1
|
Allaband C, Lingaraju A, Flores Ramos S, Kumar T, Javaheri H, Tiu MD, Dantas Machado AC, Richter RA, Elijah E, Haddad GG, Leone VA, Dorrestein PC, Knight R, Zarrinpar A. Time of sample collection is critical for the replicability of microbiome analyses. Nat Metab 2024; 6:1282-1293. [PMID: 38951660 PMCID: PMC11309016 DOI: 10.1038/s42255-024-01064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/08/2024] [Indexed: 07/03/2024]
Abstract
As the microbiome field moves from descriptive and associative research to mechanistic and interventional studies, being able to account for all confounding variables in the experimental design, which includes the maternal effect1, cage effect2, facility differences3, as well as laboratory and sample handling protocols4, is critical for interpretability of results. Despite significant procedural and bioinformatic improvements, unexplained variability and lack of replicability still occur. One underexplored factor is that the microbiome is dynamic and exhibits diurnal oscillations that can change microbiome composition5-7. In this retrospective analysis of 16S amplicon sequencing studies in male mice, we show that sample collection time affects the conclusions drawn from microbiome studies and its effect size is larger than those of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups is unique to each experiment. Sample collection times as short as only 4 hours apart can lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. The impact of diurnal rhythms on the outcomes and study design of other fields is unknown but likely significant.
Collapse
Affiliation(s)
- Celeste Allaband
- Division of Biomedical Sciences, University of California, San Diego, La Jolla, CA, USA
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Amulya Lingaraju
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Stephany Flores Ramos
- Division of Biomedical Sciences, University of California, San Diego, La Jolla, CA, USA
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tanya Kumar
- Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Haniyeh Javaheri
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Maria D Tiu
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | | | - R Alexander Richter
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Emmanuel Elijah
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Gabriel G Haddad
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Hospital, San Diego, CA, USA
| | - Vanessa A Leone
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Division of Gastroenterology, Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, CA, USA.
- Institute of Diabetes and Metabolic Health, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
2
|
Isokääntä H, Pinto da Silva L, Karu N, Kallonen T, Aatsinki AK, Hankemeier T, Schimmel L, Diaz E, Hyötyläinen T, Dorrestein PC, Knight R, Orešič M, Kaddurah-Daouk R, Dickens AM, Lamichhane S. Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization. Anal Chem 2024; 96:8893-8904. [PMID: 38782403 PMCID: PMC11154662 DOI: 10.1021/acs.analchem.3c04436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Metabolites from feces provide important insights into the functionality of the gut microbiome. As immediate freezing is not always feasible in gut microbiome studies, there is a need for sampling protocols that provide the stability of the fecal metabolome and microbiome at room temperature (RT). Here, we investigated the stability of various metabolites and the microbiome (16S rRNA) in feces collected in 95% ethanol (EtOH) and commercially available sample collection kits with specific preservatives OMNImet•GUT/OMNIgene•GUT. To simulate field-collection scenarios, the samples were stored at different temperatures at varying durations (24 h + 4 °C, 24 h RT, 36 h RT, 48 h RT, and 7 days RT) and compared to aliquots immediately frozen at -80 °C. We applied several targeted and untargeted metabolomics platforms to measure lipids, polar metabolites, endocannabinoids, short-chain fatty acids (SCFAs), and bile acids (BAs). We found that SCFAs in the nonstabilized samples increased over time, while a stable profile was recorded in sample aliquots stored in 95% EtOH and OMNImet•GUT. When comparing the metabolite levels between aliquots stored at room temperature and at +4 °C, we detected several changes in microbial metabolites, including multiple BAs and SCFAs. Taken together, we found that storing samples at RT and stabilizing them in 95% EtOH yielded metabolomic results comparable to those from flash freezing. We also found that the overall composition of the microbiome did not vary significantly between different storage types. However, notable differences were observed in the α diversity. Altogether, the stability of the metabolome and microbiome in 95% EtOH provided results similar to those of the validated commercial collection kits OMNImet•GUT and OMNIgene•GUT, respectively.
Collapse
Affiliation(s)
- Heidi Isokääntä
- Research
Center for Infections and Immunity, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Lucas Pinto da Silva
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
| | - Naama Karu
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Teemu Kallonen
- Department
of Clinical Microbiology, Laboratory Division, Turku University Hospital, Kiinamyllynkatu 10 D, 20520 Turku, Finland
- Clinical
Microbiome Bank, Microbe Center, University
Hospital and University of Turku, 20520 Turku, Finland
| | - Anna-Katariina Aatsinki
- Centre
for
Population Health Research, University of
Turku, Kiinamyllynkatu
10A, 20520 Turku, Finland
| | - Thomas Hankemeier
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Leyla Schimmel
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Edgar Diaz
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Tuulia Hyötyläinen
- School
of Science and Technology, Örebro
University, 70281 Örebro, Sweden
| | - Pieter C. Dorrestein
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093-6607, United States
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California,
San Diego, 9500 Gilman, La Jolla, California 92093-0657, United States
| | - Rob Knight
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093-6607, United States
| | - Matej Orešič
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden
| | - Rima Kaddurah-Daouk
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Alex M. Dickens
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
- Department of Chemistry, University of
Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Santosh Lamichhane
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
| |
Collapse
|
3
|
Moura F, Romeiro C, Petriz B, Cavichiolli N, Almeida JA, Castro A, Franco OL. Endurance exercise associated with a fructooligosaccharide diet modulates gut microbiota and increases colon absorptive area. J Gastroenterol Hepatol 2024; 39:1145-1154. [PMID: 38642000 DOI: 10.1111/jgh.16563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND AND AIM Fructooligosaccharide (FOS) supplementation can stimulate beneficial intestinal bacteria growth, but little is known about its influence on training performance. Therefore, this study analyzed FOS and exercise effects on gut microbiota and intestinal morphology of C57Bl/6 mice. METHODS Forty male mice were divided into four groups: standard diet-sedentary (SDS), standard diet-exercised (SDE), FOS supplemented (7.5% FOS)-sedentary (FDS), and FOS supplemented-exercised (FDE), n = 10 each group. Exercise training consisted of 60 min/day, 3 days/week, for 12 weeks. RESULTS SDE and FDE groups had an increase in aerobic performance compared to the pretraining period and SDS and FDS groups (P < 0.01), respectively. Groups with FOS increased colonic crypts size (P < 0.05). The FDE group presented rich microbiota (α-diversity) compared to other groups. The FDE group also acquired a greater microbial abundance (β-diversity) than other groups. The FDE group had a decrease in the Ruminococcaceae (P < 0.002) and an increase in Roseburia (P < 0.003), Enterorhabdus (P < 0.004) and Anaerotruncus (P < 0.006). CONCLUSIONS These findings suggest that aerobic exercise associated with FOS supplementation modulates gut microbiota and can increase colonic crypt size without improving endurance exercise performance.
