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Hertz S, Anderson JM, Nielsen HL, Schachtschneider C, McCauley KE, Özçam M, Larsen L, Lynch SV, Nielsen H. Fecal microbiota is associated with extraintestinal manifestations in inflammatory bowel disease. Ann Med 2024; 56:2338244. [PMID: 38648495 PMCID: PMC11036898 DOI: 10.1080/07853890.2024.2338244] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/17/2024] [Indexed: 04/25/2024] Open
Abstract
INTRODUCTION A large proportion of patients with inflammatory bowel disease (IBD) experience IBD-related inflammatory conditions outside of the gastrointestinal tract, termed extraintestinal manifestations (EIMs) which further decreases quality of life and, in extreme cases, can be life threatening. The pathogenesis of EIMs remains unknown, and although gut microbiota alterations are a well-known characteristic of patients with IBD, its relationship with EIMs remains sparsely investigated. This study aimed to compare the gut microbiota of patients with IBD with and without EIMs. METHODS A total of 131 Danish patients with IBD were included in the study, of whom 86 had a history of EIMs (IBD-EIM) and 45 did not (IBD-C). Stool samples underwent 16S rRNA sequencing. Amplicon sequence variants (ASVs) were mapped to the Silva database. Diversity indices and distance matrices were compared between IBD-EIM and IBD-C. Differentially abundant ASVs were identified using a custom multiple model statistical analysis approach, and modules of co-associated bacteria were identified using sparse correlations for compositional data (SparCC) and related to patient EIM status. RESULTS Patients with IBD and EIMs exhibited increased disease activity, body mass index, increased fecal calprotectin levels and circulating monocytes and neutrophils. Microbiologically, IBD-EIM exhibited lower fecal microbial diversity than IBD-C (Mann-Whitney's test, p = .01) and distinct fecal microbiota composition (permutational multivariate analysis of variance; weighted UniFrac, R2 = 0.018, p = .01). A total of 26 ASVs exhibited differential relative abundances between IBD-EIM and IBD-C, including decreased Agathobacter and Blautia and increased Eggerthella lenta in the IBD-EIM group. SparCC analysis identified 27 bacterial co-association modules, three of which were negatively related to EIM (logistic regression, p < .05) and included important health-associated bacteria, such as Agathobacter and Faecalibacterium. CONCLUSIONS The fecal microbiota in IBD patients with EIMs is distinct from that in IBD patients without EIM and could be important for EIM pathogenesis.
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Affiliation(s)
- Sandra Hertz
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline Moltzau Anderson
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Hans Linde Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Claire Schachtschneider
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Kathryn E. McCauley
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Mustafa Özçam
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Lone Larsen
- Department of Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Aalborg University, Aalborg, Denmark
| | - Susan V. Lynch
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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McCauley KE, Durack J, Lynch KV, Fadrosh DW, Fujimura KE, Vundla F, Özçam M, LeBeau P, Caltroni A, Burns P, Tran HT, Bacharier LB, Kattan M, O'Connor GT, Wood RA, Togias A, Boushey HA, Jackson DJ, Gern JE, Lynch SV. Early-life Nasal Microbiota Dynamics Relate to Longitudinal Respiratory Phenotypes in Urban Children. J Allergy Clin Immunol 2024:S0091-6749(24)00195-7. [PMID: 38423369 DOI: 10.1016/j.jaci.2023.12.032] [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: 07/28/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 03/02/2024]
Abstract
BACKGROUND Five distinct respiratory phenotypes based on latent classes of longitudinal patterns of wheezing, allergic sensitization and pulmonary function measured from 0-7 years have been described in urban children. OBJECTIVE To determine whether distinct respiratory phenotypes associate with early-life upper respiratory microbiota development and environmental microbial exposures. METHODS Microbiota profiling was performed using 16S rRNA-based sequencing of nasal samples collected at 12 (n=120) or 36 (n=142) months of age and paired house dust samples collected at 3 months (12-month, N=73; 36-month, N=90) from all four centers in the Urban Environment and Childhood Asthma (URECA) cohort. RESULTS In these high-risk urban children, nasal microbiota increased in diversity between 12 and 36 months of age (ß= 2.04, P=0.006). Age-related changes in microbiota evenness differed significantly by respiratory phenotypes (Interaction P=0.0007) increasing most in the transient-wheeze group. At 12 months of age, respiratory illness (R2=0.055, p=0.0001) and dominant bacterial genus (R2=0.59, p=0.0001) explained variance in nasal microbiota composition and enrichment of Moraxella and Haemophilus members was associated with both transient- and high-wheeze phenotypes. By 36 months, nasal microbiota significantly associated with respiratory phenotypes (R2=0.019, P=0.0376) and Moraxella dominated microbiota associated specifically with atopy-associated respiratory phenotypes. CONCLUSION Nasal microbiota development over the course of early childhood and composition at three years of age associates with longitudinal respiratory phenotypes. These data provide evidence for an early-life window of airway microbiota development that is influenced by environmental microbial exposures in infancy and associated with wheeze- and atopy-associated respiratory phenotypes through 7 years of age.
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Affiliation(s)
- Kathryn E McCauley
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Juliana Durack
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Kole V Lynch
- Department of Medicine, University of California, San Francisco, CA, USA.
| | - Douglas W Fadrosh
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Kei E Fujimura
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Faith Vundla
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Mustafa Özçam
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Petra LeBeau
- Rho Federal Systems Division Inc., Durham, NC, USA; Now employed at PPD, part of Thermo Fisher Scientific, Wilmington, NC, USA
| | | | | | - Hoang T Tran
- Rho Federal Systems Division Inc., Durham, NC, USA
| | - Leonard B Bacharier
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Meyer Kattan
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Robert A Wood
- Departments of Pediatrics and Allergy and Immunology, Johns Hopkins University, Baltimore, MD
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Homer A Boushey
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, CA, USA.
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Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Rep Med 2024; 5:101350. [PMID: 38134931 PMCID: PMC10829755 DOI: 10.1016/j.xcrm.2023.101350] [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: 03/28/2023] [Revised: 09/15/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023]
Abstract
Every year, 11% of infants are born preterm with significant health consequences, with the vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) preterm birth (PTB; <37 weeks) or (2) early preterm birth (ePTB; <32 weeks) from 9 vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from public raw data via phylogenetic harmonization. The predictive models are validated on two independent unpublished datasets representing 331 samples from 148 pregnant individuals. The top-performing models (among 148 and 121 submissions from 318 teams) achieve area under the receiver operator characteristic (AUROC) curve scores of 0.69 and 0.87 predicting PTB and ePTB, respectively. Alpha diversity, VALENCIA community state types, and composition are important features in the top-performing models, most of which are tree-based methods. This work is a model for translation of microbiome data into clinically relevant predictive models and to better understand preterm birth.
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Affiliation(s)
- Jonathan L Golob
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA.
| | - Tomiko T Oskotsky
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
| | - Alice S Tang
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Alennie Roldan
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | - Connie W Y Ha
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; March of Dimes Prematurity Research Center at Stanford University, Stanford, CA, USA
| | | | - Antonio Parraga-Leo
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia, Spain; IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Camilla Wibrand
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Boris Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Gaia Andreoletti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Idit Kosti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Jifan Gao
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhoujingpeng Wei
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Pierfrancesco Novielli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy
| | - Donato Romano
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy
| | - Ester Pantaleo
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Alfonso Monaco
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Mirco Vacca
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Maria De Angelis
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Roberto Bellotti
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Sabina Tangaro
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy
| | - Abigail Kuntzleman
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Isaac Bigcraft
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Stephen Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Daehun Bae
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Eunyoung Kim
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jongbum Jeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Kevin R Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA
| | - Sherrianne Ng
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Patricia Diaz-Gimeno
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Phillip R Bennett
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Gustavo Stolovitzky
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA; Thomas J. Watson Research Center, IBM, Yorktown Heights, NY, USA; Sema4, Stamford, CT, USA
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Nardhy Gomez-Lopez
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Detroit Medical Center, Detroit, MI, USA; Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Center for Academic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - James C Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marina Sirota
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
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4
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Wu KC, McCauley KE, Lynch SV, Nayak RR, King NJ, Patel S, Kim TY, Condra K, Fadrosh D, Nguyen D, Lin DL, Lynch K, Rogers SJ, Carter JT, Posselt AM, Stewart L, Schafer AL. Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy. J Bone Miner Res 2024:zjad017. [PMID: 38477719 DOI: 10.1093/jbmr/zjad017] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 03/14/2024]
Abstract
Laparoscopic sleeve gastrectomy (LSG), the most common bariatric surgical procedure, leads to durable weight loss and improves obesity-related comorbidities. However, it induces abnormalities in bone metabolism. One unexplored potential contributor is the gut microbiome, which influences bone metabolism and is altered after surgery. We characterized the relationship between the gut microbiome and skeletal health in severe obesity and after LSG. In a prospective cohort study, 23 adults with severe obesity underwent skeletal health assessment and stool collection preoperatively and 6 mo after LSG. Gut microbial diversity and composition were characterized using 16S rRNA gene sequencing, and fecal concentrations of short-chain fatty acids (SCFA) were measured with LC-MS/MS. Spearman's correlations and PERMANOVA analyses were applied to assess relationships between the gut microbiome and bone health measures including serum bone turnover markers (C-terminal telopeptide of type 1 collagen [CTx] and procollagen type 1 N-terminal propeptide [P1NP]), areal BMD, intestinal calcium absorption, and calciotropic hormones. Six months after LSG, CTx and P1NP increased (by median 188% and 61%, P < .01) and femoral neck BMD decreased (mean -3.3%, P < .01). Concurrently, there was a decrease in relative abundance of the phylum Firmicutes. Although there were no change in overall microbial diversity or fecal SCFA concentrations after LSG, those with greater within-subject change in gut community microbial composition (β-diversity) postoperatively had greater increases in P1NP level (ρ = 0.48, P = .02) and greater bone loss at the femoral neck (ρ = -0.43, P = .04). In addition, within-participant shifts in microbial richness/evenness (α-diversity) were associated with changes in IGF-1 levels (ρ = 0.56, P < .01). The lower the postoperative fecal butyrate concentration, the lower the IGF-1 level (ρ = 0.43, P = .04). Meanwhile, the larger the decrease in butyrate concentration, the higher the postoperative CTx (ρ = -0.43, P = .04). These findings suggest that LSG-induced gut microbiome alteration may influence skeletal outcomes postoperatively, and microbial influences on butyrate formation and IGF-1 are possible mechanisms.
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Affiliation(s)
- Karin C Wu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Kathryn E McCauley
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Renuka R Nayak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Nicole J King
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Sheena Patel
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, United States
| | - Tiffany Y Kim
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Katherine Condra
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Doug Fadrosh
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Dat Nguyen
- The Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Din L Lin
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Kole Lynch
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Stanley J Rogers
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Jonathan T Carter
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Andrew M Posselt
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Lygia Stewart
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
- Surgical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Anne L Schafer
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, United States
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5
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Schoeps VA, Zhou X, Horton MK, Zhu F, McCauley KE, Nasr Z, Virupakshaiah A, Gorman MP, Benson LA, Weinstock‐Guttman B, Waldman A, Banwell BL, Bar‐Or A, Marrie RA, van Domselaar G, O'Mahony J, Mirza AI, Bernstein CN, Yeh EA, Casper TC, Lynch SV, Tremlett H, Baranzini S, Waubant E. Short-chain fatty acid producers in the gut are associated with pediatric multiple sclerosis onset. Ann Clin Transl Neurol 2024; 11:169-184. [PMID: 37955284 PMCID: PMC10791026 DOI: 10.1002/acn3.51944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/14/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023] Open
Abstract
OBJECTIVE The relationship between multiple sclerosis and the gut microbiome has been supported by animal models in which commensal microbes are required for the development of experimental autoimmune encephalomyelitis. However, observational study findings in humans have only occasionally converged when comparing multiple sclerosis cases and controls which may in part reflect confounding by comorbidities and disease duration. The study of microbiome in pediatric-onset multiple sclerosis offers unique opportunities as it is closer to biological disease onset and minimizes confounding by comorbidities and environmental exposures. METHODS A multicenter case-control study in which 35 pediatric-onset multiple sclerosis cases were 1:1 matched to healthy controls on age, sex, self-reported race, ethnicity, and recruiting site. Linear mixed effects models, weighted correlation network analyses, and PICRUSt2 were used to identify microbial co-occurrence networks and for predicting functional abundances based on marker gene sequences. RESULTS Two microbial co-occurrence networks (one reaching significance after adjustment for multiple comparisons; q < 0.2) were identified, suggesting interdependent bacterial taxa that exhibited association with disease status. Both networks indicated a potentially protective effect of higher relative abundance of bacteria observed in these clusters. Functional predictions from the significant network suggested a contribution of short-chain fatty acid producers through anaerobic fermentation pathways in healthy controls. Consistent family-level findings from an independent Canadian-US study (19 case/control pairs) included Ruminococaccaeae and Lachnospiraceae (p < 0.05). Macronutrient intake was not significantly different between cases and controls, minimizing the potential for dietary confounding. INTERPRETATION Our results suggest that short-chain fatty acid producers may be important contributors to multiple sclerosis onset.
