multiple mechanisms. One such mechanism involves the local recruitment and expansion of myeloid derived suppressor cells (MDSCs) within the tumor microenvironment. We investigated the role of the CCR2/MCP-1 axis in MDSC-associated tumor progression using the TC1 lung tumor cell line implanted into syngeneic C57BL/6 mice. Phenotypic profiling of TC1 tumors revealed maximal expression of CCR2 by tumor resident MDSCs (p<0.01 vs. neutrophils, tumor-associated macrophages/TAM or T cells), and MCP-1 by transplanted tumor cells (p<0.01 vs. all types of leukocytes), respectively. Additionally, utilization of CCR2 knockout (CCR2KO) mice showed the dependence of progression of TC1 tumor on CCR2 signaling (p<0.01). Tumors in CCR2KO mice had fewer CCR2lowMDSCs (p<0.01), CD4 T cells (p<0.01), and Foxp3+ Treg cells (p<0.05). Conversely, CD8 T cell infiltration was significantly augmented in tumors from CCR2KO mice (p<0.05), and these CD8 T cells were capable of making higher levels of IFN-γ (p<0.01) and granzyme-B (p<0.05) upon restimulation than CD8 T cells from WT tumor-bearing mice. These effects were tumor-specific and not the result of genetic ablation of CCR2 on T cells, since the adoptive transfer of WT or CCR2KO cells into B2D6/F1 mice showed that CCR2KO cells had comparable activation, proliferation, inflammatory cytokine production, and Treg-mediated suppressive function as WT cells (all p>0.05). We next used a thioglycolate-induced peritonitis model of inflammation to validate the role of CCR2 and MCP-1 in trafficking of CCR2+ cells to the site of inflammation. We showed the ability of a CCR2 antagonist to inhibit trafficking of CCR2+ cells to the site of inflammation, in a dose-dependent manner, with a maximal effect at a dose of 10 mg/kg (p<0.05). We then tested the compound at this inhibitory concentration for its ability to impair CCR2+ cell recruitment to MCP-1 expressing TC1 tumors. Use of the CCR2 antagonist blocked growth TC1 tumors (p<0.001) and markedly suppressed intratumoral MDSC numbers (p<0.01), while boosting the numbers of cytotoxic CD8 T cells (p<0.005) and intratumoral expression of IFN-γ, TNF-α, granzyme-B and perforin (all p<0.01). In summary, fully complementary genetic and pharmacologic data indicate that CCR2 targeting may be an important new component of immuno-oncology based therapies.
Note: This abstract was not presented at the meeting.
Citation Format: Payal Mittal, Liqing Wang, Tatiana Akimova, Craig A. Leach, Jose C. Clemente, Mathew Sender, Yao Chen, Brandon Turenen, Wayne W. Hancock. Inhibiting the CCR2/MCP-1 chemokine pathway blocks MDSC recruitment and promotes anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1965.
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Hirten RP, Grinspan A, Fu SC, Luo Y, Suarez-Farinas M, Rowland J, Contijoch EJ, Mogno I, Yang N, Luong T, Labrias PR, Peter I, Cho JH, Sands BE, Colombel JF, Faith JJ, Clemente JC. Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease. Inflamm Bowel Dis 2019; 25:969-979. [PMID: 30852592 PMCID: PMC6499938 DOI: 10.1093/ibd/izy398] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Recurrent and severe Clostridium difficile infections (CDI) are treated with fecal microbiota transplant (FMT). Uncertainty exists regarding FMT effectiveness for CDI with underlying inflammatory bowel disease (IBD) and regarding its effects on disease activity and effectiveness in transferring the donor microbiota to patients with and without IBD. METHODS Subjects with and without IBD who underwent FMT for recurrent or severe CDI between 2013 and 2016 at The Mount Sinai Hospital were followed for up to 6 months. The primary outcome was CDI recurrence 6 months after FMT. Secondary outcomes were (1) CDI recurrence 2 months after FMT; (2) frequency of IBD flare after FMT; (3) microbiota engraftment after FMT; (and 4) predictors of CDI recurrence. RESULTS One hundred thirty-four patients, 46 with IBD, were treated with FMT. Follow-up was available in 83 and 118 patients at 6 and 2 months, respectively. There was no difference in recurrence in patients with and without IBD at 6 months (38.7% vs 36.5%; P > 0.99) and 2 months (22.5% vs 17.9%; P = 0.63). Proton pump inhibitor use, severe CDI, and comorbid conditions were predictors of recurrence. Pre-FMT microbiota was not predictive of CDI recurrence. Subjects with active disease requiring medication escalation had reduced engraftment, with no difference in engraftment based on CDI recurrence or IBD endoscopic severity at FMT. CONCLUSIONS Inflammatory bowel disease did not affect CDI recurrence rates 6 months after FMT. Pre-FMT microbiota was not predictive of recurrence, and microbial engraftment was impacted in those requiring IBD treatment escalation, though not by CDI recurrence or IBD disease severity.
