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Kamath S, Stringer AM, Prestidge CA, Joyce P. Targeting the gut microbiome to control drug pharmacomicrobiomics: the next frontier in oral drug delivery. Expert Opin Drug Deliv 2023; 20:1315-1331. [PMID: 37405390 DOI: 10.1080/17425247.2023.2233900] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
INTRODUCTION The trillions of microorganisms that comprise the gut microbiome form dynamic bidirectional interactions with orally administered drugs and host health. These relationships can alter all aspects of drug pharmacokinetics and pharmacodynamics (PK/PD); thus, there is a desire to control these interactions to maximize therapeutic efficacy. Attempts to modulate drug-gut microbiome interactions have spurred advancements within the field of 'pharmacomicrobiomics' and are poised to become the next frontier of oral drug delivery. AREAS COVERED This review details the bidirectional interactions that exist between oral drugs and the gut microbiome, with clinically relevant case examples outlining a clear motive for controlling pharmacomicrobiomic interactions. Specific focus is attributed to novel and advanced strategies that have demonstrated success in mediating drug-gut microbiome interactions. EXPERT OPINION Co-administration of gut-active supplements (e.g. pro- and pre-biotics), innovative drug delivery vehicles, and strategic polypharmacy serve as the most promising and clinically viable approaches for controlling pharmacomicrobiomic interactions. Targeting the gut microbiome through these strategies presents new opportunities for improving therapeutic efficacy by precisely mediating PK/PD, while mitigating metabolic disturbances caused by drug-induced gut dysbiosis. However, successfully translating preclinical potential into clinical outcomes relies on overcoming key challenges related to interindividual variability in microbiome composition and study design parameters.
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Affiliation(s)
- Srinivas Kamath
- UniSa Clinical & Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Andrea M Stringer
- UniSa Clinical & Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Clive A Prestidge
- UniSa Clinical & Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Paul Joyce
- UniSa Clinical & Health Sciences, University of South Australia, Adelaide, South Australia, Australia
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2
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Cao Y, Wang L, Ke S, Kelly CP, Pollock NR, Villafuerte Gálvez JA, Daugherty K, Xu H, Yao J, Chen Y, Liu YY, Chen X. Analysis of Intestinal Mycobiota of Patients with Clostridioides difficile Infection among a Prospective Inpatient Cohort. Microbiol Spectr 2022; 10:e0136222. [PMID: 35867408 PMCID: PMC9430669 DOI: 10.1128/spectrum.01362-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/23/2022] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) is a burden to health care systems worldwide. Gut microbiota dysbiosis associated with CDI has been well accepted. However, contribution of fungal mycobiota to CDI has recently gained research interest. Here, we report the gut mycobiota composition of 149 uniquely well characterized participants from a prospective clinical cohort and evaluate the discriminating ability of gut mycobiota to classify CDI and non-CDI patients. Fecal samples were divided into two groups: (i) CDI (inpatients who had clinically significant diarrhea and positive nucleic acid amplification testing [NAAT] and received subsequent CDI therapy, n = 58) and (ii) non-CDI, which can be further divided into three subgroups: (a) carrier (inpatients with positive stool NAAT but without diarrhea; n = 28); (b) diarrhea (inpatients with negative stool NAAT; n = 31); and (c) control (inpatients with negative stool NAAT and without diarrhea; n = 32). Fecal mycobiota composition was analyzed by internal transcribed spacer 2 (ITS2) sequencing. In comparison to non-CDI patients, CDI patients tend to have gut mycobiota with lower biodiversity, weaker fungi correlations, and weaker correlations between fungi and host immune factors. Notably, 11 genera (Saccharomyces, Penicillium, Aspergillus, Cystobasidium, Cladosporium, and so on) were significantly enriched in non-CDI patients, and Pichia and Suhomyces were enriched in patients with CDI, while 1 two genera, Cystobasidium and Exophiala, had higher abundance in patients with diarrhea compared with CDI (linear discriminant analysis [LDA] > 3.0; P < 0.05). Ascomycota and Basidiomycota (or Candida and Saccharomyces) exhibited a strong negative correlation (r ≤ -0.714 or r ≤ -0.387; P < 0.05), and the ratios of Ascomycota to Basidiomycota or genera Candida to Saccharomyces were dramatically higher in CDI patients than in non-CDI patients (P < 0.05). A disease-specific pattern with much weaker fungal abundance correlations was observed in the CDI group compared to that in the non-CDI and diarrhea groups, suggesting that these correlations may contribute to the development of CDI. Our findings provided specific markers of stool fungi that distinguish CDI from all non-CDI hospitalized patients. This study's potential clinical utility for better CDI diagnosis warrants further investigation. IMPORTANCE Clostridioides difficile is an opportunistic bacterial pathogen that causes a serious and potentially life-threatening infection of the human gut. It remains an existing challenge to distinguish active infection of CDI from diarrhea with non-CDI causes. A few large prospective studies from recent years suggest that there is no single optimal test for the diagnosis of CDI. Previous research has concentrated on the relationship between bacteria and CDI, while the roles of fungi, as a significant proportion of the gut microbial ecosystem, remain understudied. In this study, we report a series of fungal markers that may add diagnostic values for the development of a more systematic approach to accurate CDI diagnosis. These results help open the door for better understanding of the relationship between host immune factors and the fungal community in the context of CDI pathogenesis.