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Affiliation(s)
- Vinicius A. Schoeps
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Xiaoyuan Zhou
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Mary K. Horton
- Division of EpidemiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Feng Zhu
- Division of NeurologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Kathryn E. McCauley
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Zahra Nasr
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Akash Virupakshaiah
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Mark P. Gorman
- Department of NeurologyBoston Children's HospitalBostonMassachusettsUSA
| | - Leslie A. Benson
- Department of NeurologyBoston Children's HospitalBostonMassachusettsUSA
| | | | - Amy Waldman
- Department of NeurologyChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Brenda L. Banwell
- Department of NeurologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Amit Bar‐Or
- Department of NeurologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ruth Ann Marrie
- Department of Internal MedicineUniversity of ManitobaWinnipegManitobaCanada
| | - Gary van Domselaar
- Department of Internal MedicineUniversity of ManitobaWinnipegManitobaCanada
| | - Julia O'Mahony
- Department of Internal MedicineUniversity of ManitobaWinnipegManitobaCanada
| | - Ali I. Mirza
- Division of NeurologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | | | - E. Ann Yeh
- The Hospital for Sick ChildrenUniversity of TorontoTorontoOntarioCanada
| | | | - Susan V. Lynch
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Helen Tremlett
- Division of NeurologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Sergio Baranzini
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Emmanuelle Waubant
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
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6
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Yong GJM, Porsche CE, Sitarik AR, Fujimura KE, McCauley K, Nguyen DT, Levin AM, Woodcroft KJ, Ownby DR, Rundle AG, Johnson CC, Cassidy-Bushrow A, Lynch SV. Precocious infant fecal microbiome promotes enterocyte barrier dysfuction, altered neuroendocrine signaling and associates with increased childhood obesity risk. Gut Microbes 2024; 16:2290661. [PMID: 38117587 PMCID: PMC10761186 DOI: 10.1080/19490976.2023.2290661] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023] Open
Abstract
Early life gut microbiome composition has been correlated with childhood obesity, though microbial functional contributions to disease origins remain unclear. Here, using an infant birth cohort (n = 349) we identify a distinct fecal microbiota composition in 1-month-old infants with the lowest rate of exclusive breastfeeding, that relates with higher relative risk for obesity and overweight phenotypes at two years. Higher-risk infant fecal microbiomes exhibited accelerated taxonomic and functional maturation and broad-ranging metabolic reprogramming, including reduced concentrations of neuro-endocrine signals. In vitro, exposure of enterocytes to fecal extracts from higher-risk infants led to upregulation of genes associated with obesity and with expansion of nutrient sensing enteroendocrine progenitor cells. Fecal extracts from higher-risk infants also promoted enterocyte barrier dysfunction. These data implicate dysregulation of infant microbiome functional development, and more specifically promotion of enteroendocrine signaling and epithelial barrier impairment in the early-life developmental origins of childhood obesity.
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Affiliation(s)
- Germaine J. M. Yong
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA, USA
- Asian Microbiome Library Pte Ltd, Singapore and Singapore Institute of Food and Biotechnology Innovation, Singapore, Singapore
| | - Cara E. Porsche
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Alexandra R. Sitarik
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Kei E. Fujimura
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA, USA
- Genetic Disease Laboratory, California Department of Public Health, San Francisco, CA, USA
| | - Kathryn McCauley
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Dat T. Nguyen
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA, USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Albert M. Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | | | - Dennis R. Ownby
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Augusta University, Augusta, GA, USA
| | - Andrew G. Rundle
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Christine C. Johnson
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | | | - Susan V. Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA, USA
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7
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Montassier E, Kitsios GD, Radder JE, Le Bastard Q, Kelly BJ, Panzer A, Lynch SV, Calfee CS, Dickson RP, Roquilly A. Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia. Nat Med 2023; 29:2793-2804. [PMID: 37957375 DOI: 10.1038/s41591-023-02617-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/17/2023] [Accepted: 09/27/2023] [Indexed: 11/15/2023]
Abstract
Respiratory microbial dysbiosis is associated with acute respiratory distress syndrome (ARDS) and hospital-acquired pneumonia (HAP) in critically ill patients. However, we lack reproducible respiratory microbiome signatures that can increase our understanding of these conditions and potential treatments. Here, we analyze 16S rRNA sequencing data from 2,177 respiratory samples collected from 1,029 critically ill patients (21.7% with ARDS and 26.3% with HAP) and 327 healthy controls, sourced from 17 published studies. After data harmonization and pooling of individual patient data, we identified microbiota signatures associated with ARDS, HAP and prolonged mechanical ventilation. Microbiota signatures for HAP and prolonged mechanical ventilation were characterized by depletion of a core group of microbes typical of healthy respiratory samples, and the ARDS microbiota signature was distinguished by enrichment of potentially pathogenic respiratory microbes, including Pseudomonas and Staphylococcus. Using machine learning models, we identified clinically informative, three- and four-factor signatures that predicted ARDS, HAP and prolonged mechanical ventilation with relatively high accuracy (area under the curve of 0.751, 0.72 and 0.727, respectively). We validated the signatures in an independent prospective cohort of 136 patients on mechanical ventillation and found that patients with microbiome signatures associated with ARDS, HAP or prolonged mechanical ventilation had longer times to successful extubation than patients lacking these signatures (hazard ratios of 1.56 (95% confidence interval (CI) 1.07-2.27), 1.51 (95% CI 1.02-2.23) and 1.50 (95% CI 1.03-2.18), respectively). Thus, we defined and validated robust respiratory microbiome signatures associated with ARDS and HAP that may help to identify promising targets for microbiome therapeutic modulation in critically ill patients.
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Affiliation(s)
- Emmanuel Montassier
- Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes Université, Inserm, CHU Nantes, Nantes, France.
- Service des Urgences, Nantes Université, CHU Nantes, Nantes, France.
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah E Radder
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Brendan J Kelly
- Department of Medicine, Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA, USA
| | - Ariane Panzer
- Department of Medicine, Division of Gastroenterology, University of California, San Francisco, CA, USA
| | - Susan V Lynch
- Department of Medicine, Division of Gastroenterology, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | - Robert P Dickson
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Health System, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, MI, USA
| | - Antoine Roquilly
- Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes Université, Inserm, CHU Nantes, Nantes, France.
- Service d'Anesthesie Réanimation, Nantes Université, CHU Nantes, Nantes, France.
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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8
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Steininger H, Moltzau-Anderson J, Lynch SV. Contributions of the early-life microbiome to childhood atopy and asthma development. Semin Immunol 2023; 69:101795. [PMID: 37379671 DOI: 10.1016/j.smim.2023.101795] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/13/2023] [Indexed: 06/30/2023]
Abstract
The rapid rise in atopy and asthma in industrialized nations has led to the identification of early life environmental factors that promote these conditions and spurred research into how such exposures may mediate the trajectory to childhood disease development. Over the past decade, the human microbiome has emerged as a key determinant of human health. This is largely due to the increasing appreciation for the myriad of non-mutually exclusive mechanisms by which microbes tune and train host immunity. Microbiomes, particularly those in early life, are shaped by extrinsic and intrinsic factors, including many of the exposures known to influence allergy and asthma risk. This has led to the over-arching hypothesis that such exposures mediate their effect on childhood atopy and asthma by altering the functions and metabolic productivity of microbiomes that shape immune function during this critical developmental period. The capacity to study microbiomes at the genetic and molecular level in humans from the pre-natal period into childhood with well-defined clinical outcomes, offers an unprecedented opportunity to identify early-life and inter-generational determinants of atopy and asthma outcomes. Moreover, such studies provide an integrative microbiome research framework that can be applied to other chronic inflammatory conditions. This review attempts to capture key studies in the field that offer insights into the developmental origins of childhood atopy and asthma, providing novel insights into microbial mediators of maladaptive immunity and chronic inflammatory disease in childhood.
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Affiliation(s)
- Holly Steininger
- Division of Gastroenterology, University of California, San Francisco, USA; Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, USA
| | - Jacqueline Moltzau-Anderson
- Division of Gastroenterology, University of California, San Francisco, USA; Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, USA; Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, USA.
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9
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Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio 2023; 14:e0088923. [PMID: 37294090 PMCID: PMC10470529 DOI: 10.1128/mbio.00889-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 06/10/2023] Open
Abstract
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2-positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls. These results were confirmed and extended in the K18-humanized angiotensin-converting enzyme 2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the USA), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila. Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2, it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | - Preston Tasoff
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | | | - Victoria Wong Murray
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | - Jordan E. Bisanz
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
| | - Yulin Hswen
- Department of Epidemiology and Biostatistics and the Bakar Computational Health Institute, University of California San Francisco, San Francisco, California, USA
| | - Connie W. Y. Ha
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | - Irene P. Chen
- Gladstone Institutes, San Francisco, California, USA
| | - Susan V. Lynch
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
- Department of Pediatrics, University of California San Francisco, University of California, San Francisco, California, USA
| | - Melanie Ott
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Gladstone Institutes, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
| | - Sulggi Lee
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
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10
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Panzer AR, Sitarik AR, Fadrosh D, Havstad SL, Jones K, Davidson B, Finazzo S, Wegienka GR, Woodcroft K, Lukacs NW, Levin AM, Ownby DR, Johnson CC, Lynch SV, Zoratti EM. The impact of prenatal dog keeping on infant gut microbiota development. Clin Exp Allergy 2023; 53:833-845. [PMID: 36916778 DOI: 10.1111/cea.14303] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 05/20/2022] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/15/2023]
Abstract
INTRODUCTION Prenatal and early-life dog exposure has been linked to reduced childhood allergy and asthma. A potential mechanism includes altered early immune development in response to changes in the gut microbiome among dog-exposed infants. We thus sought to determine whether infants born into homes with indoor dog(s) exhibit altered gut microbiome development. METHODS Pregnant women living in homes with dogs or in pet-free homes were recruited in southeast Michigan. Infant stool samples were collected at intervals between 1 week and 18 months after birth and microbiome was assessed using 16S ribosomal sequencing. Perinatal maternal vaginal/rectal swabs and stool samples were sequenced from a limited number of mothers. Mixed effect adjusted models were used to assess stool microbial community trajectories comparing infants from dog-keeping versus pet-free homes with adjustment for relevant covariates. RESULTS Infant gut microbial composition among vaginally born babies became less similar to the maternal vaginal/rectal microbiota and more similar to the maternal gut microbiota with age-related accumulation of bacterial species with advancing age. Stool samples from dog-exposed infants were microbially more diverse (p = .041) through age 18 months with enhanced diversity most apparent between 3 and 6 months of age. Statistically significant effects of dog exposure on β-diversity metrics were restricted to formula-fed children. Across the sample collection period, dog exposure was associated with Fusobacterium genera enrichment, as well as enrichment of Collinsella, Ruminococcus, Clostridaceae and Lachnospiraceae OTUs. CONCLUSION Prenatal/early-life dog exposure is associated with an altered gut microbiome during infancy and supports a potential mechanism explaining lessened atopy and asthma risk. Further research directly linking specific dog-attributable changes in the infant gut microbiome to the risk of allergic disorders is needed.
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Affiliation(s)
- Ariane R Panzer
- Department of Medicine, University of California, San Francisco, California, USA
| | - Alexandra R Sitarik
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Doug Fadrosh
- Department of Medicine, University of California, San Francisco, California, USA
| | - Suzanne L Havstad
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Kyra Jones
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Brent Davidson
- Department of Women's Health, Henry Ford Health System, Detroit, Michigan, USA
| | - Salvatore Finazzo
- Department of Obstetrics and Gynecology, Henry Ford Wyandotte Hospital, Wyandotte, Michigan, USA
| | - Ganesa R Wegienka
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Kimberley Woodcroft
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Nicholas W Lukacs
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
- Center for Bioinformatics, Henry Ford Health System, Detroit, Michigan, USA
| | - Dennis R Ownby
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
| | - Christine C Johnson
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, USA
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, California, USA
| | - Edward M Zoratti
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, USA
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11
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Sitarik AR, Johnson CC, Levin AM, Lynch SV, Ownby DR, Rundle AG, Straughen JK, Wegienka G, Woodcroft KJ, Cassidy-Bushrow AE. Progression of C-reactive protein from birth through preadolescence varies by mode of delivery. Front Pediatr 2023; 11:1155852. [PMID: 37388285 PMCID: PMC10304017 DOI: 10.3389/fped.2023.1155852] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/05/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction Delivery via caesarean section (C-section) has been associated with an increased risk of childhood chronic diseases such as obesity and asthma, which may be due to underlying systemic inflammation. However, the impact of specific C-section types may be differential, as emergency C-sections typically involve partial labor and/or membrane rupture. Our objectives were to determine if mode of delivery associates with longitudinal profiles of high sensitivity CRP (hs-CRP) -a marker of systemic inflammation-from birth through preadolescence, and to examine if CRP mediates the association between mode of delivery and preadolescent body mass index (BMI). Methods Data from the WHEALS birth cohort (N = 1,258) were analyzed; 564 of the 1,258 children in the cohort had data available for analysis. Longitudinal plasma samples (birth through 10-years of age) from 564 children from were assayed for hs-CRP levels. Maternal medical records were abstracted to obtain mode of delivery. Growth mixture models (GMMs) were used to determine classes of hs-CRP trajectories. Poisson regression with robust error variance was used to calculate risk ratios (RRs). Results Two hs-CRP trajectory classes were identified: class 1 (76% of children) was characterized by low hs-CRP, while class 2 (24% of children) was characterized by high and steadily increasing hs-CRP. In multivariable models, children delivered via planned C-section had 1.15 times higher risk of being in hs-CRP class 2, compared to vaginal deliveries (p = 0.028), while no association was found for unplanned C-section deliveries [RR (95% CI) = 0.96 (0.84, 1.09); p = 0.49]. Further, the effect of planned C-section on BMI z-score at age 10 was significantly mediated by hs-CRP class (percent mediated = 43.4%). Conclusions These findings suggest potentially beneficial effects of experiencing partial or full labor, leading to a lower trajectory of systemic inflammation throughout childhood and decreased BMI during preadolescence. These findings may have implications for chronic disease development later in life.
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Affiliation(s)
- Alexandra R. Sitarik
- Department of Public Health Sciences, Henry Ford Health, Detroit, MI, United States
| | - Christine C. Johnson
- Department of Public Health Sciences, Henry Ford Health, Detroit, MI, United States
| | - Albert M. Levin
- Department of Public Health Sciences, Henry Ford Health, Detroit, MI, United States
| | - Susan V. Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA, United States
| | - Dennis R. Ownby
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Andrew G. Rundle
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | | | - Ganesa Wegienka
- Department of Public Health Sciences, Henry Ford Health, Detroit, MI, United States
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12
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Cassidy-Bushrow AE, Sitarik AR, Johnson CC, Johnson-Hooper TM, Kassem Z, Levin AM, Lynch SV, Ownby DR, Phillips JM, Yong GJM, Wegienka G, Straughen JK. Early-life gut microbiota and attention deficit hyperactivity disorder in preadolescents. Pediatr Res 2023; 93:2051-2060. [PMID: 35440767 PMCID: PMC9582043 DOI: 10.1038/s41390-022-02051-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 12/13/2021] [Accepted: 12/31/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Gut microbiota maturation coincides with nervous system development. Cross-sectional data suggest gut microbiota of individuals with and without attention deficit hyperactivity disorder (ADHD) differs. We hypothesized that infant gut microbiota composition is associated with later ADHD development in our on-going birth cohort study, WHEALS. METHODS Gut microbiota was profiled using 16S ribosomal RNA and the internal transcribed spacer region 2 (ITS2) sequencing in stool samples from 1 month and 6 months of age. ADHD was defined by parent-reported or medical record doctor diagnosis at age 10. RESULTS A total of 314 children had gut microbiota and ADHD data; 59 (18.8%) had ADHD. After covariate adjustment, bacterial phylogenetic diversity (p = 0.017) and bacterial composition (unweighted UniFrac p = 0.006, R2 = 0.9%) at age 6 months were associated with development of ADHD. At 1 month of age, 18 bacterial and 3 fungal OTUs were associated with ADHD development. At 6 months of age, 51 bacterial OTUs were associated with ADHD; 14 of the order Lactobacillales. Three fungal OTUs at 6 months of age were associated with ADHD development. CONCLUSIONS Infant gut microbiota is associated with ADHD development in pre-adolescents. Further studies replicating these findings and evaluating potential mechanisms of the association are needed. IMPACT Cross-sectional studies suggest that the gut microbiota of individuals with and without ADHD differs. We found evidence that the bacterial gut microbiota of infants at 1 month and 6 months of age is associated with ADHD at age 10 years. We also found novel evidence that the fungal gut microbiota in infancy (ages 1 month and 6 months) is associated with ADHD at age 10 years. This study addresses a gap in the literature in providing longitudinal evidence for an association of the infant gut microbiota with later ADHD development.