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Affiliation(s)
- Robert P Hirten
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shih-Chen Fu
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Yuying Luo
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Rowland
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eduardo J Contijoch
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Ilaria Mogno
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Nancy Yang
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tramy Luong
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Philippe R Labrias
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Inga Peter
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Judy H Cho
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Bruce E Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York NY, USA
| | - Jose C Clemente
- Icahn Institute for Genomics & Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York NY, USA
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Paramsothy S, Nielsen S, Kamm MA, Deshpande NP, Faith JJ, Clemente JC, Paramsothy R, Walsh AJ, van den Bogaerde J, Samuel D, Leong RWL, Connor S, Ng W, Lin E, Borody TJ, Wilkins MR, Colombel JF, Mitchell HM, Kaakoush NO. Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis. Gastroenterology 2019; 156:1440-1454.e2. [PMID: 30529583 DOI: 10.1053/j.gastro.2018.12.001] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy. METHODS We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multidonor FMT or placebo enemas, 5 d/wk for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 large-bowel biopsy samples from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT, if applicable. We analyzed 105 fecal samples from the 14 individual donors (n = 55), who in turn contributed to 21 multidonor batches (n = 50). Bacteria in colonic and fecal samples were analyzed by both 16S ribosomal RNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics, and 60 fecal samples were analyzed for metabolome features. RESULTS FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared with patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans compared with patients who did not achieve remission after FMT and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia species and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus species in donor stool was associated with no response to FMT. CONCLUSIONS In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov, Number NCT01896635.
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Affiliation(s)
- Sudarshan Paramsothy
- University of New South Wales, Sydney, Australia; Icahn School of Medicine at Mount Sinai, New York, New York; St Vincent's Hospital, Sydney, Australia; Nambour General Hospital, Nambour, Australia; Bankstown-Lidcombe Hospital, Sydney, Australia
| | | | - Michael A Kamm
- St Vincent's Hospital and University of Melbourne, Melbourne, Australia
| | | | | | | | | | | | | | | | | | | | - Watson Ng
- Liverpool Hospital, Sydney, Australia
| | - Enmoore Lin
- Centre for Digestive Diseases, Sydney, Australia
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Contijoch EJ, Britton GJ, Yang C, Mogno I, Li Z, Ng R, Llewellyn SR, Hira S, Johnson C, Rabinowitz KM, Barkan R, Dotan I, Hirten RP, Fu SC, Luo Y, Yang N, Luong T, Labrias PR, Lira S, Peter I, Grinspan A, Clemente JC, Kosoy R, Kim-Schulze S, Qin X, Castillo A, Hurley A, Atreja A, Rogers J, Fasihuddin F, Saliaj M, Nolan A, Reyes-Mercedes P, Rodriguez C, Aly S, Santa-Cruz K, Peters L, Suárez-Fariñas M, Huang R, Hao K, Zhu J, Zhang B, Losic B, Irizar H, Song WM, Di Narzo A, Wang W, Cohen BL, DiMaio C, Greenwald D, Itzkowitz S, Lucas A, Marion J, Maser E, Ungaro R, Naymagon S, Novak J, Shah B, Ullman T, Rubin P, George J, Legnani P, Telesco SE, Friedman JR, Brodmerkel C, Plevy S, Cho JH, Colombel JF, Schadt EE, Argmann C, Dubinsky M, Kasarskis A, Sands B, Faith JJ. Gut microbiota density influences host physiology and is shaped by host and microbial factors. eLife 2019; 8:e40553. [PMID: 30666957 PMCID: PMC6342524 DOI: 10.7554/elife.40553] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022] Open
Abstract
To identify factors that regulate gut microbiota density and the impact of varied microbiota density on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, and therapeutic interventions. Physiologic features of the host (carrying capacity) and the fitness of the gut microbiota shape microbiota density. Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohn's disease, ulcerative colitis, and ileal pouch-anal anastomosis. The gut microbiota in recurrent Clostridium difficile infection had lower density and reduced fitness that were restored by fecal microbiota transplantation. Understanding the interplay between microbiota and disease in terms of microbiota density, host carrying capacity, and microbiota fitness provide new insights into microbiome structure and microbiome targeted therapeutics. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR, Ng R, Li Z, Mortha A, Merad M, Das A, Gevers D, McGovern DPB, Singh N, Braun J, Jacobs JP, Clemente JC, Grinspan A, Sands BE, Colombel JF, Dubinsky MC, Faith JJ. Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt + Regulatory T Cells and Exacerbate Colitis in Mice. Immunity 2019; 50:212-224.e4. [PMID: 30650377 PMCID: PMC6512335 DOI: 10.1016/j.immuni.2018.12.015] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/03/2018] [Accepted: 12/13/2018] [Indexed: 12/13/2022]