Collapse
Affiliation(s)
- Filipe Moura
- Postgraduate Program in Physical Education, Catholic University of Brasília, Brasília, Brazil
- Laboratory of Molecular Physiology of Exercise, University Center UDF, Brasília, Brazil
- Center for Proteomic and Biochemical Analysis, Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
| | - Caroline Romeiro
- Postgraduate Program in Physical Education, Catholic University of Brasília, Brasília, Brazil
| | - Bernardo Petriz
- Laboratory of Molecular Physiology of Exercise, University Center UDF, Brasília, Brazil
- Center for Proteomic and Biochemical Analysis, Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
| | - Nathalia Cavichiolli
- S-Inova Biotech, Postgraduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Brazil
| | | | - Alinne Castro
- S-Inova Biotech, Postgraduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Brazil
| | - Octavio L Franco
- Postgraduate Program in Physical Education, Catholic University of Brasília, Brasília, Brazil
- Center for Proteomic and Biochemical Analysis, Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
- S-Inova Biotech, Postgraduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Brazil
| |
Collapse
|
4
|
Ma X, Brinker E, Lea CR, Delmain D, Chamorro ED, Martin DR, Graff EC, Wang X. Evaluation of fecal sample collection methods for feline gut microbiome profiling: fecal loop vs. litter box. Front Microbiol 2024; 15:1337917. [PMID: 38800749 PMCID: PMC11127567 DOI: 10.3389/fmicb.2024.1337917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/12/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Microbial population structures within fecal samples are vital for disease screening, diagnosis, and gut microbiome research. The two primary methods for collecting feline fecal samples are: (1) using a fecal loop, which retrieves a rectal sample using a small, looped instrument, and (2) using the litter box, which collects stool directly from the litter. Each method has its own advantages and disadvantages and is suitable for different research objectives. Methods and results Whole-genome shotgun metagenomic sequencing were performed on the gut microbiomes of fecal samples collected using these two methods from 10 adult cats housed in the same research facility. We evaluated the influence of collection methods on feline microbiome analysis, particularly their impact on DNA extraction, metagenomic sequencing yield, microbial composition, and diversity in subsequent gut microbiome analyses. Interestingly, fecal sample collection using a fecal loop resulted in a lower yield of microbial DNA compared to the litterbox method (p = 0.004). However, there were no significant differences between the two groups in the proportion of host contamination (p = 0.106), virus contamination (p = 0.232), relative taxonomy abundance of top five phyla (Padj > 0.638), or the number of microbial genes covered (p = 0.770). Furthermore, no significant differences were observed in alpha-diversity, beta-diversity, the number of taxa identified at each taxonomic level, and the relative abundance of taxonomic units. Discussion These two sample collection methods do not affect microbial population structures within fecal samples and collecting fecal samples directly from the litterbox within 6 hours after defecation can be considered a reliable approach for microbiome research.
Collapse
Affiliation(s)
- Xiaolei Ma
- School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Emily Brinker
- Department of Comparative Pathobiology, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
| | - Christopher R. Lea
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Diane Delmain
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Erin D. Chamorro
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Douglas R. Martin
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Emily C. Graff
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| |
Collapse
|
5
|
Budden KF, Shukla SD, Bowerman KL, Vaughan A, Gellatly SL, Wood DLA, Lachner N, Idrees S, Rehman SF, Faiz A, Patel VK, Donovan C, Alemao CA, Shen S, Amorim N, Majumder R, Vanka KS, Mason J, Haw TJ, Tillet B, Fricker M, Keely S, Hansbro N, Belz GT, Horvat J, Ashhurst T, van Vreden C, McGuire H, Fazekas de St Groth B, King NJC, Crossett B, Cordwell SJ, Bonaguro L, Schultze JL, Hamilton-Williams EE, Mann E, Forster SC, Cooper MA, Segal LN, Chotirmall SH, Collins P, Bowman R, Fong KM, Yang IA, Wark PAB, Dennis PG, Hugenholtz P, Hansbro PM. Faecal microbial transfer and complex carbohydrates mediate protection against COPD. Gut 2024; 73:751-769. [PMID: 38331563 DOI: 10.1136/gutjnl-2023-330521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024]
Abstract
OBJECTIVE Chronic obstructive pulmonary disease (COPD) is a major cause of global illness and death, most commonly caused by cigarette smoke. The mechanisms of pathogenesis remain poorly understood, limiting the development of effective therapies. The gastrointestinal microbiome has been implicated in chronic lung diseases via the gut-lung axis, but its role is unclear. DESIGN Using an in vivo mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT), we characterised the faecal microbiota using metagenomics, proteomics and metabolomics. Findings were correlated with airway and systemic inflammation, lung and gut histopathology and lung function. Complex carbohydrates were assessed in mice using a high resistant starch diet, and in 16 patients with COPD using a randomised, double-blind, placebo-controlled pilot study of inulin supplementation. RESULTS FMT alleviated hallmark features of COPD (inflammation, alveolar destruction, impaired lung function), gastrointestinal pathology and systemic immune changes. Protective effects were additive to smoking cessation, and transfer of CS-associated microbiota after antibiotic-induced microbiome depletion was sufficient to increase lung inflammation while suppressing colonic immunity in the absence of CS exposure. Disease features correlated with the relative abundance of Muribaculaceae, Desulfovibrionaceae and Lachnospiraceae family members. Proteomics and metabolomics identified downregulation of glucose and starch metabolism in CS-associated microbiota, and supplementation of mice or human patients with complex carbohydrates improved disease outcomes. CONCLUSION The gut microbiome contributes to COPD pathogenesis and can be targeted therapeutically.
Collapse
Affiliation(s)
- Kurtis F Budden
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Shakti D Shukla
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Kate L Bowerman
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Annalicia Vaughan
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, QLD, Australia
| | - Shaan L Gellatly
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - David L A Wood
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Nancy Lachner
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Saima Firdous Rehman
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Vyoma K Patel
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Chantal Donovan
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Charlotte A Alemao
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Sj Shen
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Nadia Amorim
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Rajib Majumder
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Kanth S Vanka
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Jazz Mason
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Tatt Jhong Haw
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Bree Tillet
- Frazer Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Michael Fricker
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Simon Keely
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Nicole Hansbro
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Gabrielle T Belz
- Frazer Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Jay Horvat
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Thomas Ashhurst
- Sydney Cytometry, Charles Perkins Centre, Centenary Institute and The University of Sydney, Sydney, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
| | - Caryn van Vreden
- Sydney Cytometry, Charles Perkins Centre, Centenary Institute and The University of Sydney, Sydney, NSW, Australia
- Ramaciotti Facility for Human Systems Biology, Charles Perkins Centre and The University of Sydney, Sydney, NSW, Australia
| | - Helen McGuire
- Ramaciotti Facility for Human Systems Biology, Charles Perkins Centre and The University of Sydney, Sydney, NSW, Australia
| | - Barbara Fazekas de St Groth
- Ramaciotti Facility for Human Systems Biology, Charles Perkins Centre and The University of Sydney, Sydney, NSW, Australia
| | - Nicholas J C King
- Sydney Cytometry, Charles Perkins Centre, Centenary Institute and The University of Sydney, Sydney, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Ramaciotti Facility for Human Systems Biology, Charles Perkins Centre and The University of Sydney, Sydney, NSW, Australia
- Discipline of Pathology, Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Ben Crossett
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW, Australia
| | - Stuart J Cordwell
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW, Australia
- School of Life and Environmental Sciences, Charles Perkins Centre and The University of Sydney, Sydney, NSW, Australia
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | | | - Elizabeth Mann
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases and Department of Molecular and Translational Science, Hudson Institute of Medical Research and Monash University, Melbourne, VIC, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Leopoldo N Segal
- Division of Pulmonary and Critical Care Medicine, Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Translational Respiratory Research Laboratory, Singapore
| | - Peter Collins
- Mater Research Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Department of Dietetics & Food Services, Mater Hospital, Brisbane, QLD, Australia
| | - Rayleen Bowman
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, QLD, Australia
| | - Kwun M Fong
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, QLD, Australia
| | - Ian A Yang
- UQ Thoracic Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, QLD, Australia
| | - Peter A B Wark
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs and Immune Health Research Program, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| |
Collapse
|
6
|
Chakraborty N. Metabolites: a converging node of host and microbe to explain meta-organism. Front Microbiol 2024; 15:1337368. [PMID: 38505556 PMCID: PMC10949987 DOI: 10.3389/fmicb.2024.1337368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024] Open
Abstract
Meta-organisms encompassing the host and resident microbiota play a significant role in combatting diseases and responding to stress. Hence, there is growing traction to build a knowledge base about this ecosystem, particularly to characterize the bidirectional relationship between the host and microbiota. In this context, metabolomics has emerged as the major converging node of this entire ecosystem. Systematic comprehension of this resourceful omics component can elucidate the organism-specific response trajectory and the communication grid across the ecosystem embodying meta-organisms. Translating this knowledge into designing nutraceuticals and next-generation therapy are ongoing. Its major hindrance is a significant knowledge gap about the underlying mechanisms maintaining a delicate balance within this ecosystem. To bridge this knowledge gap, a holistic picture of the available information has been presented with a primary focus on the microbiota-metabolite relationship dynamics. The central theme of this article is the gut-brain axis and the participating microbial metabolites that impact cerebral functions.