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Affiliation(s)
- Andrea E Cassidy-Bushrow
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA.
- Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI, USA.
| | | | - Christine Cole Johnson
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
- Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI, USA
| | - Tisa M Johnson-Hooper
- Department of Pediatrics, Henry Ford Hospital, Detroit, MI, USA
- Center for Autism and Developmental Disabilities, Henry Ford Hospital, Detroit, MI, USA
| | - Zeinab Kassem
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Dennis R Ownby
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Augusta University, Augusta, GA, USA
| | - Jannel M Phillips
- Center for Autism and Developmental Disabilities, Henry Ford Hospital, Detroit, MI, USA
- Department of Psychiatry and Behavioral Health Services, Division of Neuropsychology, Henry Ford Hospital, Detroit, MI, USA
| | - Germaine J M Yong
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Ganesa Wegienka
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
- Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI, USA
| | - Jennifer K Straughen
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
- Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI, USA
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13
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Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee Li YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. medRxiv 2023:2023.03.07.23286920. [PMID: 36945505 PMCID: PMC10029035 DOI: 10.1101/2023.03.07.23286920] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Globally, every year about 11% of infants are born preterm, defined as a birth prior to 37 weeks of gestation, with significant and lingering health consequences. Multiple studies have related the vaginal microbiome to preterm birth. We present a crowdsourcing approach to predict: (a) preterm or (b) early preterm birth from 9 publicly available vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from raw sequences via an open-source tool, MaLiAmPi. We validated the crowdsourced models on novel datasets representing 331 samples from 148 pregnant individuals. From 318 DREAM challenge participants we received 148 and 121 submissions for our two separate prediction sub-challenges with top-ranking submissions achieving bootstrapped AUROC scores of 0.69 and 0.87, respectively. Alpha diversity, VALENCIA community state types, and composition (via phylotype relative abundance) were important features in the top performing models, most of which were tree based methods. This work serves as the foundation for subsequent efforts to translate predictive tests into clinical practice, and to better understand and prevent preterm birth.
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Affiliation(s)
- Jonathan L Golob
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Tomiko T Oskotsky
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Alice S Tang
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Alennie Roldan
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | | | - Connie W Y Ha
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
| | | | - Antonio Parraga-Leo
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Camilla Wibrand
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
| | - Gaia Andreoletti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Idit Kosti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | | | | | - Jifan Gao
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Zhoujingpeng Wei
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Pierfrancesco Novielli
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Donato Romano
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Ester Pantaleo
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
| | - Nicola Amoroso
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Alfonso Monaco
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Mirco Vacca
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Maria De Angelis
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Roberto Bellotti
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Sabina Tangaro
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Abigail Kuntzleman
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
| | - Isaac Bigcraft
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Stephen Techtmann
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Daehun Bae
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Eunyoung Kim
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | | | - Soobok Joe
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Kevin R Theis
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
| | - Sherrianne Ng
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
| | - Yun S Lee Li
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Patricia Diaz-Gimeno
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Phillip R Bennett
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - David A MacIntyre
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Gustavo Stolovitzky
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
| | | | - Nardhy Gomez-Lopez
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Roberto Romero
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
| | - Nima Aghaeepour
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
| | - Adi L Tarca
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - James C Costello
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Marina Sirota
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
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14
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Parraga-Leo A, Oskotsky TT, Oskotsky B, Wibrand C, Roldan A, Tang A, Ha CWY, Wong RJ, Minot SS, Andreoletti G, Kosti I, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Lynch SV, Romero R, Tarca AL, Stevenson DK, Aghaeepour N, Golob J, Sirota M. VMAP: Vaginal Microbiome Atlas During Pregnancy. medRxiv 2023:2023.03.21.23286947. [PMID: 36993193 PMCID: PMC10055588 DOI: 10.1101/2023.03.21.23286947] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The vaginal microbiome has been shown to be associated with pregnancy outcomes including preterm birth (PTB) risk. Here we present VMAP: Vaginal Microbiome Atlas during Pregnancy (http://vmapapp.org), an application to visualize features of 3,909 vaginal microbiome samples of 1,416 pregnant individuals from 11 studies, aggregated from raw public and newly generated sequences via an open-source tool, MaLiAmPi. Our visualization tool (http://vmapapp.org) includes microbial features such as various measures of diversity, VALENCIA community state types (CST), and composition (via phylotypes and taxonomy). This work serves as a resource for the research community to further analyze and visualize vaginal microbiome data in order to better understand both healthy term pregnancies and those associated with adverse outcomes.
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Affiliation(s)
- Antonio Parraga-Leo
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia, Spain
- Instituto de Investigación Sanitaria La Fe (IIS La Fe), IVI Foundation, Valencia, Spain
| | - Tomiko T Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Boris Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Camilla Wibrand
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia, Spain
| | - Alennie Roldan
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Alice Tang
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Connie W Y Ha
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, California. USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
| | - Samuel S Minot
- Data Core, Fred Hutchinson Cancer Center. Seattle, WA. USA
| | - Gaia Andreoletti
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Kevin R Theis
- Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK
| | - Sherrianne Ng
- Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Patricia Diaz-Gimeno
- Instituto de Investigación Sanitaria La Fe (IIS La Fe), IVI Foundation, Valencia, Spain
| | - Phillip R Bennett
- Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Division of the Institute of Reproduction and Developmental Biology, Imperial College London, UK
- March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, California. USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI. USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI. USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI. USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI. USA; Detroit Medical Center, Detroit, MI. USA
- Department of Obstetrics and Gynecology, Florida International University, Miami, FL. USA
| | - Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI. USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI. USA; Detroit Medical Center, Detroit, MI. USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI. USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, MI. USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- Center for Academic Medicine, Stanford University School of Medicine, Stanford, California
| | - Nima Aghaeepour
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA. USA
- Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA. USA
| | - Jonathan Golob
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
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15
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Snyder BM, Gebretsadik T, Rohrig NB, Wu P, Dupont WD, Dabelea DM, Fry RC, Lynch SV, McEvoy CT, Paneth NS, Ryckman KK, Gern JE, Hartert TV. The Associations of Maternal Health Characteristics, Newborn Metabolite Concentrations, and Child Body Mass Index among US Children in the ECHO Program. Metabolites 2023; 13:510. [PMID: 37110168 PMCID: PMC10144800 DOI: 10.3390/metabo13040510] [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: 03/14/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
We aimed first to assess associations between maternal health characteristics and newborn metabolite concentrations and second to assess associations between metabolites associated with maternal health characteristics and child body mass index (BMI). This study included 3492 infants enrolled in three birth cohorts with linked newborn screening metabolic data. Maternal health characteristics were ascertained from questionnaires, birth certificates, and medical records. Child BMI was ascertained from medical records and study visits. We used multivariate analysis of variance, followed by multivariable linear/proportional odds regression, to determine maternal health characteristic-newborn metabolite associations. Significant associations were found in discovery and replication cohorts of higher pre-pregnancy BMI with increased C0 and higher maternal age at delivery with increased C2 (C0: discovery: aβ 0.05 [95% CI 0.03, 0.07]; replication: aβ 0.04 [95% CI 0.006, 0.06]; C2: discovery: aβ 0.04 [95% CI 0.003, 0.08]; replication: aβ 0.04 [95% CI 0.02, 0.07]). Social Vulnerability Index, insurance, and residence were also associated with metabolite concentrations in a discovery cohort. Associations between metabolites associated with maternal health characteristics and child BMI were modified from 1-3 years (interaction: p < 0.05). These findings may provide insights on potential biologic pathways through which maternal health characteristics may impact fetal metabolic programming and child growth patterns.
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Affiliation(s)
- Brittney M. Snyder
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Tebeb Gebretsadik
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Nina B. Rohrig
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Pingsheng Wu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - William D. Dupont
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Dana M. Dabelea
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Susan V. Lynch
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Cindy T. McEvoy
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Nigel S. Paneth
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, East Lansing, MI 48912, USA
| | - Kelli K. Ryckman
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health—Bloomington, Bloomington, IN 47405, USA
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Tina V. Hartert
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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Vercelli D, Lynch SV. Interactions between host epigenetics and microbiota: Who does what to whom, when, and why? J Allergy Clin Immunol 2023:S0091-6749(23)00138-0. [PMID: 36720286 DOI: 10.1016/j.jaci.2023.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/31/2023]
Affiliation(s)
- Donata Vercelli
- Department of Cellular and Molecular Medicine, Tucson, Ariz; Asthma and Airway Disease Research Center, Tucson, Ariz; Arizona Center for the Biology of Complex Diseases, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz.
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, San Francisco, Calif; Department of Pediatrics, University of California San Francisco, San Francisco, Calif; Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, Calif.
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Harringer EOS, Durack J, Piceno Y, Andersen V, Lynch SV. Gluten Degradation by the Gut Microbiota of Ulcerative Colitis Patients. Microorganisms 2022; 11:microorganisms11010012. [PMID: 36677307 PMCID: PMC9867242 DOI: 10.3390/microorganisms11010012] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Several studies have reported improved disease symptomatology in ulcerative colitis (UC) patients consuming a gluten free diet. This observation coupled with diversity depletion in the gut microbiota of UC patients led us to hypothesize that UC-associated enteric microbes differentially metabolize dietary gluten to produce immunogenic products that promote inflammation. Gluten concentration in stool was determined using gluten-specific ELISA, and gluten intake was assessed by food frequency questionnaire (FFQ) in UC (n = 12) and healthy controls (HC; n = 13). Gluten-metabolizing bacteria were isolated on minimal media supplemented with 1% gluten from UC and HC and identified by 16S rRNA profiling. Cell-free culture media from gluten metabolizing gut bacterial isolates was assessed for immunogenicity in vitro using HT29 colonocytes. Compared to HC, UC patients did not consume gluten differently (Mann−Whitney; p > 0.10) and exhibited equivalent levels of gluten in their feces (Mann−Whitney; p = 0.163). The profile of gluten-degrading bacteria isolated from UC stool was distinct (Chi-square; p ≤ 0.0001). Compared with Enterococcus isolates, products of gluten degradation by Bacillus strains induced higher IL8 and lower occludin (Mann−Whitney; p = 0.002 and p = 0.059, respectively) gene expression in colonocytes irrespective of whether they originated from UC or healthy gut. Members of HC and UC microbiota exhibit gluten-degrading ability, metabolites of which influence genes involved in inflammation and barrier function in enteric colonocyte cultures. Preliminary findings of this study warrant further investigations into the mechanisms by which gut microbiota contribute to UC pathogenesis through gluten degradation.
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Affiliation(s)
- Emma Olivia Schultz Harringer
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA 94143, USA
- Molecular Diagnostics and Clinical Research Unit, IRS-Centre Soenderjylland, University Hospital of Southern Denmark, 6200 Aabenraa, Denmark
| | - Juliana Durack
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yvette Piceno
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Vibeke Andersen
- Molecular Diagnostics and Clinical Research Unit, IRS-Centre Soenderjylland, University Hospital of Southern Denmark, 6200 Aabenraa, Denmark
- Institute of Regional Research, University of Southern Denmark, 5000 Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Susan V. Lynch
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA 94143, USA
- Correspondence: ; Tel.: +1-415-476-6784
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Upadhyay V, Suryawanshi R, Tasoff P, McCavitt-Malvido M, Kumar GR, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha C, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. bioRxiv 2022:2022.12.07.519508. [PMID: 36523400 PMCID: PMC9753784 DOI: 10.1101/2022.12.07.519508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila . Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.
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DeVries A, McCauley K, Fadrosh D, Fujimura KE, Stern DA, Lynch SV, Vercelli D. Maternal prenatal immunity, neonatal trained immunity, and early airway microbiota shape childhood asthma development. Allergy 2022; 77:3617-3628. [PMID: 35841380 PMCID: PMC9712226 DOI: 10.1111/all.15442] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 01/28/2022] [Revised: 05/25/2022] [Accepted: 06/11/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND The path to childhood asthma is thought to initiate in utero and be further promoted by postnatal exposures. However, the underlying mechanisms remain underexplored. We hypothesized that prenatal maternal immune dysfunction associated with increased childhood asthma risk (revealed by low IFN-γ:IL-13 secretion during the third trimester of pregnancy) alters neonatal immune training through epigenetic mechanisms and promotes early-life airway colonization by asthmagenic microbiota. METHODS We examined epigenetic, immunologic, and microbial features potentially related to maternal prenatal immunity (IFN-γ:IL-13 ratio) and childhood asthma in a birth cohort of mother-child dyads sampled pre-, peri-, and postnatally (N = 155). Epigenome-wide DNA methylation and cytokine production were assessed in cord blood mononuclear cells (CBMC) by array profiling and ELISA, respectively. Nasopharyngeal microbiome composition was characterized at age 2-36 months by 16S rRNA sequencing. RESULTS Maternal prenatal immune status related to methylome profiles in neonates born to non-asthmatic mothers. A module of differentially methylated CpG sites enriched for microbe-responsive elements was associated with childhood asthma. In vitro responsiveness to microbial products was impaired in CBMCs from neonates born to mothers with the lowest IFN-γ:IL-13 ratio, suggesting defective neonatal innate immunity in those who developed asthma during childhood. These infants exhibited a distinct pattern of upper airway microbiota development characterized by early-life colonization by Haemophilus that transitioned to a Moraxella-dominated microbiota by age 36 months. CONCLUSIONS Maternal prenatal immune status shapes asthma development in her child by altering the epigenome and trained innate immunity at birth, and is associated with pathologic upper airway microbial colonization in early life.