Abstract
Microbiota are thought to influence the development and progression of inflammatory bowel disease (IBD), but determining generalizable effects of microbiota on IBD etiology requires larger-scale functional analyses. We colonized germ-free mice with intestinal microbiotas from 30 healthy and IBD donors and determined the homeostatic intestinal T cell response to each microbiota. Compared to microbiotas from healthy donors, transfer of IBD microbiotas into germ-free mice increased numbers of intestinal Th17 cells and Th2 cells and decreased numbers of RORγt+ Treg cells. Colonization with IBD microbiotas exacerbated disease in a model where colitis is induced upon transfer of naive T cells into Rag1-/- mice. The proportions of Th17 and RORγt+ Treg cells induced by each microbiota were predictive of human disease status and accounted for disease severity in the Rag1-/- colitis model. Thus, an impact on intestinal Th17 and RORγt+ Treg cell compartments emerges as a unifying feature of IBD microbiotas, suggesting a general mechanism for microbial contribution to IBD pathogenesis.
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Affiliation(s)
- Graham J Britton
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eduardo J Contijoch
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ilaria Mogno
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia H Vennaro
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sean R Llewellyn
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruby Ng
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhihua Li
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arthur Mortha
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anuk Das
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Dermot P B McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Namita Singh
- Pediatric Gastroenterology and Inflammatory Bowel Disease, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jonathan Braun
- UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jose C Clemente
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce E Sands
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla C Dubinsky
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Pediatric Gastroenterology and Hepatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Tsay JCJ, Wu BG, Badri MH, Clemente JC, Shen N, Meyn P, Li Y, Yie TA, Lhakhang T, Olsen E, Murthy V, Michaud G, Sulaiman I, Tsirigos A, Heguy A, Pass H, Weiden MD, Rom WN, Sterman DH, Bonneau R, Blaser MJ, Segal LN. Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer. Am J Respir Crit Care Med 2018; 198:1188-1198. [PMID: 29864375 PMCID: PMC6221574 DOI: 10.1164/rccm.201710-2118oc] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 06/04/2018] [Indexed: 12/17/2022] Open
Abstract
RATIONALE In lung cancer, upregulation of the PI3K (phosphoinositide 3-kinase) pathway is an early event that contributes to cell proliferation, survival, and tissue invasion. Upregulation of this pathway was recently described as associated with enrichment of the lower airways with bacteria identified as oral commensals. OBJECTIVES We hypothesize that host-microbe interactions in the lower airways of subjects with lung cancer affect known cancer pathways. METHODS Airway brushings were collected prospectively from subjects with lung nodules at time of diagnostic bronchoscopy, including 39 subjects with final lung cancer diagnoses and 36 subjects with noncancer diagnoses. In addition, samples from 10 healthy control subjects were included. 16S ribosomal RNA gene amplicon sequencing and paired transcriptome sequencing were performed on all airway samples. In addition, an in vitro model with airway epithelial cells exposed to bacteria/bacterial products was performed. MEASUREMENTS AND MAIN RESULTS The composition of the lower airway transcriptome in the patients with cancer was significantly different from the control subjects, which included up-regulation of ERK (extracellular signal-regulated kinase) and PI3K signaling pathways. The lower airways of patients with lung cancer were enriched for oral taxa (Streptococcus and Veillonella), which was associated with up-regulation of the ERK and PI3K signaling pathways. In vitro exposure of airway epithelial cells to Veillonella, Prevotella, and Streptococcus led to upregulation of these same signaling pathways. CONCLUSIONS The data presented here show that several transcriptomic signatures previously identified as relevant to lung cancer pathogenesis are associated with enrichment of the lower airway microbiota with oral commensals.