Collapse
Affiliation(s)
- Nabarun Chakraborty
- Medical Readiness Systems Biology, CMPN, WRAIR, Silver Spring, MD, United States
| |
Collapse
|
7
|
Iribarren C, Savolainen O, Sapnara M, Törnblom H, Simrén M, Magnusson MK, Öhman L. Temporal stability of fecal metabolomic profiles in irritable bowel syndrome. Neurogastroenterol Motil 2024; 36:e14741. [PMID: 38243381 DOI: 10.1111/nmo.14741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 11/15/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND The potential of the fecal metabolome to serve as a biomarker for irritable bowel syndrome (IBS) depends on its stability over time. Therefore, this study aimed to determine the temporal dynamics of the fecal metabolome, and the potential relationship with stool consistency, in patients with IBS and healthy subjects. METHODS Fecal samples were collected in two cohorts comprising patients with IBS and healthy subjects. For Cohort A, fecal samples collected during 5 consecutive days were analyzed by gas chromatography-tandem mass spectrometry (GC-MS/MS). For Cohort B, liquid chromatography-MS (LC-MS) was used to analyze fecal samples collected at week 0 (healthy and IBS) and at week 4 (patients only). Stool consistency was determined by the Bristol Stool Form scale. KEY RESULTS Fecal samples were collected from Cohort A (seven healthy subjects and eight IBS patients), and Cohort B (seven healthy subjects and 11 IBS patients). The fecal metabolome of IBS patients was stable short-term (Cohort A, 5 days and within the same day) and long-term (Cohort B, 4 weeks). A similar trend was observed over 5 days in the healthy subjects of Cohort A. The metabolome dissimilarity was larger between than within participants over time in both healthy subjects and IBS patients. Further analyses showed that patients had greater range of stool forms (types) than healthy subjects, with no apparent influence on metabolomic dynamics. CONCLUSION & INFERENCES The fecal metabolome is stable over time within IBS patients as well as healthy subjects. This supports the concept of a stable fecal metabolome in IBS despite fluctuations in stool consistency, and the use of single timepoint sampling to further explore how the fecal metabolome is related to IBS pathogenesis.
Collapse
Affiliation(s)
- Cristina Iribarren
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Maria Sapnara
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Maria K Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
8
|
Pernigoni N, Guo C, Gallagher L, Yuan W, Colucci M, Troiani M, Liu L, Maraccani L, Guccini I, Migliorini D, de Bono J, Alimonti A. The potential role of the microbiota in prostate cancer pathogenesis and treatment. Nat Rev Urol 2023; 20:706-718. [PMID: 37491512 DOI: 10.1038/s41585-023-00795-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
The human body hosts a complex and dynamic population of trillions of microorganisms - the microbiota - which influences the body in homeostasis and disease, including cancer. Several epidemiological studies have associated specific urinary and gut microbial species with increased risk of prostate cancer; however, causal mechanistic data remain elusive. Studies have associated bacterial generation of genotoxins with the occurrence of TMPRSS2-ERG gene fusions, a common, early oncogenic event during prostate carcinogenesis. A subsequent study demonstrated the role of the gut microbiota in prostate cancer endocrine resistance, which occurs, at least partially, through the generation of androgenic steroids fuelling oncogenic signalling via the androgen receptor. These studies present mechanistic evidence of how the host microbiota might be implicated in prostate carcinogenesis and tumour progression. Importantly, these findings also reveal potential avenues for the detection and treatment of prostate cancer through the profiling and modulation of the host microbiota. The latter could involve approaches such as the use of faecal microbiota transplantation, prebiotics, probiotics, postbiotics or antibiotics, which can be used independently or combined with existing treatments to reverse therapeutic resistance and improve clinical outcomes in patients with prostate cancer.
Collapse
Affiliation(s)
- Nicolò Pernigoni
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Christina Guo
- Institute of Cancer Research, London, UK
- Royal Marsden Hospital, London, UK
| | | | - Wei Yuan
- Institute of Cancer Research, London, UK
| | - Manuel Colucci
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Martina Troiani
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Lei Liu
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Luisa Maraccani
- Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine, Padova, Italy
| | - Ilaria Guccini
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Denis Migliorini
- Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland
- Swiss Cancer Center Léman, Lausanne and Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
| | - Johann de Bono
- Institute of Cancer Research, London, UK
- Royal Marsden Hospital, London, UK
| | - Andrea Alimonti
- Institute of Oncology Research, Bellinzona, Switzerland.
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.
- Veneto Institute of Molecular Medicine, Padova, Italy.
- Oncology Institute of Southern Switzerland, EOC, Bellinzona, Switzerland.
- Department of Medicine, University of Padova, Padova, Italy.
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
9
|
Grosicki GJ, Langan SP, Bagley JR, Galpin AJ, Garner D, Hampton‐Marcell JT, Allen JM, Robinson AT. Gut check: Unveiling the influence of acute exercise on the gut microbiota. Exp Physiol 2023; 108:1466-1480. [PMID: 37702557 PMCID: PMC10988526 DOI: 10.1113/ep091446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/04/2023] [Indexed: 09/14/2023]
Abstract
The human gastrointestinal microbiota and its unique metabolites regulate a diverse array of physiological processes with substantial implications for human health and performance. Chronic exercise training positively modulates the gut microbiota and its metabolic output. The benefits of chronic exercise for the gut microbiota may be influenced by acute changes in microbial community structure and function that follow a single exercise bout (i.e., acute exercise). Thus, an improved understanding of changes in the gut microbiota that occur with acute exercise could aid in the development of evidence-based exercise training strategies to target the gut microbiota more effectively. In this review, we provide a comprehensive summary of the existing literature on the acute and very short-term (<3 weeks) exercise responses of the gut microbiota and faecal metabolites in humans. We conclude by highlighting gaps in the literature and providing recommendations for future research in this area. NEW FINDINGS: What is the topic of this review? The chronic benefits of exercise for the gut microbiota are likely influenced by acute changes in microbial community structure and function that follow a single exercise bout. This review provides a summary of the existing literature on acute exercise responses of the gut microbiota and its metabolic output in humans. What advances does it highlight? Acute aerobic exercise appears to have limited effects on diversity of the gut microbiota, variable effects on specific microbial taxa, and numerous effects on the metabolic activity of gut microbes with possible implications for host health and performance.