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Affiliation(s)
- Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Lamei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ciarán P. Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R. Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Javier A. Villafuerte Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
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Habib A, Lo S, Villageois-Tran K, Petitjean M, Malik SA, Armand-Lefèvre L, Ruppé E, Zahra R. Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan. PLoS One 2022; 17:e0270707. [PMID: 35802735 PMCID: PMC9269877 DOI: 10.1371/journal.pone.0270707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Carbapenems are considered last-line beta-lactams for the treatment of infections caused by multidrug-resistant Gram-negative bacteria. However, their activity is compromised by the rising prevalence of carbapenemase-producing Enterobacterales (CPE), which are especially marked in the Indian subcontinent. In Pakistan, previous reports have warned about the possible spread of CPE in the community, but data are still partial. This study was carried out to analyse the prevalence of CPE, the genetic characterisation, and phylogenetic links among the spreading CPE in the community. In this cohort study, we collected 306 rectal swabs from patients visiting Benazir Bhutto hospital, Rawalpindi. CPEs were screened by using ertapenem-supplemented MacConkey agar. Identification was performed by using conventional biochemical tests, and genomes were sequenced using Illumina chemistry. Antibiotic resistance genes, plasmid incompatibility groups, and Escherichia coli phylogroups were determined in silico. Sequence types were determined by using MLST tool. The prevalence of CPE carriage observed was 14.4% (44/306 samples). The most common carbapenemase-encoding gene was bla-NDM-5 (n = 58) followed by blaNDM-1 (n = 7), blaNDM (non-assigned variant, n = 4), blaOXA-181 (n = 3), blaOXA-232 (n = 3) and blaNDM-7 (n = 1). Most of the CPE were E. coli (55/64, 86%), and the genomic analysis revealed a pauciclonal diffusion of E. coli with ST167 (n = 14), 405 (n = 10), 940 (n = 8), 648 (n = 6) and 617 (n = 5). We obtained a second sample from 94 patients during their hospital stay in whom carriage was negative at admission and found that 7 (7.4%) acquired a CPE. Our results indicate that the prevalence of CPE carriage in the Pakistani urban community was high and driven by the dissemination of some E. coli clones, with ST167 being the most frequent. The high CPE carriage in the community poses a serious public health threat and calls for implementation of adequate preventive measures.
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Affiliation(s)
- Amina Habib
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Stéphane Lo
- Université de Paris, IAME, INSERM, Paris, France
- APHP, Laboratoire de Bactériologie, Hôpital Bichat, Paris, France
| | - Khanh Villageois-Tran
- Université de Paris, IAME, INSERM, Paris, France
- APHP, Laboratoire de Bactériologie, Hôpital Beaujon, Clichy, France
| | | | - Shaheen Akhtar Malik
- Accident and Emergency Department, Benazir Bhutto Hospital, Rawalpindi, Pakistan
| | - Laurence Armand-Lefèvre
- Université de Paris, IAME, INSERM, Paris, France
- APHP, Laboratoire de Bactériologie, Hôpital Bichat, Paris, France
| | - Etienne Ruppé
- Université de Paris, IAME, INSERM, Paris, France
- APHP, Laboratoire de Bactériologie, Hôpital Bichat, Paris, France
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- * E-mail:
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Wattier RL, Esbenshade AJ. From "More is Better" to "Less is More": A Commentary on Antimicrobial Use in Pediatric Oncology. J Pediatric Infect Dis Soc 2022; 11:229-238. [PMID: 35099542 DOI: 10.1093/jpids/piab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/09/2021] [Indexed: 11/14/2022]
Abstract
Reducing avoidable antimicrobial exposure to pediatric patients with cancer is achievable and necessary to promote optimal short- and long-term outcomes. Multiple evidence-based practices are already well established but should be more consistently implemented. Important opportunities exist to further improve the evidence to guide selective antimicrobial use in pediatric oncology.
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Affiliation(s)
- Rachel L Wattier
- Department of Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco, San Francisco, California, USA
| | - Adam J Esbenshade
- Department of Pediatrics, Division of Hematology/Oncology, Vanderbilt University, Nashville, Tennessee, USA
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5
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van de Velde ME, El Hassani SEM, Kaspers GJL, Broertjes J, Benninga MA, de Boer NKH, Budding AE, de Meij TGJ. Prediction of Bloodstream Infection in Pediatric Acute Leukemia by Microbiota and Volatile Organic Compounds Analysis. J Pediatr Hematol Oncol 2022; 44:e152-e159. [PMID: 34133377 DOI: 10.1097/mph.0000000000002210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/28/2021] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Bloodstream infections (BSIs) cause treatment-related mortality in pediatric acute leukemia. We explored the potential of intestinal microbiota and fecal volatile organic compounds (VOCs) analyses to predict BSI. METHODS In this case-control study, fecal samples of pediatric acute leukemia patients were collected. Microbiota composition and fecal VOC profiles of BSI cases and matched non-BSI controls were compared. RESULTS In total, 6 patients were included, of which 1 developed BSI and 1 neutropenic fever. Both showed reduced microbial diversity and stability of Bacteroidetes. In the BSI case, Pantoea was identified 15 days before BSI. Significant differences in fecal VOC profiles were measured between the case and controls. CONCLUSION Microbiota and fecal VOC could serve as biomarkers to predict BSI in pediatric leukemia.