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Affiliation(s)
- Avery DeVries
- Asthma and Airway Disease Research CenterThe University of ArizonaTucsonArizonaUSA
- The BIO5 InstituteThe University of ArizonaTucsonArizonaUSA
| | - Kathryn McCauley
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Benioff Center for Microbiome MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Douglas Fadrosh
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Kei E. Fujimura
- Genetic Disease LabCalifornia Department of Public HealthRichmondCaliforniaUSA
| | - Debra A. Stern
- Asthma and Airway Disease Research CenterThe University of ArizonaTucsonArizonaUSA
| | - Susan V. Lynch
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Benioff Center for Microbiome MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Donata Vercelli
- Asthma and Airway Disease Research CenterThe University of ArizonaTucsonArizonaUSA
- The BIO5 InstituteThe University of ArizonaTucsonArizonaUSA
- Department of Cellular and Molecular MedicineThe University of ArizonaTucsonArizonaUSA
- Arizona Center for the Biology of Complex DiseasesThe University of ArizonaTucsonArizonaUSA
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20
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Huang YJ, Porsche C, Kozik AJ, Lynch SV. Microbiome-Immune Interactions in Allergy and Asthma. J Allergy Clin Immunol Pract 2022; 10:2244-2251. [PMID: 35724951 PMCID: PMC10566566 DOI: 10.1016/j.jaip.2022.05.038] [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] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/13/2022] [Accepted: 05/28/2022] [Indexed: 06/13/2023]
Abstract
The human microbiota has been established as a key regulator of host health, in large part owing to its constant interaction with and impact on host immunity. A range of environmental exposures spanning from the prenatal period through adulthood are known to affect the composition and molecular productivity of microbiomes across mucosal and dermal tissues with short- and long-term consequences for host immune function. Here we review recent findings in the field that provide insights into how microbial-immune interactions promote and sustain immune dysfunction associated with allergy and asthma. We consider both early life microbiome perturbation and the molecular underpinnings of immune dysfunction associated with subsequent allergy and asthma development in childhood, as well as microbiome features that relate to phenotypic attributes of allergy and asthma in older patients with established disease.
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Affiliation(s)
- Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor, Mich; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Mich.
| | - Cara Porsche
- Department of Medicine, University of California San Francisco, San Francisco, Calif
| | - Ariangela J Kozik
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Michigan, Ann Arbor, Mich
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, San Francisco, Calif.
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21
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McCauley KE, Rackaityte E, LaMere B, Fadrosh DW, Fujimura KE, Panzer AR, Lin DL, Lynch KV, Halkias J, Mendoza VF, Burt TD, Bendixsen C, Barnes K, Kim H, Jones K, Ownby DR, Johnson CC, Seroogy CM, Gern JE, Boushey HA, Lynch SV. Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy. Cell Rep Med 2022; 3:100713. [PMID: 35932762 PMCID: PMC9418802 DOI: 10.1016/j.xcrm.2022.100713] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 08/21/2021] [Revised: 04/27/2022] [Accepted: 07/13/2022] [Indexed: 04/17/2023]
Abstract
Maternal asthma status, prenatal exposures, and infant gut microbiota perturbation are associated with heightened risk of atopy and asthma risk in childhood, observations hypothetically linked by intergenerational microbial transmission. Using maternal vaginal (n = 184) and paired infant stool (n = 172) samples, we identify four compositionally and functionally distinct Lactobacillus-dominated vaginal microbiota clusters (VCs) that relate to prenatal maternal health and exposures and infant serum immunoglobulin E (IgE) status at 1 year. Variance in bacteria shared between mother and infant pairs relate to VCs, maternal allergy/asthma status, and infant IgE levels. Heritable bacterial gene pathways associated with infant IgE include fatty acid synthesis and histamine and tryptophan degradation. In vitro, vertically transmitted Lactobacillus jensenii strains induce immunosuppressive phenotypes on human antigen-presenting cells. Murine supplementation with L. jensenii reduces lung eosinophils, neutrophilic expansion, and the proportion of interleukin-4 (IL-4)+ CD4+ T cells. Thus, bacterial and atopy heritability are intimately linked, suggesting a microbial component of intergenerational disease transmission.
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Affiliation(s)
- Kathryn E McCauley
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brandon LaMere
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Douglas W Fadrosh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kei E Fujimura
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ariane R Panzer
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Din L Lin
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kole V Lynch
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joanna Halkias
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ventura F Mendoza
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Process Development, PACT Pharma, South San Francisco, CA, USA
| | - Trevor D Burt
- Division of Neonatology and the Children's Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, NC 27705, USA
| | | | - Kathrine Barnes
- Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Haejin Kim
- Henry Ford Health System, Detroit, MI 48202, USA
| | - Kyra Jones
- Henry Ford Health System, Detroit, MI 48202, USA
| | | | | | - Christine M Seroogy
- University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - James E Gern
- University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Homer A Boushey
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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22
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Chang CCJ, Somohano K, Zemsky C, Uhlemann AC, Liebmann J, Cioffi GA, Al-Aswad LA, Lynch SV, Winn BJ. Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome. Invest Ophthalmol Vis Sci 2022; 63:32. [PMID: 36036910 PMCID: PMC9434984 DOI: 10.1167/iovs.63.9.32] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To investigate the ocular surface microbiome of patients with unilateral or asymmetric glaucoma being treated with topical ophthalmic medications in one eye and to determine whether microbial community changes were related to measures of ocular surface disease. Methods V3-V4 16S rRNA sequencing was conducted on ocular surface swabs collected from both eyes of 17 subjects: 10 patients with asymmetric/unilateral glaucoma using topical glaucoma therapy on only one eye and seven age-matched, healthy controls with no history of ocular disease or eyedrop use. Samples were categorized into three groups: patients’ glaucomatous eye treated with eyedrops, patients’ contralateral eye without eyedrops, and healthy control eyes. Comparisons were made for microbial diversity and composition, with differences in composition tested for association with ocular surface disease measures including tear meniscus height, tear break-up time, and Dry Eye Questionnaire. Results Samples obtained from the patients’ treated and untreated eyes both had significantly greater alpha-diversity and relative abundance of gram-negative organisms compared to healthy controls. The microbial composition of patient eyes was associated with decreased tear meniscus height and tear break-up time, whereas metagenomic predictions, based on 16S rRNA data, suggested increased synthesis of lipopolysaccharide. Conclusions The ocular surface microbiome of patients taking unilateral preserved glaucoma drops is characterized by a highly diverse array of gram-negative bacteria that is significantly different from the predominantly gram-positive microbes detected on healthy control eyes. These compositional differences were associated with decreased tear film measures and distinct inferred protein synthesis pathways, suggesting a potential link between microbial alterations and ocular surface inflammation.
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Affiliation(s)
- Chih-Chiun J Chang
- Department of Ophthalmology, University of California San Francisco, San Francisco, California, United States
| | - Karina Somohano
- Department of Ophthalmology, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States
| | - Christine Zemsky
- Department of Ophthalmology, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States
| | - Anne-Catrin Uhlemann
- Department of Internal Medicine, Division of Infectious Disease, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States
| | - Jeffrey Liebmann
- Department of Ophthalmology, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States
| | - George A Cioffi
- Department of Ophthalmology, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States
| | - Lama A Al-Aswad
- Department of Ophthalmology, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States.,Department of Ophthalmology, New York University Langone Health, New York, New York, United States
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Bryan J Winn
- Department of Ophthalmology, University of California San Francisco, San Francisco, California, United States.,Department of Ophthalmology, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States.,Ophthalmology Section, Surgical Service, San Francisco Veterans Affairs Medical Center, San Francisco, California, United States
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23
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Ray KJ, Santee C, McCauley K, Panzer AR, Lynch SV. Gut Bifidobacteria enrichment following oral Lactobacillus-supplementation is associated with clinical improvements in children with cystic fibrosis. BMC Pulm Med 2022; 22:287. [PMID: 35902830 PMCID: PMC9330662 DOI: 10.1186/s12890-022-02078-9] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 06/23/2022] [Indexed: 11/23/2022] Open
Abstract
Background Relationships between gut microbiomes and airway immunity have been established in murine and human studies of allergy and asthma. Early life Lactobacillus supplementation alters the composition and metabolic productivity of the gut microbiome. However, little is known of how Lactobacillus supplementation impacts the gut microbiota in children with cystic fibrosis (CF) and whether specific microbiota states that arise following gut microbiome manipulation relate to pulmonary outcomes. Methods Stool samples were collected from CF patients enrolled in a multi-center, double-blind, randomized placebo-controlled trial of daily Lactobacillus rhamnosus strain GG (LGG) probiotic supplementation over a 12-month period. Fecal 16S rRNA biomarker sequencing was used to profile fecal bacterial microbiota and analyses were performed in QiiME. Results Bifidobacteria-dominated fecal microbiota were more likely to arise in LGG-treated children with CF (P = 0.04). Children with Bifidobacteria-dominated gut microbiota had a reduced rate of pulmonary exacerbations (IRR = 0.55; 95% CI 0.25 to 0.82; P = 0.01), improved pulmonary function (+ 20.00% of predicted value FEV1; 95% CI 8.05 to 31.92; P = 0.001), lower intestinal inflammation (Calprotectin; Coef = − 16.53 μg g−1 feces; 95% CI − 26.80 to − 6.26; P = 0.002) and required fewer antibiotics (IRR = 0.43; 95% CI 0.22 to 0.69; P = 0.04) compared to children with Bacteroides-dominated microbiota who were less likely to have received LGG. Conclusions The majority of pediatric CF patients in this study possessed a Bacteroides- or Bifidobacteria-dominated gut microbiota. Bifidobacteria-dominated gut microbiota were more likely to be associated with LGG-supplementation and with better clinical outcomes.
Supplementary Information The online version contains supplementary material available at 10.1186/s12890-022-02078-9.
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Affiliation(s)
- Kathryn J Ray
- Department of Epidemiology and Biostatistics, University of California San Francisco (UCSF), San Francisco, USA.,Francis I Proctor Foundation, University of California San Francisco (UCSF), San Francisco, USA
| | - Clark Santee
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), 513 Parnassus Ave, S357D, San Francisco, CA, 94143, USA
| | - Kathryn McCauley
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), 513 Parnassus Ave, S357D, San Francisco, CA, 94143, USA
| | - Ariane R Panzer
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), 513 Parnassus Ave, S357D, San Francisco, CA, 94143, USA
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California San Francisco (UCSF), 513 Parnassus Ave, S357D, San Francisco, CA, 94143, USA.
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24
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McCauley KE, Flynn K, Calatroni A, DiMassa V, LaMere B, Fadrosh DW, Lynch KV, Gill MA, Pongracic JA, Khurana Hershey GK, Kercsmar CM, Liu AH, Johnson CC, Kim H, Kattan M, O'Connor GT, Bacharier LB, Teach SJ, Gergen PJ, Wheatley LM, Togias A, LeBeau P, Presnell S, Boushey HA, Busse WW, Gern JE, Jackson DJ, Altman MC, Lynch SV. Seasonal airway microbiome and transcriptome interactions promote childhood asthma exacerbations. J Allergy Clin Immunol 2022; 150:204-213. [PMID: 35149044 DOI: 10.1016/j.jaci.2022.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 11/16/2021] [Revised: 01/07/2022] [Accepted: 01/27/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND Seasonal variation in respiratory illnesses and exacerbations in pediatric populations with asthma is well described, though whether upper airway microbes play season-specific roles in these events is unknown. OBJECTIVE We hypothesized that nasal microbiota composition is seasonally dynamic and that discrete microbe-host interactions modify risk of asthma exacerbation in a season-specific manner. METHODS Repeated nasal samples from children with exacerbation-prone asthma collected during periods of respiratory health (baseline; n = 181 samples) or first captured respiratory illness (n = 97) across all seasons, underwent bacterial (16S ribosomal RNA gene) and fungal (internal transcribed spacer region 2) biomarker sequencing. Virus detection was performed by multiplex PCR. Paired nasal transcriptome data were examined for seasonal dynamics and integrative analyses. RESULTS Upper airway bacterial and fungal microbiota and rhinovirus detection exhibited significant seasonal dynamics. In seasonally adjusted analysis, variation in both baseline and respiratory illness microbiota related to subsequent exacerbation. Specifically, in the fall, when respiratory illness and exacerbation events were most frequent, several Moraxella and Haemophilus members were enriched both in virus-positive respiratory illnesses and those that progressed to exacerbations. The abundance of 2 discrete bacterial networks, characteristically comprising either Streptococcus or Staphylococcus, exhibited opposing interactions with an exacerbation-associated SMAD3 nasal epithelial transcriptional module to significantly increase the odds of subsequent exacerbation (odds ratio = 14.7, 95% confidence interval = 1.50-144, P = .02; odds ratio = 39.17, 95% confidence interval = 2.44-626, P = .008, respectively). CONCLUSIONS Upper airway microbiomes covary with season and with seasonal trends in respiratory illnesses and asthma exacerbations. Seasonally adjusted analyses reveal specific bacteria-host interactions that significantly increase risk of asthma exacerbation in these children.
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Affiliation(s)
| | - Kaitlin Flynn
- Systems Immunology Program, Benaroya Research Institute, Seattle, Wash
| | | | - Vincent DiMassa
- Department of Medicine, University of California, San Francisco, Calif
| | - Brandon LaMere
- Department of Medicine, University of California, San Francisco, Calif
| | - Douglas W Fadrosh
- Department of Medicine, University of California, San Francisco, Calif
| | - Kole V Lynch
- Department of Medicine, University of California, San Francisco, Calif
| | - Michelle A Gill
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex
| | | | | | | | - Andrew H Liu
- Department of Allergy and Immunology, Children's Hospital Colorado, Unversity of Colorado School of Medicine, Aurora, Colo
| | | | | | - Meyer Kattan
- Columbia University College of Physicians and Surgeons, New York, NY
| | - George T O'Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Mass
| | - Leonard B Bacharier
- Division of Allergy, Immunology, and Pulmonary Medicine, Washington University, St Louis, Mo
| | | | - Peter J Gergen
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Lisa M Wheatley
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Alkis Togias
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | | | - Scott Presnell
- Systems Immunology Program, Benaroya Research Institute, Seattle, Wash
| | - Homer A Boushey
- Department of Medicine, University of California, San Francisco, Calif
| | - William W Busse
- University of Wisconsin School of Medicine and Public Health, Madison, Wisc
| | - James E Gern
- University of Wisconsin School of Medicine and Public Health, Madison, Wisc
| | - Daniel J Jackson
- University of Wisconsin School of Medicine and Public Health, Madison, Wisc
| | - Matthew C Altman
- Systems Immunology Program, Benaroya Research Institute, Seattle, Wash; Department of Allergy and Infectious Diseases, University of Washington, Seattle, Wash.