Collapse
Affiliation(s)
| | - Sean P. Langan
- Korey Stringer Institute, Department of KinesiologyUniversity of ConnecticutStorrsCTUSA
| | - James R. Bagley
- Muscle Physiology LaboratorySan Francisco State UniversitySan FranciscoCAUSA
| | - Andrew J. Galpin
- Center for Sport PerformanceCalifornia State University, FullertonFullertonCAUSA
| | - Dan Garner
- BioMolecular Athlete, LLCWilmingtonDEUSA
| | | | - Jacob M. Allen
- Department of Kinesiology and Community HealthUniversity of Illinois at Urbana‐ChampaignUrbanaIL
| | - Austin T. Robinson
- Neurovascular Physiology Laboratory, School of KinesiologyAuburn UniversityAuburnALUSA
| |
Collapse
|
10
|
Ahmed RO, Ali A, Leeds T, Salem M. Fecal Microbiome Analysis Distinguishes Bacterial Taxa Biomarkers Associated with Red Fillet Color in Rainbow Trout. Microorganisms 2023; 11:2704. [PMID: 38004716 PMCID: PMC10673235 DOI: 10.3390/microorganisms11112704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
The characteristic reddish-pink fillet color of rainbow trout is an important marketing trait. The gastrointestinal microbiome is vital for host health, immunity, and nutrient balance. Host genetics play a crucial role in determining the gut microbiome, and the host-microbiome interaction impacts the host's phenotypic expression. We hypothesized that fecal microbiota could be used to predict fillet color in rainbow trout. Fish were fed Astaxanthin-supplemented feed for six months, after which 16s rDNA sequencing was used to investigate the fecal microbiome composition in rainbow trout families with reddish-pink fillet coloration (red fillet group, average saturation index = 26.50 ± 2.86) compared to families with pale white fillet color (white fillet group, average saturation index = 21.21 ± 3.53). The linear discriminant analysis effect size (LEFse) tool was used to identify bacterial biomarkers associated with fillet color. The alpha diversity measure shows no difference in the red and white fillet groups. Beta diversity principal component analysis showed clustering of the samples along the white versus red fillet group. The red fillet group has enrichment (LDA score > 1.5) of taxa Leuconostoc lactis, Corynebacterium variabile, Jeotgalicoccus halotolerans, and Leucobacter chromiireducens. In contrast, the white fillet group has an enriched presence of mycoplasma, Lachnoclostridium, and Oceanobacillus indicireducens. The enriched bacterial taxa in the red fillet group have probiotic functions and can generate carotenoid pigments. Bacteria taxa enriched in the white fillet group are either commensal, parasitic, or capable of reducing indigo dye. The study identified specific bacterial biomarkers differentially abundant in fish families of divergent fillet color that could be used in genetic selection to improve feed carotenoid retention and reddish-pink fillet color. This work extends our understanding of carotenoid metabolism in rainbow trout through the interaction between gut microbiota and fillet color.
Collapse
Affiliation(s)
- Ridwan O. Ahmed
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| | - Ali Ali
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| | - Tim Leeds
- United States Department of Agriculture Kearneysville, National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, Kearneysville, WV 25430, USA;
| | - Mohamed Salem
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (R.O.A.); (A.A.)
| |
Collapse
|
11
|
Muralitharan RR, Snelson M, Meric G, Coughlan MT, Marques FZ. Guidelines for microbiome studies in renal physiology. Am J Physiol Renal Physiol 2023; 325:F345-F362. [PMID: 37440367 DOI: 10.1152/ajprenal.00072.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023] Open
Abstract
Gut microbiome research has increased dramatically in the last decade, including in renal health and disease. The field is moving from experiments showing mere association to causation using both forward and reverse microbiome approaches, leveraging tools such as germ-free animals, treatment with antibiotics, and fecal microbiota transplantations. However, we are still seeing a gap between discovery and translation that needs to be addressed, so that patients can benefit from microbiome-based therapies. In this guideline paper, we discuss the key considerations that affect the gut microbiome of animals and clinical studies assessing renal function, many of which are often overlooked, resulting in false-positive results. For animal studies, these include suppliers, acclimatization, baseline microbiota and its normalization, littermates and cohort/cage effects, diet, sex differences, age, circadian differences, antibiotics and sweeteners, and models used. Clinical studies have some unique considerations, which include sampling, gut transit time, dietary records, medication, and renal phenotypes. We provide best-practice guidance on sampling, storage, DNA extraction, and methods for microbial DNA sequencing (both 16S rRNA and shotgun metagenome). Finally, we discuss follow-up analyses, including tools available, metrics, and their interpretation, and the key challenges ahead in the microbiome field. By standardizing study designs, methods, and reporting, we will accelerate the findings from discovery to translation and result in new microbiome-based therapies that may improve renal health.
Collapse
Affiliation(s)
- Rikeish R Muralitharan
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Melbourne, Victoria, Australia
- Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Matthew Snelson
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Guillaume Meric
- Cambridge-Baker Systems Genomics Initiative, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Cardiovascular Research Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Melinda T Coughlan
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
| | - Francine Z Marques
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Melbourne, Victoria, Australia
- Heart Failure Research Group, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Victorian Heart Institute, Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
12
|
So D, Yao CK, Gill PA, Thwaites PA, Ardalan ZS, McSweeney CS, Denman SE, Chrimes AF, Muir JG, Berean KJ, Kalantar‐Zadeh K, Gibson PR. Detection of changes in regional colonic fermentation in response to supplementing a low FODMAP diet with dietary fibres by hydrogen concentrations, but not by luminal pH. Aliment Pharmacol Ther 2023; 58:417-428. [PMID: 37386938 PMCID: PMC10946934 DOI: 10.1111/apt.17629] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/04/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND Carbohydrate fermentation plays a pivotal role in maintaining colonic health with excessive proximal and deficient distal fermentation being detrimental. AIMS To utilise telemetric gas- and pH-sensing capsule technologies for defining patterns of regional fermentation following dietary manipulations, alongside conventional techniques of measuring fermentation. METHODS In a double-blind crossover trial, 20 patients with irritable bowel syndrome were fed low FODMAP diets that included no extra fibre (total fibre content 24 g/day), or additional poorly fermented fibre, alone (33 g/day) or with fermentable fibre (45 g/day) for 2 weeks. Plasma and faecal biochemistry, luminal profiles defined by tandem gas- and pH-sensing capsules, and faecal microbiota were assessed. RESULTS Plasma short-chain fatty acid (SCFA) concentrations (μmol/L) were median (IQR) 121 (100-222) with fibre combination compared with 66 (44-120) with poorly fermented fibre alone (p = 0.028) and 74 (55-125) control (p = 0.069), but no differences in faecal content were observed. Luminal hydrogen concentrations (%), but not pH, were higher in distal colon (mean 4.9 [95% CI: 2.2-7.5]) with fibre combination compared with 1.8 (0.8-2.8) with poorly fermented fibre alone (p = 0.003) and 1.9 (0.7-3.1) control (p = 0.003). Relative abundances of saccharolytic fermentative bacteria were generally higher in association with supplementation with the fibre combination. CONCLUSIONS A modest increase in fermentable plus poorly fermented fibres had minor effects on faecal measures of fermentation, despite increases in plasma SCFA and abundance of fermentative bacteria, but the gas-sensing capsule, not pH-sensing capsule, detected the anticipated propagation of fermentation distally in the colon. The gas-sensing capsule technology provides unique insights into localisation of colonic fermentation. TRIAL REGISTRATION ACTRN12619000691145.
Collapse
Affiliation(s)
- Daniel So
- Department of GastroenterologyCentral Clinical School, Monash University and Alfred HealthMelbourneAustralia
| | - Chu K. Yao
- Department of GastroenterologyCentral Clinical School, Monash University and Alfred HealthMelbourneAustralia
| | - Paul A. Gill
- Department of GastroenterologyCentral Clinical School, Monash University and Alfred HealthMelbourneAustralia
| | - Phoebe A. Thwaites
- Department of GastroenterologyCentral Clinical School, Monash University and Alfred HealthMelbourneAustralia
| | - Zaid S. Ardalan
- Department of GastroenterologyCentral Clinical School, Monash University and Alfred HealthMelbourneAustralia
| | - Chris S. McSweeney
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationSt. LuciaAustralia
| | - Stuart E. Denman
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationSt. LuciaAustralia
| | - Adam F. Chrimes
- Atmo BiosciencesMelbourneAustralia
- School of Engineering, RMIT UniversityMelbourneAustralia
| | - Jane G. Muir
- Department of GastroenterologyCentral Clinical School, Monash University and Alfred HealthMelbourneAustralia
| | - Kyle J. Berean
- Atmo BiosciencesMelbourneAustralia
- School of Engineering, RMIT UniversityMelbourneAustralia
| | - Kourosh Kalantar‐Zadeh
- School of Chemical Engineering, University of New South WalesSydneyAustralia
- Faculty of EngineeringSchool of Chemical and Biomolecular Engineering, The University of SydneySydneyAustralia
| | - Peter R. Gibson
- Department of GastroenterologyCentral Clinical School, Monash University and Alfred HealthMelbourneAustralia
| |
Collapse
|
13
|
Balderramo DC, Romagnoli PA, Granlund AVB, Catalan-Serra I. Fecal Fungal Microbiota (Mycobiome) Study as a Potential Tool for Precision Medicine in Inflammatory Bowel Disease. Gut Liver 2023; 17:505-515. [PMID: 37305948 PMCID: PMC10352062 DOI: 10.5009/gnl220537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/15/2023] [Indexed: 06/13/2023] Open
Abstract
There is growing evidence of the role of fungal microbiota in the pathogenesis of inflammatory bowel disease (IBD). Fungi can exert direct pro-inflammatory effects or modify the bacterial composition via interkingdom interactions. Although several studies have demonstrated alterations in the fecal fungal microbiota composition in IBD, there is a wide variation in the mycobiome in different populations, with no definite pattern that can define the mycobiome in IBD having yet been identified. Recent work has suggested that characterizing the fecal fungal composition may influence therapeutic decisions and help to predict outcomes in a subset of IBD patients. In this study, we review the current literature on the emerging role of the fecal mycobiome as a potential tool for precision medicine in IBD.