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Affiliation(s)
| | - Sofia El Manouni El Hassani
- Pediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam
- Department of Pediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam
| | - Gert Jan L Kaspers
- Departments of Pediatric Oncology
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jorrit Broertjes
- Department of Pediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam
| | - Marc A Benninga
- Department of Pediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam
| | - Nanne K H de Boer
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Vrije Universiteit Amsterdam, AG&M Research Institute
| | | | - Tim G J de Meij
- Pediatric Gastroenterology, Emma Children's Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam
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6
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Oldenburg M, Rüchel N, Janssen S, Borkhardt A, Gössling KL. The Microbiome in Childhood Acute Lymphoblastic Leukemia. Cancers (Basel) 2021; 13:cancers13194947. [PMID: 34638430 PMCID: PMC8507905 DOI: 10.3390/cancers13194947] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/30/2022] Open
Abstract
For almost 30 years, the term "holobiont" has referred to an ecological unit where a host (e.g., human) and all species living in or around it are considered together. The concept highlights the complex interactions between the host and the other species, which, if disturbed may lead to disease and premature aging. Specifically, the impact of microbiome alterations on the etiology of acute lymphoblastic leukemia (ALL) in children is not fully understood, but has been the focus of much research in recent years. In ALL patients, significant reductions in microbiome diversity are already observable at disease onset. It remains unclear whether such alterations at diagnosis are etiologically linked with leukemogenesis or simply due to immunological alteration preceding ALL onset. Regardless, all chemotherapeutic treatment regimens severely affect the microbiome, accompanied by severe side effects, including mucositis, systemic inflammation, and infection. In particular, dominance of Enterococcaceae is predictive of infections during chemotherapy. Long-term dysbiosis, like depletion of Faecalibacterium, has been observed in ALL survivors. Modulation of the microbiome (e.g., by fecal microbiota transplant, probiotics, or prebiotics) is currently being researched for potential protective effects. Herein, we review the latest microbiome studies in pediatric ALL patients.
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Affiliation(s)
- Marina Oldenburg
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (M.O.); (N.R.); (A.B.)
| | - Nadine Rüchel
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (M.O.); (N.R.); (A.B.)
| | - Stefan Janssen
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, 35390 Gießen, Germany;
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (M.O.); (N.R.); (A.B.)
| | - Katharina L. Gössling
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Center of Child and Adolescent Health, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (M.O.); (N.R.); (A.B.)
- Correspondence:
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7
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Bélanger V, Benmoussa A, Napartuk M, Warin A, Laverdière C, Marcoux S, Levy E, Marcil V. The Role of Oxidative Stress and Inflammation in Cardiometabolic Health of Children During Cancer Treatment and Potential Impact of Key Nutrients. Antioxid Redox Signal 2021; 35:293-318. [PMID: 33386063 DOI: 10.1089/ars.2020.8143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Significance: The 5-year survival rate of childhood cancers is now reaching 84%. However, treatments cause numerous acute and long-term side effects. These include cardiometabolic complications, namely hypertension, dyslipidemia, hyperglycemia, insulin resistance, and increased fat mass. Recent Advances: Many antineoplastic treatments can induce oxidative stress (OxS) and trigger an inflammatory response, which may cause acute and chronic side effects. Critical Issues: Clinical studies have reported a state of heightened OxS and inflammation during cancer treatment in children as the result of treatment cytotoxic action on both cancerous and noncancerous cells. Higher levels of OxS and inflammation are associated with treatment side effects and with the development of cardiometabolic complications. Key nutrients (omega-3 polyunsaturated fatty acids, dietary antioxidants, probiotics, and prebiotics) have the potential to modulate inflammatory and oxidative responses and, therefore, could be considered in the search for adverse complication prevention means as long as antineoplastic treatment efficiency is maintained. Future Directions: There is a need to better understand the relationship between cardiometabolic complications, OxS, inflammation and diet during pediatric cancer treatment, which represents the ultimate goal of this review. Antioxid. Redox Signal. 35, 293-318.