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, Calif.
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25
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Hertz S, Durack J, Kirk KF, Nielsen HL, Lin DL, Fadrosh D, Lynch K, Piceno Y, Thorlacius-Ussing O, Nielsen H, Lynch SV. Microscopic Colitis Patients Possess a Perturbed and Inflammatory Gut Microbiota. Dig Dis Sci 2022; 67:2433-2443. [PMID: 34059992 DOI: 10.1007/s10620-021-07045-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 11/23/2020] [Accepted: 05/08/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microscopic colitis (MC), an inflammatory disease of the colon, is characterized by chronic non-bloody diarrhea with characteristic inflammation and for some, collagen deposits in mucosal biopsies. The etiology of MC is unclear, although previous findings implicate luminal factors and thus the gut microbiome. However, the relationships between fecal microbiota and MC are relatively unexplored. METHODS Stool microbiota of MC (n = 15) and healthy controls (HC; n = 21) were assessed by 16S rRNA V4 amplicon sequencing and analysis performed in QIIME. Gut microbiota functions were predicted using Piphillin and inflammatory potential assessed using an in vitro HT29 colonocyte cell assay. RESULTS MC patient fecal microbiota were less diverse (Faiths index; p < 0.01) and compositionally distinct (PERMANOVA, weighted UniFrac, R2 = 0.08, p = 0.02) compared with HC subjects. MC microbiota were significantly depleted of members of the Clostridiales, enriched for Prevotella and more likely to be dominated by this genus (Chi2 = 0.03). Predicted pathways enriched in MC microbiota included those related to biosynthesis of antimicrobials, and sphingolipids, to glycan degradation, host defense evasion, and Th17 cell differentiation and activation. In vitro, exposure of cultured colonocytes to cell-free products of MC patient feces indicates reduced gene expression of IL-1B and occludin and increased GPR119 and the lymphocyte chemoattractant CCL20. CONCLUSION MC gut microbiota are distinct from HC and characterized by lower bacterial diversity and Prevotella enrichment and distinct predicted functional pathways. Limited in vitro experiments indicate that compared with cell-free products from healthy fecal microbiota, MC microbiota induce distinct responses when co-cultured with epithelial cells, implicating microbiota perturbation in MC-associated mucosal dysfunction.
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Affiliation(s)
- Sandra Hertz
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA. .,Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, 7th floor, east wing, 9000, Aalborg, Denmark.
| | - Juliana Durack
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Karina Frahm Kirk
- Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, 7th floor, east wing, 9000, Aalborg, Denmark
| | - Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Mølleparkvej 10, 6th floor, 9000, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Din L Lin
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Douglas Fadrosh
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Kole Lynch
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Yvette Piceno
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Hobrovej 18-22, 9000, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Mølleparkvej 4, 7th floor, east wing, 9000, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, 513 Parnassus Ave, S357D, Box 0538, San Francisco, CA, 94143, USA
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26
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Merana GR, Dwyer LR, Dhariwala MO, Weckel A, Gonzalez JR, Okoro JN, Cohen JN, Tamaki CM, Han J, Tasoff P, Palacios-Calderon Y, Ha CWY, Lynch SV, Segre JA, Kong HH, Kattah MG, Ma A, Scharschmidt TC. Intestinal inflammation alters the antigen-specific immune response to a skin commensal. Cell Rep 2022; 39:110891. [PMID: 35649365 PMCID: PMC9248974 DOI: 10.1016/j.celrep.2022.110891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/26/2021] [Revised: 04/08/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
Resident microbes in skin and gut predominantly impact local immune cell function during homeostasis. However, colitis-associated neutrophilic skin disorders suggest possible breakdown of this compartmentalization with disease. Using a model wherein neonatal skin colonization by Staphylococcus epidermidis facilitates generation of commensal-specific tolerance and CD4+ regulatory T cells (Tregs), we ask whether this response is perturbed by gut inflammation. Chemically induced colitis is accompanied by intestinal expansion of S. epidermidis and reduces gut-draining lymph node (dLN) commensal-specific Tregs. It also results in reduced commensal-specific Tregs in skin and skin-dLNs and increased skin neutrophils. Increased CD4+ circulation between gut and skin dLN suggests that the altered cutaneous response is initiated in the colon, and resistance to colitis-induced effects in Cd4creIl1r1fl/fl mice implicate interleukin (IL)-1 in mediating the altered commensal-specific response. These findings provide mechanistic insight into observed connections between inflammatory skin and intestinal diseases.
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Affiliation(s)
- Geil R Merana
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura R Dwyer
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Miqdad O Dhariwala
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Antonin Weckel
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeanmarie R Gonzalez
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joy N Okoro
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jarish N Cohen
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Courtney M Tamaki
- Parnassus Flow Cytometry CoLab, University of California, San Francisco, San Francisco, 94143, USA
| | - Jungmin Han
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Preston Tasoff
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA 94143, USA
| | | | - Connie W Y Ha
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julia A Segre
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Heidi H Kong
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael G Kattah
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Averil Ma
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tiffany C Scharschmidt
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA.
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27
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Spottiswoode N, Bloomstein JD, Caldera S, Sessolo A, McCauley K, Byanyima P, Zawedde J, Kalantar K, Kaswabuli S, Rutishauser RL, Lieng MK, Davis JL, Moore J, Jan A, Iwai S, Shenoy M, Sanyu I, DeRisi JL, Lynch SV, Worodria W, Huang L, Langelier CR. Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study. Lancet Microbe 2022; 3:e357-e365. [PMID: 35544096 DOI: 10.1016/s2666-5247(21)00357-8] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Pneumonia is a leading cause of death worldwide and is a major health-care challenge in people living with HIV. Despite this, the causes of pneumonia in this population remain poorly understood. We aimed to assess the feasibility of metatranscriptomics for epidemiological surveillance of pneumonia in patients with HIV in Uganda. METHODS We performed a retrospective observational study in patients with HIV who were admitted to Mulago Hospital, Kampala, Uganda between Oct 1, 2009, and Dec 31, 2011. Inclusion criteria were age 18 years or older, HIV-positivity, and clinically diagnosed pneumonia. Exclusion criteria were contraindication to bronchoscopy or an existing diagnosis of tuberculosis. Bronchoalveolar lavage fluid was collected within 72 h of admission and a combination of RNA sequencing and Mycobacterium tuberculosis culture plus PCR were performed. The primary outcome was detection of an established or possible respiratory pathogen in the total study population. FINDINGS We consecutively enrolled 217 patients during the study period. A potential microbial cause for pneumonia was identified in 211 (97%) patients. At least one microorganism of established respiratory pathogenicity was identified in 113 (52%) patients, and a microbe of possible pathogenicity was identified in an additional 98 (45%). M tuberculosis was the most commonly identified established pathogen (35 [16%] patients; in whom bacterial or viral co-infections were identified in 13 [37%]). Streptococcus mitis, although not previously reported as a cause of pneumonia in patients with HIV, was the most commonly identified bacterial organism (37 [17%] patients). Haemophilus influenzae was the most commonly identified established bacterial pathogen (20 [9%] patients). Pneumocystis jirovecii was only identified in patients with a CD4 count of less than 200 cells per mL. INTERPRETATION We show the feasibility of using metatranscriptomics for epidemiologic surveillance of pneumonia by describing the spectrum of respiratory pathogens in adults with HIV in Uganda. Applying these methods to a contemporary cohort could enable broad assessment of changes in pneumonia aetiology following the emergence of SARS-CoV-2. FUNDING US National Institutes of Health, Chan Zuckerberg Biohub.
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Affiliation(s)
- Natasha Spottiswoode
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua D Bloomstein
- Department of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - Saharai Caldera
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Abdul Sessolo
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Kathryn McCauley
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Patrick Byanyima
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | | | | | - Sylvia Kaswabuli
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Rachel L Rutishauser
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Monica K Lieng
- Department of Medicine, University of California Davis School of Medicine, Sacramento, CA, USA
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Julia Moore
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amanda Jan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health and Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shoko Iwai
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Meera Shenoy
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - Ingvar Sanyu
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Joseph L DeRisi
- Department of Biochemistry, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, San Francisco, CA, USA
| | - William Worodria
- Infectious Disease Platform, Makerere University, Kampala, Uganda
| | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles R Langelier
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N. Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis. Sci Rep 2022; 12:5517. [PMID: 35365713 PMCID: PMC8976058 DOI: 10.1038/s41598-022-09307-5] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 03/16/2022] [Indexed: 01/04/2023] Open
Abstract
Fecal microbiota transplant is a promising therapy for ulcerative colitis. Parameters maximizing effectiveness and tolerability are not yet clear, and it is not known how import the transmission of donor microbes to patients is. Here (clinicaltrails.gov: NCT03006809) we have tested the effects of antibiotic pretreatment and compared two modes of maintenance dose delivery, capsules versus enema, in a randomized, pilot, open-label, 2 × 2 factorial design with 22 patients analyzed with mild to moderate UC. Clinically, the treatment was well-tolerated with favorable safety profile. Of patients who received antibiotic pretreatment, 6 of 11 experienced remission after 6 weeks of treatment, versus 2 of 11 non-pretreated patients (log odds ratio: 1.69, 95% confidence interval: −0.25 to 3.62). No significant differences were found between maintenance dosing via capsules versus enema. In exploratory analyses, microbiome turnover at both the species and strain levels was extensive and significantly more pronounced in the pretreated patients. Associations were also revealed between taxonomic turnover and changes in the composition of primary and secondary bile acids. Together these findings suggest that antibiotic pretreatment contributes to microbiome engraftment and possibly clinical effectiveness, and validate longitudinal strain tracking as a powerful way to monitor the dynamics and impact of microbiota transfer.
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Affiliation(s)
- Byron J Smith
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | | | - Martin Zydek
- Division of Gastroenterology, University of California, San Francisco, CA, USA
| | - Bing Zhang
- Division of Gastroenterology, University of California, San Francisco, CA, USA.,Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lara Aboud Syriani
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, USA
| | - Jonathan P Terdiman
- Division of Gastroenterology, University of California, San Francisco, CA, USA
| | | | - Averil Ma
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, CA, USA.,Benioff Center for Microbiome Medicine, University of California, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Najwa El-Nachef
- Division of Gastroenterology, University of California, San Francisco, CA, USA.
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29
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Wu KC, Cao S, Weaver CM, King NJ, Patel S, Kingman H, Sellmeyer DE, McCauley K, Li D, Lynch SV, Kim TY, Black DM, Shafer MM, Özçam M, Lin DL, Rogers SJ, Stewart L, Carter JT, Posselt AM, Schafer AL. Prebiotic to Improve Calcium Absorption in Postmenopausal Women After Gastric Bypass: A Randomized Controlled Trial. J Clin Endocrinol Metab 2022; 107:1053-1064. [PMID: 34888663 PMCID: PMC8947782 DOI: 10.1210/clinem/dgab883] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT The adverse skeletal effects of Roux-en-Y gastric bypass (RYGB) are partly caused by intestinal calcium absorption decline. Prebiotics, such as soluble corn fiber (SCF), augment colonic calcium absorption in healthy individuals. OBJECTIVE We tested the effects of SCF on fractional calcium absorption (FCA), biochemical parameters, and the fecal microbiome in a post-RYGB population. METHODS Randomized, double-blind, placebo-controlled trial of 20 postmenopausal women with history of RYGB a mean 5 years prior; a 2-month course of 20 g/day SCF or maltodextrin placebo was taken orally. The main outcome measure was between-group difference in absolute change in FCA (primary outcome) and was measured with a gold standard dual stable isotope method. Other measures included tolerability, adherence, serum calciotropic hormones and bone turnover markers, and fecal microbial composition via 16S rRNA gene sequencing. RESULTS Mean FCA ± SD at baseline was low at 5.5 ± 5.1%. Comparing SCF to placebo, there was no between-group difference in mean (95% CI) change in FCA (+3.4 [-6.7, +13.6]%), nor in calciotropic hormones or bone turnover markers. The SCF group had a wider variation in FCA change than placebo (SD 13.4% vs 7.0%). Those with greater change in microbial composition following SCF treatment had greater increase in FCA (r2 = 0.72, P = 0.05). SCF adherence was high, and gastrointestinal symptoms were similar between groups. CONCLUSION No between-group differences were observed in changes in FCA or calciotropic hormones, but wide CIs suggest a variable impact of SCF that may be due to the degree of gut microbiome alteration. Daily SCF consumption was well tolerated. Larger and longer-term studies are warranted.
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Affiliation(s)
- Karin C Wu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
- Endocrine Research Unit, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, USA
- Correspondence: Karin C. Wu, MD, 1700 Owens St. RM 349, San Francisco, CA 94158, USA.
| | - Sisi Cao
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Human Sciences, the Ohio State University, Columbus, OH 43210, USA
| | - Connie M Weaver
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Nicole J King
- Endocrine Research Unit, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, USA
| | - Sheena Patel
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Hillary Kingman
- Endocrine Research Unit, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, USA
| | - Deborah E Sellmeyer
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Kathryn McCauley
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Danny Li
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Tiffany Y Kim
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
- Endocrine Research Unit, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, USA
| | - Dennis M Black
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Martin M Shafer
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Mustafa Özçam
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Din L Lin
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Stanley J Rogers
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Lygia Stewart
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
- Surgical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, USA
| | - Jonathan T Carter
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Andrew M Posselt
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Anne L Schafer
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
- Endocrine Research Unit, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
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30
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Santarossa S, Sitarik AR, Johnson CC, Li J, Lynch SV, Ownby DR, Ramirez A, Yong GLM, Cassidy-Bushrow AE. Associations of physical activity with gut microbiota in pre-adolescent children. Phys Act Nutr 2021; 25:24-37. [PMID: 35152621 PMCID: PMC8843867 DOI: 10.20463/pan.2021.0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022] Open
Abstract
[Purpose] To determine whether physical activity (PA), primarily the recommended 60 minutes of moderate-to-vigorous PA, is associated with gut bacterial microbiota in 10-year-old children. [Methods] The Block Physical Activity Screener, which provides minutes/day PA variables, was used to determine whether the child met the PA recommendations. 16S rRNA sequencing was performed on stool samples from the children to profile the composition of their gut bacterial microbiota. Differences in alpha diversity metrics (richness, Pielou’s evenness, and Faith’s phylogenetic diversity) by PA were determined using linear regression, whereas beta diversity (unweighted and weighted UniFrac) relationships were assessed using PERMANOVA. Taxon relative abundance differentials were determined using DESeq2. [Results] The analytic sample included 321 children with both PA and 16S rRNA sequencing data (mean age [SD] =10.2 [0.8] years; 54.2% male; 62.9% African American), where 189 (58.9%) met the PA recommendations. After adjusting for covariates, meeting the PA recommendations as well as minutes/day PA variables were not significantly associated with gut richness, evenness, or diversity (p ≥ 0.19). However, meeting the PA recommendations (weighted UniFrac R2 = 0.014, p = 0.001) was significantly associated with distinct gut bacterial composition. These compositional differences were partly characterized by increased abundance of Megamonas and Anaerovorax as well as specific Christensenellaceae_R-7_group taxa in children with higher PA. [Conclusion] Children who met the recommendations of PA had altered gut microbiota compositions. Whether this translates to a reduced risk of obesity or associated metabolic diseases is still unclear.