Collapse
Affiliation(s)
- Domingo C. Balderramo
- Department of Gastroenterology, Private Hospital Medical Center of Cordoba S.A., Cordoba, Argentina
| | - Pablo Alberto Romagnoli
- Universitarian Institute for Biomedical Sciences of Cordoba (IUCBC), Translational Medicine Research Center "Severo R. Amuchastegui" (CIMETSA). G.V. Medical Research Institute "Mercedes and Martin Ferreyra" (INIMEC-CONICET-UNC), Cordoba, Argentina
| | - Atle van Beelen Granlund
- Department of Gastroenterology and Hepatology, Clinic of Medicine, St. Olav’s University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine (IKOM), NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Ignacio Catalan-Serra
- Department of Clinical and Molecular Medicine (IKOM), NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Centre of Molecular Inflammation Research, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
- Department of Medicine, Gastroenterology, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| |
Collapse
|
14
|
Nordin E, Hellström PM, Dicksved J, Pelve E, Landberg R, Brunius C. Effects of FODMAPs and Gluten on Gut Microbiota and Their Association with the Metabolome in Irritable Bowel Syndrome: A Double-Blind, Randomized, Cross-Over Intervention Study. Nutrients 2023; 15:3045. [PMID: 37447371 DOI: 10.3390/nu15133045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND A mechanistic understanding of the effects of dietary treatment in irritable bowel syndrome (IBS) is lacking. Our aim was therefore to investigate how fermentable oligo- di-, monosaccharides, and polyols (FODMAPs) and gluten affected gut microbiota and circulating metabolite profiles, as well as to investigate potential links between gut microbiota, metabolites, and IBS symptoms. METHODS We used data from a double-blind, randomized, crossover study with week-long provocations of FODMAPs, gluten, and placebo in participants with IBS. To study the effects of the provocations on fecal microbiota, fecal and plasma short-chain fatty acids, the untargeted plasma metabolome, and IBS symptoms, we used Random Forest, linear mixed model and Spearman correlation analysis. RESULTS FODMAPs increased fecal saccharolytic bacteria, plasma phenolic-derived metabolites, 3-indolepropionate, and decreased isobutyrate and bile acids. Gluten decreased fecal isovalerate and altered carnitine derivatives, CoA, and fatty acids in plasma. For FODMAPs, modest correlations were observed between microbiota and phenolic-derived metabolites and 3-indolepropionate, previously associated with improved metabolic health, and reduced inflammation. Correlations between molecular data and IBS symptoms were weak. CONCLUSIONS FODMAPs, but not gluten, altered microbiota composition and correlated with phenolic-derived metabolites and 3-indolepropionate, with only weak associations with IBS symptoms. Thus, the minor effect of FODMAPs on IBS symptoms must be weighed against the effect on microbiota and metabolites related to positive health factors.
Collapse
Affiliation(s)
- Elise Nordin
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Per M Hellström
- Department of Medical Sciences, Gastroenterology/Hepatology, Uppsala University, SE-75185 Uppsala, Sweden
| | - Johan Dicksved
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Erik Pelve
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Rikard Landberg
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Carl Brunius
- Department of Life Sciences, Food and Nutrition Science, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| |
Collapse
|
15
|
Zhang Y, Liu L, Wei C, Wang X, Li R, Xu X, Zhang Y, Geng G, Dang K, Ming Z, Tao X, Xu H, Yan X, Zhang J, Hu J, Li Y. Vitamin K2 supplementation improves impaired glycemic homeostasis and insulin sensitivity for type 2 diabetes through gut microbiome and fecal metabolites. BMC Med 2023; 21:174. [PMID: 37147641 PMCID: PMC10163743 DOI: 10.1186/s12916-023-02880-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/25/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND There is insufficient evidence for the ability of vitamin K2 to improve type 2 diabetes mellitus symptoms by regulating gut microbial composition. Herein, we aimed to demonstrate the key role of the gut microbiota in the improvement of impaired glycemic homeostasis and insulin sensitivity by vitamin K2 intervention. METHODS We first performed a 6-month RCT on 60 T2DM participants with or without MK-7 (a natural form of vitamin K2) intervention. In addition, we conducted a transplantation of the MK-7-regulated microbiota in diet-induced obesity mice for 4 weeks. 16S rRNA sequencing, fecal metabolomics, and transcriptomics in both study phases were used to clarify the potential mechanism. RESULTS After MK-7 intervention, we observed notable 13.4%, 28.3%, and 7.4% reductions in fasting serum glucose (P = 0.048), insulin (P = 0.005), and HbA1c levels (P = 0.019) in type 2 diabetes participants and significant glucose tolerance improvement in diet-induced obesity mice (P = 0.005). Moreover, increased concentrations of secondary bile acids (lithocholic and taurodeoxycholic acid) and short-chain fatty acids (acetic acid, butyric acid, and valeric acid) were found in human and mouse feces accompanied by an increased abundance of the genera that are responsible for the biosynthesis of these metabolites. Finally, we found that 4 weeks of fecal microbiota transplantation significantly improved glucose tolerance in diet-induced obesity mice by activating colon bile acid receptors, improving host immune-inflammatory responses, and increasing circulating GLP-1 concentrations. CONCLUSIONS Our gut-derived findings provide evidence for a regulatory role of vitamin K2 on glycemic homeostasis, which may further facilitate the clinical implementation of vitamin K2 intervention for diabetes management. TRIAL REGISTRATION The study was registered at https://www.chictr.org.cn (ChiCTR1800019663).
Collapse
Affiliation(s)
- Yuntao Zhang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Lin Liu
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Chunbo Wei
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Xuanyang Wang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Ran Li
- Department of Nutrition, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoqing Xu
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Yingfeng Zhang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Guannan Geng
- Department of Endocrinology, the First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Keke Dang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Zhu Ming
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Xinmiao Tao
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Huan Xu
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Xuemin Yan
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Jia Zhang
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Jinxia Hu
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China
| | - Ying Li
- Department of Nutrition and Food Hygiene, the National Key Discipline, School of Public Health, Harbin Medical University, Harbin, China.
| |
Collapse
|
16
|
Liu W, Lee LP. Toward Rapid and Accurate Molecular Diagnostics at Home. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206525. [PMID: 36416278 DOI: 10.1002/adma.202206525] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/14/2022] [Indexed: 05/26/2023]
Abstract
The global outbreaks of infectious diseases have significantly driven an imperative demand for rapid and accurate molecular diagnostics. Nucleic acid amplification tests (NAATs) feature high sensitivity and high specificity; however, the labor-intensive sample preparation and nucleic acid amplification steps remain challenging in order to carry out rapid and precision molecular diagnostics at home. This review discusses the advances and challenges of automatic solutions of sample preparation integrated with on-chip nucleic acid amplification for effective and accurate molecular diagnostics at home. The sample preparation methods of whole blood, urine, saliva/nasal swab, and stool on chip are examined. Then, the repurposable integrated sample preparation on a chip using various biological samples is investigated. Finally, the on-chip NAATs that can be integrated with automated sample preparation are evaluated. The user-friendly approaches with combined sample preparation and NAATs can be the game changers for next-generation rapid and precision home diagnostics.