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Affiliation(s)
- Véronique Bélanger
- Research Centre, CHU Sainte-Justine University Health Centre, Montreal, Canada.,Department of Nutrition, Université de Montréal, Montreal, Canada.,Institute of Nutrition and Functional Foods, Laval University, Quebec City, Canada
| | - Abderrahim Benmoussa
- Research Centre, CHU Sainte-Justine University Health Centre, Montreal, Canada.,Department of Nutrition, Université de Montréal, Montreal, Canada.,Institute of Nutrition and Functional Foods, Laval University, Quebec City, Canada
| | - Mélanie Napartuk
- Research Centre, CHU Sainte-Justine University Health Centre, Montreal, Canada.,Department of Nutrition, Université de Montréal, Montreal, Canada.,Institute of Nutrition and Functional Foods, Laval University, Quebec City, Canada
| | - Alexandre Warin
- Research Centre, CHU Sainte-Justine University Health Centre, Montreal, Canada
| | | | - Sophie Marcoux
- Department of Public Health & Preventive Medicine, Université de Montréal, Montreal, Canada
| | - Emile Levy
- Research Centre, CHU Sainte-Justine University Health Centre, Montreal, Canada.,Department of Nutrition, Université de Montréal, Montreal, Canada.,Institute of Nutrition and Functional Foods, Laval University, Quebec City, Canada.,Department of Pediatrics, Université de Montréal, Montreal, Canada
| | - Valérie Marcil
- Research Centre, CHU Sainte-Justine University Health Centre, Montreal, Canada.,Department of Nutrition, Université de Montréal, Montreal, Canada.,Institute of Nutrition and Functional Foods, Laval University, Quebec City, Canada
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Dillon SM, Abdo MH, Wilson MP, Liu J, Jankowski CM, Robertson CE, Tuncil Y, Hamaker B, Frank DN, MaWhinney S, Wilson CC, Erlandson KM. A Unique Gut Microbiome-Physical Function Axis Exists in Older People with HIV: An Exploratory Study. AIDS Res Hum Retroviruses 2021; 37:542-550. [PMID: 33787299 PMCID: PMC8260890 DOI: 10.1089/aid.2020.0283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Impairments in physical function and increased systemic levels of inflammation have been observed in middle-aged and older persons with HIV (PWH). We previously demonstrated that in older persons, associations between gut microbiota and inflammation differed by HIV serostatus. To determine whether relationships between the gut microbiome and physical function measurements would also be distinct between older persons with and without HIV, we reanalyzed existing gut microbiome and short chain fatty acid (SCFA) data in conjunction with previously collected measurements of physical function and body composition from the same cohorts of older (51-74 years), nonfrail PWH receiving effective antiretroviral therapy (N = 14) and age-balanced uninfected controls (N = 22). Associations between relative abundance (RA) of the most abundant bacterial taxa or stool SCFA levels with physical function and body composition were tested using HIV-adjusted linear regression models. In older PWH, but not in controls, greater RA of Alistipes, Escherichia, Prevotella, Megasphaera, and Subdoligranulum were associated with reduced lower extremity muscle function, decreased lean mass, or lower Short Physical Performance Battery (SPPB) scores. Conversely, greater RA of Dorea, Coprococcus, and Phascolarctobacterium in older PWH were associated with better muscle function, lean mass, and SPPB scores. Higher levels of the SCFA butyrate associated with increased grip strength in both PWH and controls. Our findings indicate that in older PWH, both negative and positive associations exist between stool microbiota abundance and physical function. Different relationships were observed in older uninfected persons, suggesting features of a unique gut-physical function axis in PWH.
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Affiliation(s)
- Stephanie M. Dillon
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mona H. Abdo
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Melissa P. Wilson
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Jay Liu
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Catherine M. Jankowski
- College of Nursing, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Yunus Tuncil
- Department of Food Science, Purdue University, West Lafayette, Indiana, USA
| | - Bruce Hamaker
- Department of Food Science, Purdue University, West Lafayette, Indiana, USA
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Samantha MaWhinney
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Cara C. Wilson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kristine M. Erlandson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Cao Y, Wang L, Ke S, Gálvez JAV, Pollock NR, Barret C, Sprague R, Daugherty K, Xu H, Lin Q, Yao J, Chen Y, Kelly CP, Liu YY, Chen X. Fecal Mycobiota Combined With Host Immune Factors Distinguish Clostridioides difficile Infection From Asymptomatic Carriage. Gastroenterology 2021; 160:2328-2339.e6. [PMID: 33684427 PMCID: PMC8169571 DOI: 10.1053/j.gastro.2021.02.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/16/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Although the role of gut microbiota in Clostridioides difficile infection (CDI) has been well established, little is known about the role of mycobiota in CDI. Here, we performed mycobiome data analysis in a well-characterized human cohort to evaluate the potential of using gut mycobiota features for CDI diagnosis. METHODS Stool samples were collected from 118 hospital patients, divided into 3 groups: CDI (n = 58), asymptomatic carriers (Carrier, n = 28), and Control (n = 32). The nuclear ribosomal DNA internal transcribed spacer 2 was sequenced using the Illumina HiSeq platform to assess the fungal composition. Downstream statistical analyses (including Alpha diversity analysis, ordination analysis, differential abundance analysis, fungal correlation network analysis, and classification analysis) were then performed. RESULTS Significant differences were observed in alpha and beta diversity between patients with CDI and Carrier (P < .05). Differential abundance analysis identified 2 genera (Cladosporium and Aspergillus) enriched in Carrier. The ratio of Ascomycota to Basidiomycota was dramatically higher in patients with CDI than in Carrier and Control (P < .05). Correlations between host immune factors and mycobiota features were weaker in patients with CDI than in Carrier. Using 4 fungal operational taxonomic units combined with 6 host immune markers in the random forest classifier can achieve very high performance (area under the curve ∼92.38%) in distinguishing patients with CDI from Carrier. CONCLUSIONS Our study provides specific markers of stool fungi combined with host immune factors to distinguish patients with CDI from Carrier. It highlights the importance of gut mycobiome in CDI, which may have been underestimated. Further studies on the diagnostic applications and therapeutic potentials of these findings are warranted.
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Affiliation(s)
- Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Lamei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China,Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Shanlin Ke
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Javier A. Villafuerte Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R. Pollock
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA,Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Caitlin Barret
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Rebecca Sprague
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kaitlyn Daugherty
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hua Xu
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Qianyun Lin
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Ciaran P. Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
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10
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Rotz SJ, Dandoy CE. The microbiome in pediatric oncology. Cancer 2020; 126:3629-3637. [PMID: 32533793 DOI: 10.1002/cncr.33030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/01/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023]
Abstract
The human microbiome comprises a diverse set of microorganisms, which play a mostly cooperative role in processes such as metabolism and host defense. Next-generation genomic sequencing of bacterial nucleic acids now can contribute a much broader understanding of the diverse organisms composing the microbiome. Emerging evidence has suggested several roles of the microbiome in pediatric hematology/oncology, including susceptibility to infectious diseases, immune response to neoplasia, and contributions to the tumor microenvironment as well as changes to the microbiome from chemotherapy and antibiotics with unclear consequences. In this review, the authors have examined the evidence of the role of the microbiome in pediatric hematology/oncology, discussed how the microbiome may be modulated, and suggested key questions in need of further exploration.