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31
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Tsitsiklis A, Zha BS, Byrne A, DeVoe C, Rackaityte E, Levan S, Sunshine S, Mick E, Ghale R, Love C, Tarashansky AJ, Pisco A, Albright J, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Detweiler A, Jones NG, Wu B, Darmanis S, Lynch SV, DeRisi JL, Matthay MA, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. medRxiv 2021:2021.03.23.21253487. [PMID: 33791731 PMCID: PMC8010763 DOI: 10.1101/2021.03.23.21253487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing we assessed lower respiratory tract immune responses and microbiome dynamics in 23 COVID-19 patients, 10 of whom developed VAP, and eight critically ill uninfected controls. At a median of three days (range: 2-4 days) before VAP onset we observed a transcriptional signature of bacterial infection. At a median of 15 days prior to VAP onset (range: 8-38 days), we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.
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Fonseca W, Malinczak CA, Fujimura K, Li D, McCauley K, Li J, Best SKK, Zhu D, Rasky AJ, Johnson CC, Bermick J, Zoratti EM, Ownby D, Lynch SV, Lukacs NW, Ptaschinski C. Maternal gut microbiome regulates immunity to RSV infection in offspring. J Exp Med 2021; 218:212680. [PMID: 34613328 PMCID: PMC8500238 DOI: 10.1084/jem.20210235] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/26/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022] Open
Abstract
Development of the immune system can be influenced by diverse extrinsic and intrinsic factors that influence the risk of disease. Severe early life respiratory syncytial virus (RSV) infection is associated with persistent immune alterations. Previously, our group had shown that adult mice orally supplemented with Lactobacillus johnsonii exhibited decreased airway immunopathology following RSV infection. Here, we demonstrate that offspring of mice supplemented with L. johnsonii exhibit reduced airway mucus and Th2 cell–mediated response to RSV infection. Maternal supplementation resulted in a consistent gut microbiome in mothers and their offspring. Importantly, supplemented maternal plasma and breastmilk, and offspring plasma, exhibited decreased inflammatory metabolites. Cross-fostering studies showed that prenatal Lactobacillus exposure led to decreased Th2 cytokines and lung inflammation following RSV infection, while postnatal Lactobacillus exposure diminished goblet cell hypertrophy and mucus production in the lung in response to airway infection. These studies demonstrate that Lactobacillus modulation of the maternal microbiome and associated metabolic reprogramming enhance airway protection against RSV in neonates.
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Affiliation(s)
- Wendy Fonseca
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | | | - Kei Fujimura
- Department of Medicine-Gastroenterology, University of California, San Francisco, San Francisco, CA
| | - Danny Li
- Department of Medicine-Gastroenterology, University of California, San Francisco, San Francisco, CA
| | - Kathryn McCauley
- Department of Medicine-Gastroenterology, University of California, San Francisco, San Francisco, CA
| | - Jia Li
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI
| | | | - Diana Zhu
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Andrew J Rasky
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | | | - Jennifer Bermick
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | - Edward M Zoratti
- Division of Allergy and Clinical Immunology, Department of Medicine, Henry Ford Health System, Detroit, MI
| | - Dennis Ownby
- Department of Pediatrics, Augusta University, Augusta, GA
| | - Susan V Lynch
- Department of Medicine-Gastroenterology, University of California, San Francisco, San Francisco, CA
| | - Nicholas W Lukacs
- Department of Pathology, University of Michigan, Ann Arbor, MI.,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI
| | - Catherine Ptaschinski
- Department of Pathology, University of Michigan, Ann Arbor, MI.,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI
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Abstract
States of oral health and disease reflect the compositional and functional capacities of, as well as the interspecies interactions within, the oral microbiota. The oral cavity exists as a highly dynamic microbial environment that harbors many distinct substrata and microenvironments that house diverse microbial communities. Specific to the oral cavity, the nonshedding dental surfaces facilitate the development of highly complex polymicrobial biofilm communities, characterized not only by the distinct microbes comprising them, but cumulatively by their activities. Adding to this complexity, the oral cavity faces near-constant environmental challenges, including those from host diet, salivary flow, masticatory forces, and introduction of exogenous microbes. The composition of the oral microbiome is shaped throughout life by factors including host genetics, maternal transmission, as well as environmental factors, such as dietary habits, oral hygiene practice, medications, and systemic factors. This dynamic ecosystem presents opportunities for oral microbial dysbiosis and the development of dental and periodontal diseases. The application of both in vitro and culture-independent approaches has broadened the mechanistic understandings of complex polymicrobial communities within the oral cavity, as well as the environmental, local, and systemic underpinnings that influence the dynamics of the oral microbiome. Here, we review the present knowledge and current understanding of microbial communities within the oral cavity and the influences and challenges upon this system that encourage homeostasis or provoke microbiome perturbation, and thus contribute to states of oral health or disease.
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Affiliation(s)
- Lea Sedghi
- Department of Orofacial SciencesSchool of DentistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Vincent DiMassa
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Anthony Harrington
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Susan V. Lynch
- Department of MedicineUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Yvonne L. Kapila
- Department of Orofacial SciencesSchool of DentistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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Horton MK, McCauley K, Fadrosh D, Fujimura K, Graves J, Ness J, Wheeler Y, Gorman MP, Benson LA, Weinstock‐Guttman B, Waldman A, Rodriguez M, Tillema J, Krupp L, Belman A, Mar S, Rensel M, Chitnis T, Casper TC, Rose J, Hart J, Shao X, Tremlett H, Lynch SV, Barcellos LF, Waubant E. Gut microbiome is associated with multiple sclerosis activity in children. Ann Clin Transl Neurol 2021; 8:1867-1883. [PMID: 34409759 PMCID: PMC8419410 DOI: 10.1002/acn3.51441] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE To identify features of the gut microbiome associated with multiple sclerosis activity over time. METHODS We used 16S ribosomal RNA sequencing from stool of 55 recently diagnosed pediatric-onset multiple sclerosis patients. Microbiome features included the abundance of individual microbes and networks identified from weighted genetic correlation network analyses. Prentice-Williams-Peterson Cox proportional hazards models estimated the associations between features and three disease activity outcomes: clinical relapses and both new/enlarging T2 lesions and new gadolinium-enhancing lesions on brain MRI. Analyses were adjusted for age, sex, and disease-modifying therapies. RESULTS Participants were followed, on average, 2.1 years. Five microbes were nominally associated with all three disease activity outcomes after multiple testing correction. These included butyrate producers Odoribacter (relapse hazard ratio = 0.46, 95% confidence interval: 0.24, 0.88) and Butyricicoccus (relapse hazard ratio = 0.49, 95% confidence interval: 0.28, 0.88). Two networks of co-occurring gut microbes were significantly associated with a higher hazard of both MRI outcomes (gadolinium-enhancing lesion hazard ratios (95% confidence intervals) for Modules 32 and 33 were 1.29 (1.08, 1.54) and 1.42 (1.18, 1.71), respectively; T2 lesion hazard ratios (95% confidence intervals) for Modules 32 and 33 were 1.34 (1.15, 1.56) and 1.41 (1.21, 1.64), respectively). Metagenomic predictions of these networks demonstrated enrichment for amino acid biosynthesis pathways. INTERPRETATION Both individual and networks of gut microbes were associated with longitudinal multiple sclerosis activity. Known functions and metagenomic predictions of these microbes suggest the important role of butyrate and amino acid biosynthesis pathways. This provides strong support for future development of personalized microbiome interventions to modify multiple sclerosis disease activity.
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Affiliation(s)
- Mary K. Horton
- Division of EpidemiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Kathryn McCauley
- Department of Medicine‐ GastroenterologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Douglas Fadrosh
- Department of Medicine‐ GastroenterologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Kei Fujimura
- Department of Medicine‐ GastroenterologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Jennifer Graves
- Department of NeurosciencesUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Jayne Ness
- Division of Pediatric NeurologyUniversity of AlabamaBirminghamAlabamaUSA
| | - Yolanda Wheeler
- Division of Pediatric NeurologyUniversity of AlabamaBirminghamAlabamaUSA
| | - Mark P. Gorman
- Department of NeurologyBoston Children’s HospitalBostonMassachusettsUSA
| | - Leslie A. Benson
- Department of NeurologyBoston Children’s HospitalBostonMassachusettsUSA
| | | | - Amy Waldman
- Department of NeurologyChildren’s Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | | | | | - Lauren Krupp
- Pediatric Multiple Sclerosis CenterNew York University Langone Medical CenterNew YorkNew YorkUSA
| | - Anita Belman
- Pediatric Multiple Sclerosis CenterNew York University Langone Medical CenterNew YorkNew YorkUSA
| | - Soe Mar
- Department of NeurologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Mary Rensel
- Department of NeurologyCleveland ClinicClevelandOhioUSA
| | - Tanuja Chitnis
- Division of Child NeurologyMassachusetts General HospitalBostonMassachusettsUSA
| | | | - John Rose
- School of MedicineUniversity of Utah SchoolSalt Lake CityUtahUSA
| | - Janace Hart
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Xiaorong Shao
- Division of EpidemiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Helen Tremlett
- Department of MedicineUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Susan V. Lynch
- Department of Medicine‐ GastroenterologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Lisa F. Barcellos
- Division of EpidemiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Emmanuelle Waubant
- Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
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Abstract
Intestinal microbiome perturbation characterizes Crohn's disease (CD), though specific contributors to pathophysiology remain elusive. In a recent issue of Science, Jain et al. show that Debaryomyces hansenii impairs intestinal healing in mice via effects on type I interferon signaling and chemokine CCL5 expression in macrophages and that it is also prevalent in the inflamed mucosa of CD patients.
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Affiliation(s)
- Kevin M Magnaye
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, CA, USA.
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Lynch SV, Vercelli D. Microbiota, Epigenetics, and Trained Immunity. Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood. Am J Respir Crit Care Med 2021; 203:802-808. [PMID: 33493428 DOI: 10.1164/rccm.202010-3779pp] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, California; and
| | - Donata Vercelli
- Department of Cellular and Molecular Medicine & Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona
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Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay MA, Lynch SV, DeRisi JL, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. Res Sq 2021:rs.3.rs-380803. [PMID: 34013247 PMCID: PMC8132240 DOI: 10.21203/rs.3.rs-380803/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing (scRNA-seq) we assessed lower respiratory tract immune responses and microbiome dynamics in 28 COVID-19 patients, 15 of whom developed VAP, and eight critically ill uninfected controls. Two days before VAP onset we observed a transcriptional signature of bacterial infection. Two weeks prior to VAP onset, following intubation, we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.
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Affiliation(s)
- Alexandra Tsitsiklis
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Catherine Devoe
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Sophia Levan
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Eran Mick
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Rajani Ghale
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alejandra Jauregui
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Aartik Sarma
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Paula Hayakawa Serpa
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Thomas J. Deiss
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sidney Carrillo
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - K. Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - Aleksandra Leligdowicz
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Christenson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Norman Jones
- Department of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Bing Wu
- Genentech, Inc. San Francisco, CA, USA
| | | | - Michael A. Matthay
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Susan V. Lynch
- Department of Gastroenterology, University of California, San Francisco, CA, USA
- Benioff Center for Microbiome Medicine, University of California, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Carolyn M. Hendrickson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten N. Kangelaris
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Matthew F. Krummel
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Prescott G. Woodruff
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
- Sandler Asthma Basic Research Center, University of California, San Francisco, CA, USA
| | - David J. Erle
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Lung Biology Center, University of California, San Francisco, CA, USA
- UCSF CoLabs, University of California, San Francisco, CA, USA
| | - Oren Rosenberg
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Carolyn S. Calfee
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles R. Langelier
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Corroborating evidence refutes batch effect as explanation for fetal bacteria. Microbiome 2021; 9:10. [PMID: 33436079 PMCID: PMC7805121 DOI: 10.1186/s40168-020-00948-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 05/16/2023]
Affiliation(s)
- E Rackaityte
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - J Halkias
- Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - E M Fukui
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - V F Mendoza
- Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - C Hayzelden
- College of Science and Engineering, San Francisco State University, San Francisco, CA, USA
| | - E D Crawford
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - T D Burt
- Duke University School of Medicine, Durham, NC, USA
| | - S V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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Sitarik AR, Arora M, Austin C, Bielak LF, Eggers S, Johnson CC, Lynch SV, Kyun Park S, Hank Wu KH, Yong GJM, Cassidy-Bushrow AE. Fetal and early postnatal lead exposure measured in teeth associates with infant gut microbiota. Environ Int 2020; 144:106062. [PMID: 32871381 PMCID: PMC7572588 DOI: 10.1016/j.envint.2020.106062] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Lead (Pb) is an environmentally ubiquitous heavy metal associated with a wide range of adverse health effects in children. Both lead exposure and the early life microbiome- which plays a critical role in human development-have been linked to similar health outcomes, but it is unclear if the adverse effects of lead are partially driven by early life gut microbiota dysbiosis. The objective of this study was to examine the association between in utero and postnatal lead levels (measured in deciduous baby teeth) and early life bacterial and fungal gut microbiota in the first year of life. METHODS Data from the Wayne County Health, Environment, Allergy and Asthma Longitudinal Study (WHEALS) birth cohort were analyzed. Tooth lead levels during the 2nd and 3rd trimesters and postnatally (<1 year of age) were quantified using high-resolution microspatial mapping of dentin growth rings. Early life microbiota were measured in stool samples collected at approximately 1 and 6 months of age, using both 16S rRNA (bacterial) and ITS2 (fungal) sequencing. Of the 1,258 maternal-child pairs in WHEALS, 146 had data on both tooth metals and early life microbiome. RESULTS In utero tooth lead levels were significantly associated with gut fungal community composition at 1-month of age, where higher levels of 2nd trimester tooth lead was associated with lower abundances of Candida and Aspergillus and higher abundances of Malassezia and Saccharomyces; 3rd trimester lead was also associated with lower abundances of Candida. Though lead did not significantly associate with the overall structure of the infant gut bacterial community, it associated with the abundance of some specific bacterial taxa, including the increased abundance of Collinsella and Bilophila and a decreased abundance of Bacteroides taxa. CONCLUSIONS The observed associations between lead exposure and infant gut microbiota could play a role in the impact of lead on childhood development. Given the paucity of research examining these associations in humans-particularly for fungal microbiota-further investigation is needed.