Collapse
Affiliation(s)
- Wenpeng Liu
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| |
Collapse
|
17
|
Kool J, Tymchenko L, Shetty SA, Fuentes S. Reducing bias in microbiome research: Comparing methods from sample collection to sequencing. Front Microbiol 2023; 14:1094800. [PMID: 37065158 PMCID: PMC10101209 DOI: 10.3389/fmicb.2023.1094800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/22/2023] [Indexed: 04/01/2023] Open
Abstract
BackgroundMicrobiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results. To investigate and identify potential biases introduced by technical variations, we compared several approaches throughout the entire workflow of a microbiome study, from sample collection to sequencing, using commercially available mock communities (from bacterial strains as well as from DNA) and multiple human fecal samples, including a large set of positive controls created as a random mix of several participant samples.MethodsHuman fecal material was sampled, and aliquots were used to test two commercially available stabilization solutions (OMNIgene·GUT and Zymo Research) in comparison to samples frozen immediately upon collection. In addition, the methodology for DNA extraction, input of DNA, or the number of PCR cycles were analyzed. Furthermore, to investigate the potential batch effects in DNA extraction, sequencing, and barcoding, we included 139 positive controls.ResultsSamples preserved in both the stabilization buffers limited the overgrowth of Enterobacteriaceae when compared to unpreserved samples stored at room temperature (RT). These stabilized samples stored at RT were different from immediately frozen samples, where the relative abundance of Bacteroidota was higher and Actinobacteriota and Firmicutes were lower. As reported previously, the method used for cell disruption was a major contributor to variation in microbiota composition. In addition, a high number of cycles during PCR lead to an increase in contaminants detected in the negative controls. The DNA extraction had a significant impact on the microbial composition, also observed with the use of different Illumina barcodes during library preparation and sequencing, while no batch effect was observed in replicate runs.ConclusionOur study reaffirms the importance of the mechanical cell disruption method and immediate frozen storage as critical aspects in fecal microbiota studies. A comparison of storage conditions revealed that the bias was limited in RT samples preserved in stabilization systems, and these may be a suitable compromise when logistics are challenging due to the size or location of a study. Moreover, to reduce the effect of contaminants in fecal microbiota profiling studies, we suggest the use of ~125 pg input DNA and 25 PCR cycles as optimal parameters during library preparation.
Collapse
Affiliation(s)
- Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Liza Tymchenko
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sudarshan A. Shetty
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Groningen, Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- *Correspondence: Susana Fuentes
| |
Collapse
|
18
|
Rahman T, Sarwar PF, Potter C, Comstock SS, Klepac-Ceraj V. Role of human milk oligosaccharide metabolizing bacteria in the development of atopic dermatitis/eczema. Front Pediatr 2023; 11:1090048. [PMID: 37020647 PMCID: PMC10069630 DOI: 10.3389/fped.2023.1090048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/23/2023] [Indexed: 04/07/2023] Open
Abstract
Despite affecting up to 20% of infants in the United States, there is no cure for atopic dermatitis (AD), also known as eczema. Atopy usually manifests during the first six months of an infant's life and is one predictor of later allergic health problems. A diet of human milk may offer protection against developing atopic dermatitis. One milk component, human milk oligosaccharides (HMOs), plays an important role as a prebiotic in establishing the infant gut microbiome and has immunomodulatory effects on the infant immune system. The purpose of this review is to summarize the available information about bacterial members of the intestinal microbiota capable of metabolizing HMOs, the bacterial genes or metabolic products present in the intestinal tract during early life, and the relationship of these genes and metabolic products to the development of AD/eczema in infants. We find that specific HMO metabolism gene sets and the metabolites produced by HMO metabolizing bacteria may enable the protective role of human milk against the development of atopy because of interactions with the immune system. We also identify areas for additional research to further elucidate the relationship between the human milk metabolizing bacteria and atopy. Detailed metagenomic studies of the infant gut microbiota and its associated metabolomes are essential for characterizing the potential impact of human milk-feeding on the development of atopic dermatitis.
Collapse
Affiliation(s)
- Trisha Rahman
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Prioty F. Sarwar
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Cassie Potter
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| | - Sarah S. Comstock
- Department of Food Science & Human Nutrition, Michigan State University, East Lansing, MI, United States
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, MA, United States
| |
Collapse
|
19
|
Neveu V, Nicolas G, Amara A, Salek RM, Scalbert A. The human microbial exposome: expanding the Exposome-Explorer database with gut microbial metabolites. Sci Rep 2023; 13:1946. [PMID: 36732606 PMCID: PMC9894932 DOI: 10.1038/s41598-022-26366-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/13/2022] [Indexed: 02/04/2023] Open
Abstract
Metabolites produced by the gut microbiota play an important role in the cross-talk with the human host. Many microbial metabolites are biologically active and can pass the gut barrier and make it into the systemic circulation, where they form the gut microbial exposome, i.e. the totality of gut microbial metabolites in body fluids or tissues of the host. A major difficulty faced when studying the microbial exposome and its role in health and diseases is to differentiate metabolites solely or partially derived from microbial metabolism from those produced by the host or coming from the diet. Our objective was to collect data from the scientific literature and build a database on gut microbial metabolites and on evidence of their microbial origin. Three types of evidence on the microbial origin of the gut microbial exposome were defined: (1) metabolites are produced in vitro by human faecal bacteria; (2) metabolites show reduced concentrations in humans or experimental animals upon treatment with antibiotics; (3) metabolites show reduced concentrations in germ-free animals when compared with conventional animals. Data was manually collected from peer-reviewed publications and inserted in the Exposome-Explorer database. Furthermore, to explore the chemical space of the microbial exposome and predict metabolites uniquely formed by the microbiota, genome-scale metabolic models (GSMMs) of gut bacterial strains and humans were compared. A total of 1848 records on one or more types of evidence on the gut microbial origin of 457 metabolites was collected in Exposome-Explorer. Data on their known precursors and concentrations in human blood, urine and faeces was also collected. About 66% of the predicted gut microbial metabolites (n = 1543) were found to be unique microbial metabolites not found in the human GSMM, neither in the list of 457 metabolites curated in Exposome-Explorer, and can be targets for new experimental studies. This new data on the gut microbial exposome, freely available in Exposome-Explorer ( http://exposome-explorer.iarc.fr/ ), will help researchers to identify poorly studied microbial metabolites to be considered in future studies on the gut microbiota, and study their functionalities and role in health and diseases.
Collapse
Affiliation(s)
- Vanessa Neveu
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | - Geneviève Nicolas
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | - Adam Amara
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | - Reza M Salek
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | - Augustin Scalbert
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France.
| |
Collapse
|
20
|
Are neuromodulation interventions associated with changes in the gut microbiota? A systematic review. Neuropharmacology 2023; 223:109318. [PMID: 36334762 DOI: 10.1016/j.neuropharm.2022.109318] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
The microbiota-gut-brain axis (MGBA) refers to the bidirectional communication between the brain and the gut microbiota and recent studies have linked the MGBA to health and disease. Research has so far investigated this axis mainly from microbiota to brain but less is known about the other direction. One approach to examine the MGBA from brain to microbiota is through understanding if and how neuromodulation might impact microbiota. Neuromodulation encompasses a wide range of stimulation techniques and is used to treat neurological, psychiatric and metabolic disorders, like Parkinson's Disease, depression and obesity. Here, we performed a systematic review to investigate whether neuromodulation is associated with subsequent changes in the gut microbiota. Searches in PsycINFO and MEDLINE were performed up to March 2022. Included studies needed to be clinical or preclinical studies comparing the effects of deep brain stimulation, electroconvulsive therapy, repetitive transcranial magnetic stimulation, transcranial direct current stimulation or vagal nerve stimulation on the gut microbiota before and after treatment or between active and control groups. Seven studies were identified. Neuromodulation was associated with changes in relative bacterial abundances, but not with (changes in) α-diversity or β-diversity. Summarizing, currently reported findings suggest that neuromodulation interventions are associated with moderate changes in the gut microbiome. However, findings remain inconclusive due to the limited number and varying quality of included studies, as well as the large heterogeneity between studies. More research is required to more conclusively establish whether, and if so, via which mechanism(s) of action neuromodulation interventions might influence the gut microbiota.