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Affiliation(s)
- Seth J Rotz
- Department of Pediatric Hematology, Oncology, and Blood and Marrow Transplantation, Cleveland Clinic Children's Hospital, Cleveland, Ohio
| | - Christopher E Dandoy
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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11
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Jobira B, Frank DN, Pyle L, Silveira LJ, Kelsey MM, Garcia-Reyes Y, Robertson CE, Ir D, Nadeau KJ, Cree-Green M. Obese Adolescents With PCOS Have Altered Biodiversity and Relative Abundance in Gastrointestinal Microbiota. J Clin Endocrinol Metab 2020; 105:5709658. [PMID: 31970418 PMCID: PMC7147870 DOI: 10.1210/clinem/dgz263] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/11/2019] [Indexed: 12/31/2022]
Abstract
CONTEXT Alterations in gut microbiota relate to the metabolic syndrome, but have not been examined in at-risk obese youth with polycystic ovary syndrome (PCOS). OBJECTIVE Compare the composition and diversity of the gut microbiota and associations with metabolic and hormonal measures between 2 groups of female adolescents with equal obesity with or without PCOS. DESIGN Prospective, case-control cross-sectional study. SETTING Tertiary-care center. PARTICIPANTS A total of 58 obese female adolescents (n = 37 with PCOS; 16.1 ± 0.3 years of age; body mass index [BMI] 98.5th percentile) and (n = 21 without PCOS; 14.5 ± 0.4 years of age; BMI 98.7th percentile). OUTCOMES Bacterial diversity, percent relative abundance (%RA), and correlations with hormonal and metabolic measures. RESULTS Participants with PCOS had decreased α-diversity compared with the non-PCOS group (Shannon diversity P = 0.045 and evenness P = 0.0052). β-diversity, reflecting overall microbial composition, differed between groups (P < 0.001). PCOS had higher %RA of phyla Actinobacteria (P = 0.027), lower Bacteroidetes (P = 0.004), and similar Firmicutes and Proteobacteria. PCOS had lower %RA of families Bacteroidaceae (P < 0.001) and Porphyromonadaceae (P = 0.024) and higher Streptococcaceae (P = 0.047). Lower bacterial α-diversity was strongly associated with higher testosterone concentrations. Several individual taxa correlated with testosterone and metabolic measures within PCOS and across the entire cohort. Receiver operative curve analysis showed 6 taxa for which the %RA related to PCOS status and lower Bacteroidaceae conferred a 4.4-fold likelihood ratio for PCOS. CONCLUSION Alterations in the gut microbiota exist in obese adolescents with PCOS versus obese adolescents without PCOS and these changes relate to markers of metabolic disease and testosterone. Further work is needed to determine if microbiota changes are reflective of, or influencing, hormonal metabolism.
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Affiliation(s)
- Beza Jobira
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Daniel N Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Laura Pyle
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado
| | - Lori J Silveira
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado
| | - Megan M Kelsey
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Center for Women’s Health Research; University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Yesenia Garcia-Reyes
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Charles E Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kristen J Nadeau
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Center for Women’s Health Research; University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Melanie Cree-Green
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Center for Women’s Health Research; University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Correspondence: Melanie Cree-Green, MD, PhD, Children’s Hospital Colorado, University of Colorado Anschutz Medical Campus, PO Box 265, 13123 E 16th Ave, Aurora, Colorado 80045.
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12
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De Pietri S, Ingham AC, Frandsen TL, Rathe M, Krych L, Castro-Mejía JL, Nielsen DS, Nersting J, Wehner PS, Schmiegelow K, Hasle H, Pamp SJ, Müller K. Gastrointestinal toxicity during induction treatment for childhood acute lymphoblastic leukemia: The impact of the gut microbiota. Int J Cancer 2020; 147:1953-1962. [PMID: 32115690 DOI: 10.1002/ijc.32942] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/19/2020] [Accepted: 02/04/2020] [Indexed: 12/17/2022]
Abstract
Intestinal mucositis is a common side effect of chemotherapy leading to diarrhea, abdominal pain and increased risk of infections. The intestinal microbiota has been recognized as a key regulator of mucosal immune responses. Therefore, we hypothesized that intestinal microbial changes would be associated with enterocyte loss and systemic inflammation during induction treatment for childhood acute lymphoblastic leukemia (ALL). We prospectively included 51 children newly-diagnosed with ALL treated in Denmark in 2015-2018. Plasma C-reactive protein (CRP), plasma citrulline (marker of functional enterocytes mass) measurements and fecal samplings were performed on treatment Days 1, 8, 15, 22 and 29. Moreover, intestinal mucositis was scored by a trained nurse/physician. Fecal samples in patients and 19 healthy siblings were analyzed by 16S rRNA gene sequencing (V3-V4 region). Bacterial alpha diversity was lower in patients compared to siblings. It decreased from Day 1 to Days 8-22 and increased on Day 29. Shannon alpha diversity index was correlated with CRP on Days 15-29 (rho = -0.33-0.49; p < 0.05) and with citrulline on Days 15 and 29 (although with p values <0.06, rho = 0.32-0.34). The abundance of unclassified Enterococcus species (spp.) was correlated with CRP on Days 22-29 (rho = 0.42-0.49; p < 0.009), while the abundance of unclassified Lachnospiraceae spp. was correlated with citrulline on days 8-15 (rho = 0.48-0.62, p < 0.001). Systemic inflammation, enterocyte loss and relative abundance of unclassified Enterococcus spp. reached a peak around Day 15. In conclusion, specific changes in the microbiota were associated with the severity of enterocyte loss and systemic inflammation during chemotherapy.