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Affiliation(s)
| | | | - Michelle H. Badri
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, New York
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nan Shen
- Department of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Peter Meyn
- New York University Genomic Technology Center, New York, New York; and
| | - Yonghua Li
- Division of Pulmonary and Critical Care Medicine
| | - Ting-An Yie
- Division of Pulmonary and Critical Care Medicine
| | - Tenzin Lhakhang
- New York University Genomic Technology Center, New York, New York; and
| | - Evan Olsen
- Division of Pulmonary and Critical Care Medicine
| | - Vivek Murthy
- Division of Pulmonary and Critical Care Medicine
| | | | | | | | - Adriana Heguy
- New York University Genomic Technology Center, New York, New York; and
| | | | | | | | | | - Richard Bonneau
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, New York
- New York University Center for Data Science, New York, New York
| | - Martin J. Blaser
- Department of Medicine, New York University School of Medicine, New York, New York
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Katz Sand I, Zhu Y, Ntranos A, Clemente JC, Cekanaviciute E, Brandstadter R, Crabtree-Hartman E, Singh S, Bencosme Y, Debelius J, Knight R, Cree BAC, Baranzini SE, Casaccia P. Disease-modifying therapies alter gut microbial composition in MS. Neurol Neuroimmunol Neuroinflamm 2018; 6:e517. [PMID: 30568995 PMCID: PMC6278850 DOI: 10.1212/nxi.0000000000000517] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/10/2018] [Indexed: 11/24/2022]
Abstract
Objective To determine the effects of the disease-modifying therapies, glatiramer acetate (GA) and dimethyl fumarate (DMF), on the gut microbiota in patients with MS. Methods Participants with relapsing MS who were either treatment-naive or treated with GA or DMF were recruited. Peripheral blood mononuclear cells were immunophenotyped. Bacterial DNA was extracted from stool, and amplicons targeting the V4 region of the bacterial/archaeal 16S rRNA gene were sequenced (Illumina MiSeq). Raw reads were clustered into Operational Taxonomic Units using the GreenGenes database. Differential abundance analysis was performed using linear discriminant analysis effect size. Phylogenetic investigation of communities by reconstruction of unobserved states was used to investigate changes to functional pathways resulting from differential taxon abundance. Results One hundred sixty-eight participants were included (treatment-naive n = 75, DMF n = 33, and GA n = 60). Disease-modifying therapies were associated with changes in the fecal microbiota composition. Both therapies were associated with decreased relative abundance of the Lachnospiraceae and Veillonellaceae families. In addition, DMF was associated with decreased relative abundance of the phyla Firmicutes and Fusobacteria and the order Clostridiales and an increase in the phylum Bacteroidetes. Despite the different changes in bacterial taxa, there was an overlap between functional pathways affected by both therapies. Interpretation Administration of GA or DMF is associated with differences in gut microbial composition in patients with MS. Because those changes affect critical metabolic pathways, we hypothesize that our findings may highlight mechanisms of pathophysiology and potential therapeutic intervention requiring further investigation.