Collapse
|
21
|
McCoubrey LE, Favaron A, Awad A, Orlu M, Gaisford S, Basit AW. Colonic drug delivery: Formulating the next generation of colon-targeted therapeutics. J Control Release 2023; 353:1107-1126. [PMID: 36528195 DOI: 10.1016/j.jconrel.2022.12.029] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/26/2022]
Abstract
Colonic drug delivery can facilitate access to unique therapeutic targets and has the potential to enhance drug bioavailability whilst reducing off-target effects. Delivering drugs to the colon requires considered formulation development, as both oral and rectal dosage forms can encounter challenges if the colon's distinct physiological environment is not appreciated. As the therapeutic opportunities surrounding colonic drug delivery multiply, the success of novel pharmaceuticals lies in their design. This review provides a modern insight into the key parameters determining the effective design and development of colon-targeted medicines. Influential physiological features governing the release, dissolution, stability, and absorption of drugs in the colon are first discussed, followed by an overview of the most reliable colon-targeted formulation strategies. Finally, the most appropriate in vitro, in vivo, and in silico preclinical investigations are presented, with the goal of inspiring strategic development of new colon-targeted therapeutics.
Collapse
Affiliation(s)
- Laura E McCoubrey
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Alessia Favaron
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Atheer Awad
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Mine Orlu
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Simon Gaisford
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Abdul W Basit
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK.
| |
Collapse
|
22
|
Hiseni P, Snipen L, Wilson RC, Furu K, Hegge FT, Rudi K. Prediction of high fecal propionate-to-butyrate ratios using 16S rRNA-based detection of bacterial groups with liquid array diagnostics. Biotechniques 2023; 74:9-21. [PMID: 36601888 DOI: 10.2144/btn-2022-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Butyrate and propionate represent two of three main short-chain fatty acids produced by the intestinal microbiota. In healthy populations, their levels are reportedly equimolar, whereas a deviation in their ratio has been observed in various diseased cohorts. Monitoring such a ratio represents a valuable metric; however, it remains a challenge to adopt short-chain fatty acid detection techniques in clinical settings because of the volatile nature of these acids. Here we aimed to estimate short-chain fatty acid information indirectly through a novel, simple quantitative PCR-compatible assay (liquid array diagnostics) targeting a limited number of microbiome 16S markers. Utilizing 15 liquid array diagnostics probes to target microbiome markers selected by a model that combines partial least squares and linear discriminant analysis, the classes (normal vs high propionate-to-butyrate ratio) separated at a threshold of 2.6 with a prediction accuracy of 96%.
Collapse
Affiliation(s)
- Pranvera Hiseni
- Genetic Analysis AS, Kabelgata 8, Oslo, 0580, Norway.,Department of Chemistry, Biotechnology & Food Sciences, Norwegian University of Life Sciences, PO Box 5003, Aas, 1432, Norway
| | - Lars Snipen
- Department of Chemistry, Biotechnology & Food Sciences, Norwegian University of Life Sciences, PO Box 5003, Aas, 1432, Norway
| | - Robert C Wilson
- Department of Biotechnology, Inland Norway University of Applied Sciences, PO Box 400 Vestad, Elverum, 2418, Norway
| | - Kari Furu
- Genetic Analysis AS, Kabelgata 8, Oslo, 0580, Norway
| | | | - Knut Rudi
- Department of Chemistry, Biotechnology & Food Sciences, Norwegian University of Life Sciences, PO Box 5003, Aas, 1432, Norway.,Department of Biotechnology, Inland Norway University of Applied Sciences, PO Box 400 Vestad, Elverum, 2418, Norway
| |
Collapse
|
23
|
Hamamah S, Gheorghita R, Lobiuc A, Sirbu IO, Covasa M. Fecal microbiota transplantation in non-communicable diseases: Recent advances and protocols. Front Med (Lausanne) 2022; 9:1060581. [PMID: 36569149 PMCID: PMC9773399 DOI: 10.3389/fmed.2022.1060581] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Fecal microbiota transplant (FMT) is a therapeutic method that aims to restore normal gut microbial composition in recipients. Currently, FMT is approved in the USA to treat recurrent and refractory Clostridioides difficile infection and has been shown to have great efficacy. As such, significant research has been directed toward understanding the potential role of FMT in other conditions associated with gut microbiota dysbiosis such as obesity, type 2 diabetes mellitus, metabolic syndrome, neuropsychiatric disorders, inflammatory bowel disease, irritable bowel syndrome, decompensated cirrhosis, cancers and graft-versus-host disease. This review examines current updates and efficacy of FMT in treating conditions other than Clostridioides difficile infection. Further, protocols for administration of FMT are also discussed including storage of fecal samples in stool banks, inclusion/exclusion criteria for donors, fecal sample preparation and methods of treatment administration. Overall, understanding the mechanisms by which FMT can manipulate gut microbiota to provide therapeutic benefit as well as identifying potential adverse effects is an important step in clarifying its long-term safety and efficacy in treating multiple conditions in the future.
Collapse
Affiliation(s)
- Sevag Hamamah
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, CA, United States
| | - Roxana Gheorghita
- Department of Medicine and Biomedical Sciences, College of Medicine and Biological Science, University of Suceava, Suceava, Romania,Department of Biochemistry, Victor Babeş University of Medicine and Pharmacy Timisoara, Timişoara, Romania
| | - Andrei Lobiuc
- Department of Medicine and Biomedical Sciences, College of Medicine and Biological Science, University of Suceava, Suceava, Romania
| | - Ioan-Ovidiu Sirbu
- Department of Biochemistry, Victor Babeş University of Medicine and Pharmacy Timisoara, Timişoara, Romania,Center for Complex Network Science, Victor Babeş University of Medicine and Pharmacy Timisoara, Timişoara, Romania
| | - Mihai Covasa
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, CA, United States,Department of Medicine and Biomedical Sciences, College of Medicine and Biological Science, University of Suceava, Suceava, Romania,*Correspondence: Mihai Covasa,
| |
Collapse
|
24
|
Gut microbiome-wide association study of depressive symptoms. Nat Commun 2022; 13:7128. [PMID: 36473852 PMCID: PMC9726982 DOI: 10.1038/s41467-022-34502-3] [Citation(s) in RCA: 127] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Depression is one of the most poorly understood diseases due to its elusive pathogenesis. There is an urgency to identify molecular and biological mechanisms underlying depression and the gut microbiome is a novel area of interest. Here we investigate the relation of fecal microbiome diversity and composition with depressive symptoms in 1,054 participants from the Rotterdam Study cohort and validate these findings in the Amsterdam HELIUS cohort in 1,539 subjects. We identify association of thirteen microbial taxa, including genera Eggerthella, Subdoligranulum, Coprococcus, Sellimonas, Lachnoclostridium, Hungatella, Ruminococcaceae (UCG002, UCG003 and UCG005), LachnospiraceaeUCG001, Eubacterium ventriosum and Ruminococcusgauvreauiigroup, and family Ruminococcaceae with depressive symptoms. These bacteria are known to be involved in the synthesis of glutamate, butyrate, serotonin and gamma amino butyric acid (GABA), which are key neurotransmitters for depression. Our study suggests that the gut microbiome composition may play a key role in depression.