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Affiliation(s)
- Alexandra R Sitarik
- Department of Public Health Sciences, Henry Ford Health System, Detroit, USA.
| | - Manish Arora
- Senator Frank R Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, USA.
| | - Christine Austin
- Senator Frank R Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, USA.
| | | | - Shoshannah Eggers
- Senator Frank R Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, USA.
| | - Christine C Johnson
- Department of Public Health Sciences, Henry Ford Health System, Detroit, USA.
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, USA.
| | - Sung Kyun Park
- Department of Epidemiology, University of Michigan, Ann Arbor, USA; Department of Environmental Health Sciences, University of Michigan, Ann Arbor, USA.
| | - Kuan-Han Hank Wu
- Department of Public Health Sciences, Henry Ford Health System, Detroit, USA.
| | - Germaine J M Yong
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, USA.
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Panzer AR, Lynch SV. Gut Microbial Regulation of Autism Spectrum Disorder Symptoms. Trends Endocrinol Metab 2020; 31:809-811. [PMID: 32972817 DOI: 10.1016/j.tem.2020.09.001] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/03/2020] [Indexed: 11/27/2022]
Abstract
Relationships between gut microbiome perturbation and autism spectrum disorder (ASD) have been observed in several human studies, but the functional implications and molecular mechanisms by which microbes may influence disease symptomology remain enigmatic. A recently published study by Sharon et al. offers evidence that the gut microbiome has a causative role in ASD and highlights the importance of early-life gut microbial metabolites in shaping mammalian behavior.
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Affiliation(s)
- Ariane R Panzer
- Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA; UCSF Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA; UCSF Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, USA.
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Kassem Z, Sitarik A, Levin AM, Lynch SV, Havstad S, Fujimura K, Kozyrskyj A, Ownby DR, Johnson CC, Yong GJM, Wegienka G, Cassidy-Bushrow AE. Maternal and cord blood vitamin D level and the infant gut microbiota in a birth cohort study. Matern Health Neonatol Perinatol 2020; 6:5. [PMID: 33101701 PMCID: PMC7576815 DOI: 10.1186/s40748-020-00119-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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] [Received: 02/13/2020] [Accepted: 10/08/2020] [Indexed: 12/22/2022] Open
Abstract
Background Mounting evidence suggests both vitamin D and the early life gut microbiome influence childhood health outcomes. However, little is known about how these two important exposures are related. We aimed to examine associations between plasma 25-hydroxyvitamin D (25[OH]D) levels during pregnancy or at delivery (cord blood) and infant gut microbiota. Methods Maternal and cord blood 25[OH]D levels were assessed in a sample of pregnant women. Compositional analyses adjusted for race were run on the gut microbiota of their offspring at 1 and 6 months of age. Results Mean prenatal 25(OH)D level was 25.04 ± 11.62 ng/mL and mean cord blood 25(OH)D level was 10.88 ± 6.77 ng/mL. Increasing prenatal 25(OH)D level was significantly associated with decreased richness (p = 0.028) and diversity (p = 0.012) of the gut microbiota at 1 month of age. Both prenatal and cord 25(OH)D were significantly associated with 1 month microbiota composition. A total of 6 operational taxonomic units (OTUs) were significantly associated with prenatal 25(OH)D level (four positively and two negatively) while 11 OTUs were significantly associated with cord 25(OH)D (10 positively and one negatively). Of these, OTU 93 (Acinetobacter) and OTU 210 (Corynebacterium), were consistently positively associated with maternal and cord 25(OH)D; OTU 64 (Ruminococcus gnavus) was positively associated with prenatal 25(OH)D but negatively associated with cord 25(OH)D. Conclusions Prenatal maternal and cord blood 25(OH)D levels are associated with the early life gut microbiota. Future studies are needed to understand how vitamin D and the microbiome may interact to influence child health.
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Affiliation(s)
- Zeinab Kassem
- Department of Public Health Sciences, Henry Ford Hospital, 1 Ford Place, 5C, Detroit, MI 48202 USA
| | - Alexandra Sitarik
- Department of Public Health Sciences, Henry Ford Hospital, 1 Ford Place, 5C, Detroit, MI 48202 USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Hospital, 1 Ford Place, 5C, Detroit, MI 48202 USA
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, CA USA
| | - Suzanne Havstad
- Department of Public Health Sciences, Henry Ford Hospital, 1 Ford Place, 5C, Detroit, MI 48202 USA
| | - Kei Fujimura
- Department of Medicine, University of California, San Francisco, CA USA
| | - Anita Kozyrskyj
- Department of Pediatrics, University of Alberta, Alberta, Canada
| | - Dennis R Ownby
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Georgia Regents University, Augusta, GA USA
| | - Christine Cole Johnson
- Department of Public Health Sciences, Henry Ford Hospital, 1 Ford Place, 5C, Detroit, MI 48202 USA.,Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI USA
| | - Germaine J M Yong
- Department of Medicine, University of California, San Francisco, CA USA
| | - Ganesa Wegienka
- Department of Public Health Sciences, Henry Ford Hospital, 1 Ford Place, 5C, Detroit, MI 48202 USA.,Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI USA
| | - Andrea E Cassidy-Bushrow
- Department of Public Health Sciences, Henry Ford Hospital, 1 Ford Place, 5C, Detroit, MI 48202 USA.,Center for Urban Responses to Environmental Stressors, Wayne State University, Detroit, MI USA
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Sitarik AR, Havstad SL, Johnson CC, Jones K, Levin AM, Lynch SV, Ownby DR, Rundle AG, Straughen JK, Wegienka G, Woodcroft KJ, Yong GJM, Cassidy-Bushrow AE. Association between cesarean delivery types and obesity in preadolescence. Int J Obes (Lond) 2020; 44:2023-2034. [PMID: 32873910 PMCID: PMC7530127 DOI: 10.1038/s41366-020-00663-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 01/04/2023]
Abstract
Background/Objectives: The association between mode of delivery and childhood obesity remains inconclusive. Because few studies have separated C-section types (planned or unplanned C-section), our objective was to assess how these subtypes relate to pre-adolescent obesity. Subjects/Methods: The study consisted of 570 maternal-child pairs drawn from the WHEALS birth cohort based in Detroit, Michigan. Children were followed-up at 10 years of age where a variety of anthropometric measurements were collected. Obesity was defined based on BMI percentile (≥95th percentile), as well as through gaussian finite mixture modeling on the anthropometric measurements. Risk ratios (RRs) and 95% confidence intervals (CIs) for obesity comparing planned and unplanned C-sections to vaginal deliveries were computed, which utilized inverse probability weights to account for loss to follow-up and multiple imputation for covariate missingness. Mediation models were fit to examine the mediation role of breastfeeding. Results: After adjusting for marital status, maternal race, prenatal tobacco smoke exposure, maternal age, maternal BMI, any hypertensive disorders during pregnancy, gestational diabetes, prenatal antibiotic use, child sex, parity, and birthweight z-score, children born via planned C-section had 1.77 times higher risk of obesity (≥95th percentile), relative to those delivered vaginally ((95% CI)=(1.16,2.72); p=0.009). No association was found comparing unplanned C-section to vaginal delivery (RR (95% CI)=0.75 (0.45, 1.23); p=0.25). Results were similar but slightly stronger when obesity was defined by anthropometric class (RR (95% CI)=2.78 (1.47, 5.26); p=0.002). Breastfeeding did not mediate the association between mode of delivery and obesity. Conclusions: These findings indicate that children delivered via planned C-section—but not unplanned C-section—have a higher risk of pre-adolescent obesity, suggesting that partial labor or membrane rupture (typically experienced during unplanned C-section delivery) may offer protection. Additional research is needed to understand the biological mechanisms behind this effect, including whether microbiological differences fully or partially account for the association.
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Affiliation(s)
- Alexandra R Sitarik
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA.
| | - Suzanne L Havstad
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Christine C Johnson
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Kyra Jones
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Dennis R Ownby
- Division of Allergy & Immunology, Medical College of Georgia at Augusta University, Augusta, Georgia
| | - Andrew G Rundle
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Jennifer K Straughen
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Ganesa Wegienka
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | | | - Germaine J M Yong
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, CA, USA
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Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Viable bacterial colonization is limited in the human intestine in utero. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.83.23] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Mucosal immunity develops in the human fetal intestine by 11–14 weeks gestation, yet whether viable microbes exist in utero and interact with intestinal immunity is unknown. Structures consistent with coccoid bacterial morphology, embedded in fetal meconium were evident before mid-gestation by high-resolution scanning electron microscopy (n=4). Molecular methods indicated extremely low bacterial burden and simple profiles in fetal meconium (n=40 of 50) compared to controls (n=87). A subset of Micrococcaceae-dominated (n=9) meconium associated with proportions of lamina propria PLZF+ CD161+ CD4+ T cells and divergent intestinal epithelial transcriptomes. Fetal Micrococcus luteus was isolated only in the presence of a monocyte feeder cell line. This strain grew on placental hormones, remained viable within fetal antigen presenting cells, exhibited species-specific immunomodulatory capacity and genomic features indicating fetal adaptation. Thus, viable bacteria are highly limited and inconsistently detectable in human fetal meconium at mid-gestation.
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Durack J, Christian LS, Nariya S, Gonzalez J, Bhakta NR, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Peters SP, Rosenberg SR, Sorkness CA, Wechsler ME, Wenzel SE, White SR, Lynch SV, Boushey HA, Huang YJ. Distinct associations of sputum and oral microbiota with atopic, immunologic, and clinical features in mild asthma. J Allergy Clin Immunol 2020; 146:1016-1026. [PMID: 32298699 DOI: 10.1016/j.jaci.2020.03.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/06/2020] [Accepted: 03/02/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Whether microbiome characteristics of induced sputum or oral samples demonstrate unique relationships to features of atopy or mild asthma in adults is unknown. OBJECTIVE We sought to determine sputum and oral microbiota relationships to clinical or immunologic features in mild atopic asthma and the impact on the microbiota of inhaled corticosteroid (ICS) treatment administered to ICS-naive subjects with asthma. METHODS Bacterial microbiota profiles were analyzed in induced sputum and oral wash samples from 32 subjects with mild atopic asthma before and after inhaled fluticasone treatment, 18 atopic subjects without asthma, and 16 nonatopic healthy subjects in a multicenter study (NCT01537133). Associations with clinical and immunologic features were examined, including markers of atopy, type 2 inflammation, immune cell populations, and cytokines. RESULTS Sputum bacterial burden inversely associated with bronchial expression of type 2 (T2)-related genes. Differences in specific sputum microbiota also associated with T2-low asthma phenotype, a subgroup of whom displayed elevations in lung inflammatory mediators and reduced sputum bacterial diversity. Differences in specific oral microbiota were more reflective of atopic status. After ICS treatment of patients with asthma, the compositional structure of sputum microbiota showed greater deviation from baseline in ICS nonresponders than in ICS responders. CONCLUSIONS Novel associations of sputum and oral microbiota to immunologic features were observed in this cohort of subjects with or without ICS-naive mild asthma. These findings confirm and extend our previous report of reduced bronchial bacterial burden and compositional complexity in subjects with T2-high asthma, with additional identification of a T2-low subgroup with a distinct microbiota-immunologic relationship.
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Affiliation(s)
- Juliana Durack
- Department of Medicine, Division of Gastroenterology, University of California, San Francisco, Calif
| | - Laura S Christian
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, San Francisco, Calif
| | - Snehal Nariya
- Department of Medicine, Division of Pulmonary/Critical Care Medicine, University of California, San Francisco, Calif
| | - Jeanmarie Gonzalez
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, San Francisco, Calif
| | - Nirav R Bhakta
- Department of Medicine, Division of Pulmonary/Critical Care Medicine, University of California, San Francisco, Calif
| | - K Mark Ansel
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, San Francisco, Calif
| | - Avraham Beigelman
- Division of Pediatric Allergy, Immunology, and Pulmonary Medicine, Washington University School of Medicine, St Louis, Mo; Kipper Institute of Allergy and Immunology, Schneider Children's Medical Center of Israel, Tel Aviv University, Tel Aviv, Israel
| | - Mario Castro
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St Louis, Mo
| | - Anne-Marie Dyer
- Department of Public Health Sciences, Penn State University, Hershey, Pa
| | - Elliot Israel
- Department of Medicine, Brigham & Women's Hospital, Boston, Mass
| | - Monica Kraft
- University of Arizona, Health Sciences, Tucson, Ariz
| | | | - David T Mauger
- Department of Public Health Sciences, Penn State University, Hershey, Pa
| | | | | | | | | | - Sally E Wenzel
- University of Pittsburgh Asthma Institute at UPMC/UPSOM, Pittsburgh, Pa
| | - Steven R White
- Department of Medicine, University of Chicago, Chicago, Ill
| | - Susan V Lynch
- Department of Medicine, Division of Gastroenterology, University of California, San Francisco, Calif
| | - Homer A Boushey
- Department of Medicine, Division of Pulmonary/Critical Care Medicine, University of California, San Francisco, Calif
| | - Yvonne J Huang
- Department of Internal Medicine, Division of Pulmonary/Critical Care Medicine, University of Michigan, Ann Arbor, Mich.