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Affiliation(s)
- Ilana Katz Sand
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Yunjiao Zhu
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Achilles Ntranos
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Jose C Clemente
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Egle Cekanaviciute
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Rachel Brandstadter
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Elizabeth Crabtree-Hartman
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Sneha Singh
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Yadira Bencosme
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Justine Debelius
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Rob Knight
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Bruce A C Cree
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Sergio E Baranzini
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
| | - Patrizia Casaccia
- Department of Neurology (I.K.S., A.N., R.B., Y.B.), Department of Neuroscience (Y.Z., P.C.), and Department of Genetics & Genomic Sciences, Icahn Institute for Genomics & Multiscale Biology (J.C.C.), Icahn School of Medicine at Mount Sinai; Department of Neurology (E.C., E.C.-H., S.S., B.A.C.C., S.E.B.), Weill Institute for Neurosciences, University of California, San Francisco; E.C. is now with Universities Space Research Association, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA; Department of Pediatrics (J.D., R.K.), Department of Computer Science & Engineering (R.K.), and Center for Microbiome Innovation (R.K.), University of California, San Diego; and Neuroscience Initiative (P.C.), Advanced Research Science Center at the Graduate Center of the City University of New York
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Sulaiman I, Wu BG, Li Y, Scott AS, Malecha P, Scaglione B, Wang J, Basavaraj A, Chung S, Bantis K, Carpenito J, Clemente JC, Shen N, Bessich J, Rafeq S, Michaud G, Donington J, Naidoo C, Theron G, Schattner G, Garofano S, Condos R, Kamelhar D, Addrizzo-Harris D, Segal LN. Evaluation of the airway microbiome in nontuberculous mycobacteria disease. Eur Respir J 2018; 52:13993003.00810-2018. [PMID: 30093571 DOI: 10.1183/13993003.00810-2018] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/29/2018] [Indexed: 01/15/2023]
Abstract
Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether NTM disease was associated with a distinct airway microbiota and immune profile.297 oral wash and induced sputum samples were collected from 106 participants with respiratory symptoms and imaging abnormalities compatible with NTM. Lower airway samples were obtained in 20 participants undergoing bronchoscopy. 16S rRNA gene and nested mycobacteriome sequencing approaches characterised microbiota composition. In addition, inflammatory profiles of lower airway samples were examined.The prevalence of NTM+ cultures was 58%. Few changes were noted in microbiota characteristics or composition in oral wash and sputum samples among groups. Among NTM+ samples, 27% of the lower airway samples were enriched with Mycobacterium A mycobacteriome approach identified Mycobacterium in a greater percentage of samples, including some nonpathogenic strains. In NTM+ lower airway samples, taxa identified as oral commensals were associated with increased inflammatory biomarkers.The 16S rRNA gene sequencing approach is not sensitive in identifying NTM among airway samples that are culture-positive. However, associations between lower airway inflammation and microbiota signatures suggest a potential role for these microbes in the inflammatory process in NTM disease.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Adrienne S Scott
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Patrick Malecha
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin Scaglione
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jing Wang
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Ashwin Basavaraj
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samuel Chung
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Katrina Bantis
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Joseph Carpenito
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose C Clemente
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nan Shen
- Dept of Genetics and Genomic Sciences and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jamie Bessich
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Samaan Rafeq
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Gaetene Michaud
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jessica Donington
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Charissa Naidoo
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Grant Theron
- Medicine and Health Sciences, Stellenbosch University, DST/NRF of Excellence for Biomedical Tuberculosis Research and SA MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics Tygerberg, Cape Town, South Africa
| | - Gail Schattner
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Suzette Garofano
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Rany Condos
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - David Kamelhar
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Doreen Addrizzo-Harris