Collapse
|
25
|
Is There a Universal Endurance Microbiota? Microorganisms 2022; 10:microorganisms10112213. [DOI: 10.3390/microorganisms10112213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 11/12/2022] Open
Abstract
Billions of microbes sculpt the gut ecosystem, affecting physiology. Since endurance athletes’ performance is often physiology-limited, understanding the composition and interactions within athletes’ gut microbiota could improve performance. Individual studies describe differences in the relative abundance of bacterial taxa in endurance athletes, suggesting the existence of an “endurance microbiota”, yet the taxa identified are mostly non-overlapping. To narrow down the source of this variation, we created a bioinformatics workflow and reanalyzed fecal microbiota from four 16S rRNA gene sequence datasets associated with endurance athletes and controls, examining diversity, relative abundance, correlations, and association networks. There were no significant differences in alpha diversity among all datasets and only one out of four datasets showed a significant overall difference in bacterial community abundance. When bacteria were examined individually, there were no genera with significantly different relative abundance in all four datasets. Two genera were significantly different in two datasets (Veillonella and Romboutsia). No changes in correlated abundances were consistent across datasets. A power analysis using the variance in relative abundance detected in each dataset indicated that much larger sample sizes will be necessary to detect a modest difference in relative abundance especially given the multitude of covariates. Our analysis confirms several challenges when comparing microbiota in general, and indicates that microbes consistently or universally associated with human endurance remain elusive.
Collapse
|
26
|
Modest Conformity Between Self-Reporting of Bristol Stool Form and Fecal Consistency Measured by Stool Water Content in Irritable Bowel Syndrome and a FODMAP and Gluten Trial. Am J Gastroenterol 2022; 117:1668-1674. [PMID: 36087104 DOI: 10.14309/ajg.0000000000001942] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/29/2022] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Altered bowel habits constitute a criterion of irritable bowel syndrome (IBS), with the Bristol Stool Form Scale (BSFS) as the recommended tool for assessment of fecal consistency. However, BSFS is devoid of a comprehensive objective evaluation in subjects with IBS. Therefore, we aimed to evaluate the concordance between subjective reporting of BSFS and objective stool water content in subjects with IBS. Furthermore, we evaluated whether intake of fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) or gluten would affect stool water content. METHODS Data from a previous crossover trial in IBS with 1-week provocations of FODMAPs, gluten, or placebo were subanalyzed. After each intervention, fecal consistency was subjectively assessed using the BSFS and stool samples were collected. The stool water content was analyzed, where ≤68.5% water content was classified as hard stool, while ≥78% was classified as diarrhea. RESULTS BSFS correlated to stool water content ( r = 0.36, P < 0.0001). The BSFS score increased in parallel with increasing water content, but with considerable overlap between BSFS scores. Stool water content differed between the BSFS categories 1-2, 3-5, and 6-7 (hard, normal, and loose, respectively) ( P < 0.0001). For BSFS categories 1-2, 77% had water content ≤68.5%, whereas for BSFS categories 6-7, 52% had water content ≥78%. There was no difference in stool water content after consumption of FODMAPs, gluten, or placebo ( P = 0.94). DISCUSSION Subjective reporting of BSFS conforms only modestly with stool water content in IBS, warranting caution when subtyping IBS according to the BSFS. High intake of FODMAPs and gluten does not affect stool water content.
Collapse
|
27
|
Jones J, Reinke SN, Mousavi-Derazmahalleh M, Palmer DJ, Christophersen CT. Changes to the Gut Microbiome in Young Children Showing Early Behavioral Signs of Autism. Front Microbiol 2022; 13:905901. [PMID: 35966698 PMCID: PMC9371947 DOI: 10.3389/fmicb.2022.905901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
The human gut microbiome has increasingly been associated with autism spectrum disorder (ASD), which is a neurological developmental disorder, characterized by impairments to social interaction. The ability of the gut microbiota to signal across the gut-brain-microbiota axis with metabolites, including short-chain fatty acids, impacts brain health and has been identified to play a role in the gastrointestinal and developmental symptoms affecting autistic children. The fecal microbiome of older children with ASD has repeatedly shown particular shifts in the bacterial and fungal microbial community, which are significantly different from age-matched neurotypical controls, but it is still unclear whether these characteristic shifts are detectable before diagnosis. Early microbial colonization patterns can have long-lasting effects on human health, and pre-emptive intervention may be an important mediator to more severe autism. In this study, we characterized both the microbiome and short-chain fatty acid concentrations of fecal samples from young children between 21 and 40 months who were showing early behavioral signs of ASD. The fungal richness and acetic acid concentrations were observed to be higher with increasing autism severity, and the abundance of several bacterial taxa also changed due to the severity of ASD. Bacterial diversity and SCFA concentrations were also associated with stool form, and some bacterial families were found with differential abundance according to stool firmness. An exploratory analysis of the microbiome associated with pre-emptive treatment also showed significant differences at multiple taxonomic levels. These differences may impact the microbial signaling across the gut-brain-microbiota axis and the neurological development of the children.
Collapse
Affiliation(s)
- Jacquelyn Jones
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA, Australia
- *Correspondence: Jacquelyn Jones
| | - Stacey N. Reinke
- Centre for Integrative Metabolomics and Computational Biology, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA, Australia
| | - Debra J. Palmer
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
- School of Medicine, University of Western Australia, Crawley, WA, Australia
| | - Claus T. Christophersen
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA, Australia
- Centre for Integrative Metabolomics and Computational Biology, School of Science, Edith Cowan University, Joondalup, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| |
Collapse
|
28
|
Morgan EW, Perdew GH, Patterson AD. Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research. Toxicol Sci 2022; 187:189-213. [PMID: 35285497 PMCID: PMC9154275 DOI: 10.1093/toxsci/kfac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microbial communities on and within the host contact environmental pollutants, toxic compounds, and other xenobiotic compounds. These communities of bacteria, fungi, viruses, and archaea possess diverse metabolic potential to catabolize compounds and produce new metabolites. Microbes alter chemical disposition thus making the microbiome a natural subject of interest for toxicology. Sequencing and metabolomics technologies permit the study of microbiomes altered by acute or long-term exposure to xenobiotics. These investigations have already contributed to and are helping to re-interpret traditional understandings of toxicology. The purpose of this review is to provide a survey of the current methods used to characterize microbes within the context of toxicology. This will include discussion of commonly used techniques for conducting omic-based experiments, their respective strengths and deficiencies, and how forward-looking techniques may address present shortcomings. Finally, a perspective will be provided regarding common assumptions that currently impede microbiome studies from producing causal explanations of toxicologic mechanisms.
Collapse
Affiliation(s)
- Ethan W Morgan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gary H Perdew
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew D Patterson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
29
|
Sauceda C, Bayne C, Sudqi K, Gonzalez A, Dulai PS, Knight R, Gonzalez DJ, Gonzalez CG. Stool multi-omics for the study of host-microbe interactions in inflammatory bowel disease. Gut Microbes 2022; 14:2154092. [PMID: 36503356 PMCID: PMC9746627 DOI: 10.1080/19490976.2022.2154092] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Inflammatory Bowel Disease (IBD) is a chronic immune-mediated inflammatory disease of the gastrointestinal tract that is a growing public burden. Gut microbes and their interactions with hosts play a crucial role in disease pathogenesis and progression. These interactions are complex, spanning multiple physiological systems and data types, making comprehensive disease assessment difficult, and often overwhelming single-omic capabilities. Stool-based multi-omics is a promising approach for characterizing host-gut microbiome interactions using deep integration of technologies such as 16S rRNA sequencing, shotgun metagenomics, meta-transcriptomics, metabolomics, and metaproteomics. The wealth of information generated through multi-omic studies is poised to usher in advancements in IBD research and precision medicine. This review highlights historical and recent findings from stool-based muti-omic studies that have contributed to unraveling IBD's complexity. Finally, we discuss common pitfalls, issues, and limitations, and how future pipelines should address them to standardize multi-omics in IBD research and beyond.
Collapse
Affiliation(s)
- Consuelo Sauceda
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Charlie Bayne
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Khadijeh Sudqi
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Parambir S. Dulai
- Division of Gastroenterology and Hepatology, Northwestern University, Chicago, IL, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - David J. Gonzalez
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Carlos G. Gonzalez
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|