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Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Viable bacterial colonization is highly limited in the human intestine in utero. Nat Med 2020; 26:599-607. [PMID: 32094926 PMCID: PMC8110246 DOI: 10.1038/s41591-020-0761-3] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/10/2020] [Indexed: 02/08/2023]
Abstract
Mucosal immunity develops in the human fetal intestine by 11-14 weeks of gestation, yet whether viable microbes exist in utero and interact with the intestinal immune system is unknown. Bacteria-like morphology was identified in pockets of human fetal meconium at mid-gestation by scanning electron microscopy (n = 4), and a sparse bacterial signal was detected by 16S rRNA sequencing (n = 40 of 50) compared to environmental controls (n = 87). Eighteen taxa were enriched in fetal meconium, with Micrococcaceae (n = 9) and Lactobacillus (n = 6) the most abundant. Fetal intestines dominated by Micrococcaceae exhibited distinct patterns of T cell composition and epithelial transcription. Fetal Micrococcus luteus, isolated only in the presence of monocytes, grew on placental hormones, remained viable within antigen presenting cells, limited inflammation ex vivo and possessed genomic features linked with survival in the fetus. Thus, viable bacteria are highly limited in the fetal intestine at mid-gestation, although strains with immunomodulatory capacity are detected in subsets of specimens.
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Affiliation(s)
- E Rackaityte
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - J Halkias
- Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - E M Fukui
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - V F Mendoza
- Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - C Hayzelden
- College of Science and Engineering, San Francisco State University, San Francisco, CA, USA
| | - E D Crawford
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - K E Fujimura
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Genentech, South San Francisco, CA, USA
| | - T D Burt
- Duke University School of Medicine, Durham, NC, USA
| | - S V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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Selvig D, Piceno Y, Terdiman J, Zydek M, Umetsu SE, Balitzer D, Fadrosh D, Lynch K, Lamere B, Leith T, Kassam Z, Beck K, Lewin S, Ma A, Somsouk M, Lynch SV, El-Nachef N. Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study. Dig Dis Sci 2020; 65:1099-1106. [PMID: 31302808 DOI: 10.1007/s10620-019-05715-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/02/2019] [Indexed: 12/26/2022]
Abstract
AIMS This pilot study assessed the efficacy, safety, and microbiome dynamics of fecal microbiota transplantation (FMT) for patients with chronic pouchitis. METHODS A prospective open-label pilot study was performed at an academic center among pouchitis patients undergoing FMT. Patients received a minimum of a single FMT by pouchoscopy from healthy, screened donors. The primary outcome was clinical improvement in pouchitis assessed by patient survey at week 4. Secondary outcomes included decrease in total Pouchitis Disease Activity Index (PDAI) Score ≥ 3 at week 4, bowel movement frequency, ESR, CRP, fecal calprotectin, abdominal pain, and PDAI subscores including endoscopic and histologic changes. Stool samples were collected at baseline and 4 weeks post-FMT to assess bacterial microbiota using V4 16S rRNA sequencing. RESULTS Nineteen patients were enrolled; however, 1 patient was lost to follow-up. No patients had a major adverse event or escalation of therapy related to FMT. Total PDAI scores, endoscopic scores, and histologic scores did not decrease significantly post-FMT. However, there was a statistically significant improvement in bowel movement (BM) frequency (9.25-7.25 BM/day, p = 0.03) and trend for improvement in abdominal pain to improve post-FMT (p = 0.05). Bacterial microbiota profiling revealed no distinct community-level changes post-FMT, though a small number of specific bacterial taxa significantly differed in relative abundance. CONCLUSIONS A single FMT has a tolerable short-term safety profile and may be associated with a decrease in bowel movements in patients with chronic pouchitis; however, no robust endoscopic or histologic changes were observed.
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Affiliation(s)
- Daniel Selvig
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yvette Piceno
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan Terdiman
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Zydek
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah E Umetsu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Dana Balitzer
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Doug Fadrosh
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kole Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brandon Lamere
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Zain Kassam
- OpenBiome, Somerville, MA, USA
- Finch Therapeutics Group, Somerville, MA, USA
| | - Kendall Beck
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sara Lewin
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Averil Ma
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ma Somsouk
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Najwa El-Nachef
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ, Lynch SV. Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma. J Allergy Clin Immunol 2019; 144:1187-1197. [PMID: 31201890 PMCID: PMC6842413 DOI: 10.1016/j.jaci.2019.05.035] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [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: 11/29/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND In infants, distinct nasopharyngeal bacterial microbiotas differentially associate with the incidence and severity of acute respiratory tract infection and childhood asthma development. OBJECTIVE We hypothesized that distinct nasal airway microbiota structures also exist in children with asthma and relate to clinical outcomes. METHODS Nasal secretion samples (n = 3122) collected after randomization during the fall season from children with asthma (6-17 years, n = 413) enrolled in a trial of omalizumab (anti-IgE) underwent 16S rRNA profiling. Statistical analyses with exacerbation as the primary outcome and rhinovirus infection and respiratory illnesses as secondary outcomes were performed. Using A549 epithelial cells, we assessed nasal isolates of Moraxella, Staphylococcus, and Corynebacterium species for their capacity to induce epithelial damage and inflammatory responses. RESULTS Six nasal airway microbiota assemblages, each dominated by Moraxella, Staphylococcus, Corynebacterium, Streptococcus, Alloiococcus, or Haemophilus species, were observed. Moraxella and Staphylococcus species-dominated microbiotas were most frequently detected and exhibited temporal stability. Nasal microbiotas dominated by Moraxella species were associated with increased exacerbation risk and eosinophil activation. Staphylococcus or Corynebacterium species-dominated microbiotas were associated with reduced respiratory illness and exacerbation events, whereas Streptococcus species-dominated assemblages increased the risk of rhinovirus infection. Nasal microbiota composition remained relatively stable despite viral infection or exacerbation; only a few taxa belonging to the dominant genera exhibited relative abundance fluctuations during these events. In vitro, Moraxella catarrhalis induced significantly greater epithelial damage and inflammatory cytokine expression (IL-33 and IL-8) compared with other dominant nasal bacterial isolates tested. CONCLUSION Distinct nasal airway microbiotas of children with asthma relate to the likelihood of exacerbation, rhinovirus infection, and respiratory illnesses during the fall season.
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Affiliation(s)
- Kathryn McCauley
- Department of Medicine, University of California, San Francisco, Calif
| | - Juliana Durack
- Department of Medicine, University of California, San Francisco, Calif
| | | | - Douglas W Fadrosh
- Department of Medicine, University of California, San Francisco, Calif
| | - Din L Lin
- Department of Medicine, University of California, San Francisco, Calif
| | | | | | | | - Kei E Fujimura
- Department of Medicine, University of California, San Francisco, Calif
| | - Brandon LaMere
- Department of Medicine, University of California, San Francisco, Calif
| | - Geil Merana
- Department of Medicine, University of California, San Francisco, Calif
| | - Kole Lynch
- Department of Medicine, University of California, San Francisco, Calif
| | | | | | | | - Carolyn M Kercsmar
- Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Michelle Gill
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex; Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Andrew H Liu
- Department of Pedatrics and Pulmonology Medicine, National Jewish Health, Denver, Colo; Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colo
| | - Haejin Kim
- Department of Internal Medicine, Division of Allergy and Immunology, Henry Ford Health System, Detroit, Mich
| | - Meyer Kattan
- College of Physicians and Surgeons, Columbia University, New York, NY
| | | | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Homer A Boushey
- Department of Medicine, University of California, San Francisco, Calif
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis.
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco, Calif.
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48
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DeMuri GP, Gern JE, Eickhoff JC, Lynch SV, Wald ER. Dynamics of Bacterial Colonization With Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis During Symptomatic and Asymptomatic Viral Upper Respiratory Tract Infection. Clin Infect Dis 2019; 66:1045-1053. [PMID: 29121208 PMCID: PMC6019034 DOI: 10.1093/cid/cix941] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/06/2017] [Indexed: 12/02/2022] Open
Abstract
Background Virus is detected in about 80% of upper respiratory tract infections (URTIs) in children and is also detectable in the nasopharynx of 30% of asymptomatic children. The effect of asymptomatic viral infection on the dynamics of bacterial density and colonization of the nasopharynx has not been reported. The current study was performed to assess the presence and density of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in the nasopharynx of 4–7-year-old children during URTI and when well. Methods Nasal samples were obtained during 4 surveillance periods when children were asymptomatic and whenever they had symptoms of URTI. Respiratory viruses and bacterial pathogens were identified and quantified using polymerase chain reaction. Results The proportion of children colonized with all 3 bacteria was higher during visits for acute URTI than during asymptomatic surveillance visits. Mean bacterial densities were significantly higher at all visits for all 3 pathogens when a virus was detected. The differences between the means were 1.0, 0.4, and 0.7 log10 colony-forming unit equivalents per milliliter for S. pneumoniae, H. influenzae, and M. catarrhalis, respectively, compared with visits in which virus was not detected. The percentage of children colonized and density were also higher at asymptomatic visits in which virus was detected than at visits in which virus was not detected. Conclusion The density and frequency of colonization with S. pneumoniae, H. influenzae, and M. catarrhalis in nasal wash samples increase during periods of both symptomatic and asymptomatic viral infection. Increases in bacterial colonization observed during asymptomatic viral infection were nearly the same magnitude as when children were symptomatic.
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Affiliation(s)
- Gregory P DeMuri
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison
| | - Jens C Eickhoff
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison
| | - Susan V Lynch
- Department of Medicine, University of California, San Francisco
| | - Ellen R Wald
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison
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Talpin A, Kattah MG, Advincula R, Fadrosh D, Lynch K, LaMere B, Fujimura KE, Nagalingam NA, Malynn BA, Lynch SV, Ma A. A20 in dendritic cells restrains intestinal anti-bacterial peptide expression and preserves commensal homeostasis. PLoS One 2019; 14:e0218999. [PMID: 31295268 PMCID: PMC6622485 DOI: 10.1371/journal.pone.0218999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/13/2019] [Indexed: 12/24/2022] Open
Abstract
Microbial dysbiosis commonly occurs in patients with inflammatory bowel diseases (IBD). Exogenous causes of dysbiosis such as antibiotics and diet are well described, but host derived causes are understudied. A20 is a potent regulator of signals triggered by microbial pattern molecules, and A20 regulates susceptibility to intestinal inflammation in mice and in humans. We now report that mice lacking A20 expression in dendritic cells, A20FL/FL CD11c-Cre mice (or A20dDC mice), spontaneously develop colitogenic intestinal dysbiosis that is evident upon weaning and precedes the onset of colitis. Intestines from A20dDC mice express increased amounts of Reg3β and Reg3γ, but not Ang4. A20 deficient DCs promote gut microbiota perturbation in the absence of adaptive lymphocytes. Moreover, A20 deficient DCs directly induce expression of Reg3β and Reg3γ but not Ang 4 in normal intestinal epithelial cell enteroid cultures in the absence of other cell types. These findings reveal a pathophysiological pathway in which defective expression of an IBD susceptibility gene in DCs drives aberrant expression of anti-bacterial peptides and luminal dysbiosis that in turn confers host susceptibility to intestinal inflammation.
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Affiliation(s)
- Alice Talpin
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Michael G. Kattah
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Rommel Advincula
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Douglas Fadrosh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Kole Lynch
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Brandon LaMere
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Kei E. Fujimura
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Nabeetha A. Nagalingam
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Barbara A. Malynn
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Susan V. Lynch
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Averil Ma
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
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50
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Panzer AR, Lynch SV, Langelier C, Christie JD, McCauley K, Nelson M, Cheung CK, Benowitz NL, Cohen MJ, Calfee CS. Lung Microbiota Is Related to Smoking Status and to Development of Acute Respiratory Distress Syndrome in Critically Ill Trauma Patients. Am J Respir Crit Care Med 2019; 197:621-631. [PMID: 29035085 DOI: 10.1164/rccm.201702-0441oc] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [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: 12/20/2022] Open
Abstract
RATIONALE Cigarette smoking is associated with increased risk of acute respiratory distress syndrome (ARDS) in patients after severe trauma; however, the mechanisms underlying this association are unknown. OBJECTIVES To determine whether cigarette smoking contributes to ARDS development after trauma by altering community composition of the lung microbiota. METHODS We studied the lung microbiota of mechanically ventilated patients admitted to the ICU after severe blunt trauma. To do so, we used 16S ribosomal RNA gene amplicon sequencing of endotracheal aspirate samples obtained on ICU admission (n = 74) and at 48 hours after admission (n = 30). Cigarette smoke exposure (quantified using plasma cotinine), ARDS development, and other clinical parameters were correlated with lung microbiota composition. MEASUREMENTS AND MAIN RESULTS Smoking status was significantly associated with lung bacterial community composition at ICU admission (P = 0.007 by permutational multivariate ANOVA [PERMANOVA]) and at 48 hours (P = 0.03 by PERMANOVA), as well as with significant enrichment of potential pathogens, including Streptococcus, Fusobacterium, Prevotella, Haemophilus, and Treponema. ARDS development was associated with lung community composition at 48 hours (P = 0.04 by PERMANOVA) and was characterized by relative enrichment of Enterobacteriaceae and of specific taxa enriched at baseline in smokers, including Prevotella and Fusobacterium. CONCLUSIONS After severe blunt trauma, a history of smoking is related to lung microbiota composition, both at the time of ICU admission and at 48 hours. ARDS development is also correlated with respiratory microbial community structure at 48 hours and with taxa that are relatively enriched in smokers at ICU admission. The data derived from this pilot study suggest that smoking-related changes in the lung microbiota could be related to ARDS development after severe trauma.
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Affiliation(s)
| | - Susan V Lynch
- 1 Division of Gastroenterology, Department of Medicine
| | - Chaz Langelier
- 2 Division of Infectious Diseases, Department of Medicine
| | - Jason D Christie
- 3 Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Mary Nelson
- 4 Department of Surgery.,5 Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Christopher K Cheung
- 4 Department of Surgery.,5 Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Neal L Benowitz
- 6 Division of Clinical Pharmacology, Department of Medicine.,5 Zuckerberg San Francisco General Hospital, San Francisco, California
| | - Mitchell J Cohen
- 7 Department of Surgery, Denver Health Medical Center, Denver, Colorado; and.,8 Department of Surgery, University of Colorado, Aurora, Colorado
| | - Carolyn S Calfee
- 9 Division of Pulmonary and Critical Care Medicine, Department of Medicine.,10 Department of Anesthesia.,11 Cardiovascular Research Institute, and.,12 Center for Tobacco Control Research and Education, University of California, San Francisco, San Francisco, California
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