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA.,Dept of Medicine, New York University School of Medicine, New York, NY, USA
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Chen L, He Z, Iuga AC, Martins Filho SN, Faith JJ, Clemente JC, Deshpande M, Jayaprakash A, Colombel JF, Lafaille JJ, Sachidanandam R, Furtado GC, Lira SA. Diet Modifies Colonic Microbiota and CD4 + T-Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-Cell Expression of Interleukin 23. Gastroenterology 2018; 155:1177-1191.e16. [PMID: 29909020 PMCID: PMC6174107 DOI: 10.1053/j.gastro.2018.06.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/24/2018] [Accepted: 06/11/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Several studies have shown that signaling via the interleukin 23 (IL23) receptor is required for development of colitis. We studied the roles of IL23, dietary factors, alterations to the microbiota, and T cells in the development and progression of colitis in mice. METHODS All mice were maintained on laboratory diet 5053, unless otherwise noted. We generated mice that express IL23 in CX3CR1-positive myeloid cells (R23FR mice) upon cyclic administration of tamoxifen dissolved in diet 2019. Diets 2019 and 5053 have minor differences in the overall composition of protein, fat, fiber, minerals, and vitamins. CX3CR1CreER mice (FR mice) were used as controls. Some mice were given antibiotics, and others were raised in a germ-free environment. Intestinal tissues were collected and analyzed by histology and flow cytometry. Feces were collected and analyzed by 16S rDNA sequencing. Feces from C57/Bl6, R23FR, or FR mice were fed to FR and R23FR germ-free mice in microbiota transplant experiments. We also performed studies with R23FR/Rag-/-, R23FR/Mu-/-, and R23FR/Tcrd-/- mice. R23FR mice were given injections of antibodies against CD4 or CD8 to deplete T cells. Mesenteric lymph nodes and large intestine CD4+ cells from R23FR or FR mice in remission from colitis were transferred into Rag-/- mice. CD4+ cells were isolated from donor R23FR mice and recipient Rag-/- mice, and T-cell receptor sequences were determined. RESULTS Expression of IL23 led to development of a relapsing-remitting colitis that was dependent on the microbiota and CD4+ T cells. The relapses were caused by switching from the conventional diet used in our facility (diet 5053) to the diet 2019 and were not dependent on tamoxifen after the first cycle. The switch in the diet modified the microbiota but did not alter levels of IL23 in intestinal tissues compared with mice that remained on the conventional diet. Mesenteric lymph nodes and large intestine CD4+ cells from R23FR mice in remission, but not from FR mice, induced colitis after transfer into Rag-/- mice, but only when these mice were placed on the diet 2019. The CD4+ T-cell receptor repertoire of Rag-/- mice with colitis (fed the 2019 diet) was less diverse than that from donor mice and Rag-/- mice without colitis (fed the 5053 diet) because of expansion of dominant T-cell clones. CONCLUSIONS We developed mice that express IL23 in CX3CR1-positive myeloid cells (R23FR mice) and found that they are more susceptible to diet-induced colitis than mice that do not express IL23. The R23FR mice have a population of CD4+ T cells that becomes activated in response to dietary changes and alterations to the intestinal microbiota. The results indicate that alterations in the diet, intestinal microbiota, and IL23 signaling can contribute to pathogenesis of inflammatory bowel disease.
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Affiliation(s)
- Lili Chen
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhengxiang He
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alina Cornelia Iuga
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Sebastião N. Martins Filho
- Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil,Department of Pathology and Laboratory Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jose C. Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madhura Deshpande
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan J. Lafaille
- Department of Pathology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Ravi Sachidanandam
- Girihlet Inc. Oakland, CA 94609, USA,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Glaucia C. Furtado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio A. Lira
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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48
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Fernandez DM, Clemente JC, Giannarelli C. Physical Activity, Immune System, and the Microbiome in Cardiovascular Disease. Front Physiol 2018; 9:763. [PMID: 30013482 PMCID: PMC6036301 DOI: 10.3389/fphys.2018.00763] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/30/2018] [Indexed: 12/23/2022] Open
Abstract
Cardiovascular health is a primary research focus, as it is a leading contributor to mortality and morbidity worldwide, and is prohibitively costly for healthcare. Atherosclerosis, the main driver of cardiovascular disease, is now recognized as an inflammatory disorder. Physical activity (PA) may have a more important role in cardiovascular health than previously expected. This review overviews the contribution of PA to cardiovascular health, the inflammatory role of atherosclerosis, and the emerging evidence of the microbiome as a regulator of inflammation.