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Affiliation(s)
- Silvia De Pietri
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anna C Ingham
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas L Frandsen
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mathias Rathe
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark.,Odense Patient Data Explorative Network (OPEN), Odense University Hospital, Odense, Denmark
| | - Lukasz Krych
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Nersting
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peder S Wehner
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Institute of Clinical Medicine, Faculty of Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Hasle
- Department of Paediatrics, Aarhus University Hospital, Aarhus, Denmark
| | - Sünje J Pamp
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Klaus Müller
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Institute of Clinical Medicine, Faculty of Medicine, University of Copenhagen, Copenhagen, Denmark.,Institute for Inflammation Research, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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13
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Takahashi S, Luo Y, Ranjit S, Xie C, Libby AE, Orlicky DJ, Dvornikov A, Wang XX, Myakala K, Jones BA, Bhasin K, Wang D, McManaman JL, Krausz KW, Gratton E, Ir D, Robertson CE, Frank DN, Gonzalez FJ, Levi M. Bile acid sequestration reverses liver injury and prevents progression of nonalcoholic steatohepatitis in Western diet-fed mice. J Biol Chem 2020; 295:4733-4747. [PMID: 32075905 DOI: 10.1074/jbc.ra119.011913] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease is a rapidly rising problem in the 21st century and is a leading cause of chronic liver disease that can lead to end-stage liver diseases, including cirrhosis and hepatocellular cancer. Despite this rising epidemic, no pharmacological treatment has yet been established to treat this disease. The rapidly increasing prevalence of nonalcoholic fatty liver disease and its aggressive form, nonalcoholic steatohepatitis (NASH), requires novel therapeutic approaches to prevent disease progression. Alterations in microbiome dynamics and dysbiosis play an important role in liver disease and may represent targetable pathways to treat liver disorders. Improving microbiome properties or restoring normal bile acid metabolism may prevent or slow the progression of liver diseases such as NASH. Importantly, aberrant systemic circulation of bile acids can greatly disrupt metabolic homeostasis. Bile acid sequestrants are orally administered polymers that bind bile acids in the intestine, forming nonabsorbable complexes. Bile acid sequestrants interrupt intestinal reabsorption of bile acids, decreasing their circulating levels. We determined that treatment with the bile acid sequestrant sevelamer reversed the liver injury and prevented the progression of NASH, including steatosis, inflammation, and fibrosis in a Western diet-induced NASH mouse model. Metabolomics and microbiome analysis revealed that this beneficial effect is associated with changes in the microbiota population and bile acid composition, including reversing microbiota complexity in cecum by increasing Lactobacillus and decreased Desulfovibrio The net effect of these changes was improvement in liver function and markers of liver injury and the positive effects of reversal of insulin resistance.
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Affiliation(s)
- Shogo Takahashi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057.,National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhuan Luo
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057.,Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California at Irvine, Irvine, California 92697
| | - Cen Xie
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrew E Libby
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
| | - David J Orlicky
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Alexander Dvornikov
- Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California at Irvine, Irvine, California 92697
| | - Xiaoxin X Wang
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
| | - Komuraiah Myakala
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
| | - Bryce A Jones
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057.,Department of Pharmacology and Physiology, Georgetown University, Washington, D.C., 20057
| | - Kanchan Bhasin
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
| | - Dong Wang
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - James L McManaman
- Division of Reproductive Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045.,Graduate Program in Integrated Physiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Kristopher W Krausz
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Enrico Gratton
- Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California at Irvine, Irvine, California 92697
| | - Diana Ir
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Charles E Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045
| | - Frank J Gonzalez
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., 20057
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14
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Kelly CJ, Alexeev EE, Farb L, Vickery TW, Zheng L, Eric L C, Kitzenberg DA, Battista KD, Kominsky DJ, Robertson CE, Frank DN, Stabler SP, Colgan SP. Oral vitamin B 12 supplement is delivered to the distal gut, altering the corrinoid profile and selectively depleting Bacteroides in C57BL/6 mice. Gut Microbes 2019; 10:654-662. [PMID: 31062653 PMCID: PMC6866687 DOI: 10.1080/19490976.2019.1597667] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Vitamin B12 is a critical nutrient for humans as well as microbes. Due to saturable uptake, high dose oral B12 supplements are largely unabsorbed and reach the distal gut where they are available to interact with the microbiota. The aim of this study was to determine if oral B12 supplementation in mice alters 1) the concentration of B12 and related corrinoids in the distal gut, 2) the fecal microbiome, 3) short chain fatty acids (SCFA), and 4) susceptibility to experimental colitis. C57BL/6 mice (up to 24 animals/group) were supplemented with oral 3.94 µg/ml cyanocobalamin (B12), a dose selected to approximate a single 5 mg supplement for a human. Active vitamin B12 (cobalamin), and four B12-analogues ([ADE]CN-Cba, [2Me-ADE]CN-Cba, [2MeS-ADE]CN-Cba, CN-Cbi) were analyzed in cecal and fecal contents using liquid chromatography/mass spectrometry (LC/MS), in parallel with evaluation of fecal microbiota, cecal SCFA, and susceptibility to dextran sodium sulfate (DSS) colitis. At baseline, active B12 was a minor constituent of overall cecal (0.86%) and fecal (0.44%) corrinoid. Oral B12 supplementation increased active B12 at distal sites by >130-fold (cecal B12 increased from 0.08 to 10.60 ng/mg, fecal B12 increased from 0.06 to 7.81 ng/ml) and reduced microbe-derived fecal corrinoid analogues ([ADE]CN-Cba, [2Me-ADE]CN-Cba, [2MeS-ADE]CN-Cba). Oral B12 had no effect on cecal SCFA. Microbial diversity was unaffected by this intervention, however a selective decrease in Bacteroides was observed with B12 treatment. Lastly, no difference in markers of DSS-induced colitis were detected with B12 treatment.
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Affiliation(s)
- Caleb J Kelly
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA,CONTACT Sean P. Colgan Mucosal Inflammation Program, University of Colorado, 12700 East 19th Ave. MS B-146, Aurora, CO 80045, USA
| | - Erica E Alexeev
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Linda Farb
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Thad W Vickery
- Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado Microbiome Research Consortium, Aurora, CO, USA
| | - Leon Zheng
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Campbell Eric L
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA,Centre for Experimental Medicine, Queens University, Belfast, UK
| | - David A Kitzenberg
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Kayla D Battista
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Douglas J Kominsky
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Centre for Experimental Medicine, Queens University, Belfast, UK,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Charles E Robertson
- Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado Microbiome Research Consortium, Aurora, CO, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado Microbiome Research Consortium, Aurora, CO, USA
| | - Sally P Stabler
- Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Sean P Colgan
- Mucosal Inflammation Program, University of Colorado, Aurora, CO, USA,Department of Medicine, University of Colorado, Aurora, CO, USA
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15
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Liu J, Johnson R, Dillon S, Kroehl M, Frank DN, Tuncil YE, Zhang X, Ir D, Robertson CE, Seifert S, Higgins J, Hamaker B, Wilson CC, Erlandson KM. Among older adults, age-related changes in the stool microbiome differ by HIV-1 serostatus. EBioMedicine 2019; 40:583-594. [PMID: 30685386 PMCID: PMC6413415 DOI: 10.1016/j.ebiom.2019.01.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 12/18/2022] Open
Abstract
Background HIV-1 infection and physiological aging are independently linked to elevated systemic inflammation and changes in enteric microbial communities (dysbiosis). However, knowledge of the direct effect of HIV infection on the aging microbiome and potential links to systemic inflammation is lacking. Methods In a cross-sectional study of older people living with HIV (PLWH) (median age 61.5 years, N = 14) and uninfected controls (median 58 years, n = 22) we compared stool microbiota, levels of microbial metabolites (short-chain fatty acid levels, SCFA) and systemic inflammatory biomarkers by HIV serostatus and age. Findings HIV and age were independently associated with distinct changes in the stool microbiome. For example, abundances of Enterobacter and Paraprevotella were higher and Eggerthella and Roseburia lower among PLWH compared to uninfected controls. Age-related microbiome changes also differed by HIV serostatus. Some bacteria with inflammatory potential (e.g. Escherichia) increased with age among PLWH, but not controls. Stool SCFA levels were similar between the two groups yet patterns of associations between individual microbial taxa and SCFA levels differed. Abundance of various genera including Escherichia and Bifidobacterium positively associated with inflammatory biomarkers (e.g. soluble Tumor Necrosis Factor Receptors) among PLWH, but not among controls. Interpretation The age effect on the gut microbiome and associations between microbiota and microbial metabolites or systemic inflammation differed based on HIV serostatus, raising important implications for the impact of therapeutic interventions, dependent on HIV serostatus or age.
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Affiliation(s)
- Jay Liu
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rachel Johnson
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Stephanie Dillon
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Miranda Kroehl
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, USA
| | - Daniel N Frank
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yunus E Tuncil
- Food Engineering Department, Ordu University, Ordu, Turkey; Department of Food Science, Purdue University, Lafayette, IN, USA
| | - Xiaowei Zhang
- Department of Food Science, Purdue University, Lafayette, IN, USA
| | - Diana Ir
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charles E Robertson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sharon Seifert
- Department of Pharmacology, Children's Hospital Colorado, Aurora, CO, USA
| | - Janine Higgins
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bruce Hamaker
- Department of Food Science, Purdue University, Lafayette, IN, USA
| | - Cara C Wilson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Kristine M Erlandson
- Department of Medicine, Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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16
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D'Argenio V. The Prenatal Microbiome: A New Player for Human Health. High Throughput 2018; 7:ht7040038. [PMID: 30544936 PMCID: PMC6306741 DOI: 10.3390/ht7040038] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 02/06/2023] Open
Abstract
The last few years have featured an increasing interest in the study of the human microbiome and its correlations with health status. Indeed, technological advances have allowed the study of microbial communities to reach a previously unthinkable sensitivity, showing the presence of microbes also in environments usually considered as sterile. In this scenario, microbial communities have been described in the amniotic fluid, the umbilical blood cord, and the placenta, denying a dogma of reproductive medicine that considers the uterus like a sterile womb. This prenatal microbiome may play a role not only in fetal development but also in the predisposition to diseases that may develop later in life, and also in adulthood. Thus, the aim of this review is to report the current knowledge regarding the prenatal microbiome composition, its association with pathological processes, and the future perspectives regarding its manipulation for healthy status promotion and maintenance.