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Affiliation(s)
- Dawn M. Fernandez
- Department of Medicine, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Chiara Giannarelli
- Department of Medicine, Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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Llewellyn SR, Britton GJ, Contijoch EJ, Vennaro OH, Mortha A, Colombel JF, Grinspan A, Clemente JC, Merad M, Faith JJ. Interactions Between Diet and the Intestinal Microbiota Alter Intestinal Permeability and Colitis Severity in Mice. Gastroenterology 2018; 154:1037-1046.e2. [PMID: 29174952 PMCID: PMC5847454 DOI: 10.1053/j.gastro.2017.11.030] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS It is not clear how the complex interactions between diet and the intestinal microbiota affect development of mucosal inflammation or inflammatory bowel disease. We investigated interactions between dietary ingredients, nutrients, and the microbiota in specific pathogen-free (SPF) and germ-free (GF) mice given more than 40 unique diets; we quantified individual and synergistic effects of dietary macronutrients and the microbiota on intestinal health and development of colitis. METHODS C56BL/6J SPF and GF mice were placed on custom diets containing different concentrations and sources of protein, fat, digestible carbohydrates, and indigestible carbohydrates (fiber). After 1 week, SPF and GF mice were given dextran sulfate sodium (DSS) to induce colitis. Disease severity was determined based on the percent weight change from baseline, and modeled as a function of the concentration of each macronutrient in the diet. In unchallenged mice, we measured intestinal permeability by feeding mice labeled dextran and measuring levels in blood. Feces were collected and microbiota were analyzed by 16S rDNA sequencing. We collected colons from mice and performed transcriptome analyses. RESULTS Fecal microbiota varied with diet; the concentration of protein and fiber had the strongest effect on colitis development. Among 9 fiber sources tested, psyllium, pectin, and cellulose fiber reduced the severity of colitis in SPF mice, whereas methylcellulose increased severity. Increasing dietary protein increased the density of the fecal microbiota and the severity of colitis in SPF mice, but not in GF mice or mice given antibiotics. Psyllium fiber reduced the severity of colitis through microbiota-dependent and microbiota-independent mechanisms. Combinatorial perturbations to dietary casein protein and psyllium fiber in parallel accounted for most variation in gut microbial density and intestinal permeability in unchallenged mice, as well as the severity of DSS-induced colitis; changes in 1 ingredient could be offset by changes in another. CONCLUSIONS In an analysis of the effects of different dietary components and the gut microbiota on mice with and without DSS-induced colitis, we found complex mixtures of nutrients affect intestinal permeability, gut microbial density, and development of intestinal inflammation.
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Affiliation(s)
- Sean R. Llewellyn
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Graham J. Britton
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Eduardo J. Contijoch
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Olivia H. Vennaro
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Arthur Mortha
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jose C. Clemente
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Miriam Merad
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Department of Oncological Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jeremiah J. Faith
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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Abstract
The role of the gut microbiome in models of inflammatory and autoimmune disease is now well characterized. Renewed interest in the human microbiome and its metabolites, as well as notable advances in host mucosal immunology, has opened multiple avenues of research to potentially modulate inflammatory responses. The complexity and interdependence of these diet-microbe-metabolite-host interactions are rapidly being unraveled. Importantly, most of the progress in the field comes from new knowledge about the functional properties of these microorganisms in physiology and their effect in mucosal immunity and distal inflammation. This review summarizes the preclinical and clinical evidence on how dietary, probiotic, prebiotic, and microbiome based therapeutics affect our understanding of wellness and disease, particularly in autoimmunity.
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Affiliation(s)
- Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julia Manasson
- Department of Medicine, Division of Rheumatology, New York University School of Medicine and Hospital for Joint Diseases, New York, NY 10003, USA
| | - Jose U Scher
- Department of Medicine, Division of Rheumatology, New York University School of Medicine and Hospital for Joint Diseases, New York, NY 10003, USA
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