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Affiliation(s)
- Valeria D'Argenio
- CEINGE-BiotecnologieAvanzate, via G. Salvatore via G. Salvatore 486, 80145 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via Pansini 5, 80131 Naples, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, via Pansini 5, 80131 Naples, Italy.
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17
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García-Arroyo FE, Gonzaga G, Muñoz-Jiménez I, Blas-Marron MG, Silverio O, Tapia E, Soto V, Ranganathan N, Ranganathan P, Vyas U, Irvin A, Ir D, Robertson CE, Frank DN, Johnson RJ, Sánchez-Lozada LG. Probiotic supplements prevented oxonic acid-induced hyperuricemia and renal damage. PLoS One 2018; 13:e0202901. [PMID: 30142173 PMCID: PMC6108486 DOI: 10.1371/journal.pone.0202901] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/11/2018] [Indexed: 02/07/2023] Open
Abstract
Hyperuricemia is highly prevalent and especially common in subjects with metabolic, cardiovascular and renal diseases. In chronic kidney disease, hyperuricemia is extremely common, and uric acid (UA) excretion relies on gut uricolysis by gut microbiota. Current therapy for lowering serum UA includes drugs that may produce undesired secondary effects. Therefore, this pilot study was designed to evaluate the potential of two probiotic supplements to reduce systemic uric acid concentrations. Secondary objectives were to assess whether the hypouricemic effect related to a therapeutic benefit on the hyperuricemia-induced renal damage and hypertension. Analysis of fecal microbiota was also performed. Groups of 6 rats each were followed for 5 weeks and allocated in the following treatment groups: C = Control; HU-ND = Oxonic acid-induced hyperuricemia (HU) +regular diet; HU-P = HU+placebo; HU-F1 = HU+ probiotics formula 1 and HU-F2 = HU+ probiotics formula 2. We confirmed that oxonic acid-induced hyperuricemia produced hypertension and renal functional and structural changes, along with modest changes in the overall composition of fecal microbiota. Both probiotic-containing diets prevented HU, elevated UA urinary excretion and intrarenal UA accumulation induced by oxonic acid. The hypouricemic effect conferred by probiotic supplementation also prevented the renal changes and hypertension caused by hyperuricemia. However, probiotic treatment did not restore the fecal microbiota. In conclusion, we demonstrated for the first time the ability of probiotics containing uricolytic bacteria to lower serum uric acid in hyperuricemic animals with beneficial consequences on blood pressure and renal disease. As probiotics supplements are innocuous for human health, we recommend clinical studies to test if probiotic supplements could benefit hyperuricemic individuals.
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Affiliation(s)
| | - Guillermo Gonzaga
- Laboratory of Renal Physiopathology, INC Ignacio Chavez, Mexico City, Mexico
| | - Itzel Muñoz-Jiménez
- Laboratory of Renal Physiopathology, INC Ignacio Chavez, Mexico City, Mexico
| | | | - Octaviano Silverio
- Laboratory of Renal Physiopathology, INC Ignacio Chavez, Mexico City, Mexico
| | - Edilia Tapia
- Laboratory of Renal Physiopathology, INC Ignacio Chavez, Mexico City, Mexico
| | - Virgilia Soto
- Dept.of Pathology, INC Ignacio Chavez, Mexico City, Mexico
| | | | | | - Usha Vyas
- Kibow Biotech, Newtown Square, PA, United States of America
| | - Anthony Irvin
- Kibow Biotech, Newtown Square, PA, United States of America
| | - Diana Ir
- Division of Infectious Diseases, University of Colorado, Aurora, CO, United States of America
| | - Charles E. Robertson
- Division of Infectious Diseases, University of Colorado, Aurora, CO, United States of America
| | - Daniel N. Frank
- Division of Infectious Diseases, University of Colorado, Aurora, CO, United States of America
| | - Richard J. Johnson
- Renal Diseases and Hypertension, University of Colorado, Aurora, CO, United States of America
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18
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Nycz BT, Dominguez SR, Friedman D, Hilden JM, Ir D, Robertson CE, Frank DN. Correction: Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients. PLoS One 2018; 13:e0197530. [PMID: 29746574 PMCID: PMC5945044 DOI: 10.1371/journal.pone.0197530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0191232.].
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Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies. Int J Mol Sci 2018; 19:ijms19020383. [PMID: 29382070 PMCID: PMC5855605 DOI: 10.3390/ijms19020383] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/21/2018] [Accepted: 01/24/2018] [Indexed: 12/21/2022] Open
Abstract
The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i.e., shotgun metagenomics and metatranscriptomics, are becoming more widely used. Methods standardization and the development of specific pipelines for data analysis are required to contribute to and increase our understanding of the human microbiome relationship with health and disease status.
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