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Maier L, Stein-Thoeringer C, Ley RE, Brötz-Oesterhelt H, Link H, Ziemert N, Wagner S, Peschel A. Integrating research on bacterial pathogens and commensals to fight infections-an ecological perspective. Lancet Microbe 2024:S2666-5247(24)00049-1. [PMID: 38608681 DOI: 10.1016/s2666-5247(24)00049-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 04/14/2024]
Abstract
The incidence of antibiotic-resistant bacterial infections is increasing, and development of new antibiotics has been deprioritised by the pharmaceutical industry. Interdisciplinary research approaches, based on the ecological principles of bacterial fitness, competition, and transmission, could open new avenues to combat antibiotic-resistant infections. Many facultative bacterial pathogens use human mucosal surfaces as their major reservoirs and induce infectious diseases to aid their lateral transmission to new host organisms under some pathological states of the microbiome and host. Beneficial bacterial commensals can outcompete specific pathogens, thereby lowering the capacity of the pathogens to spread and cause serious infections. Despite the clinical relevance, however, the understanding of commensal-pathogen interactions in their natural habitats remains poor. In this Personal View, we highlight directions to intensify research on the interactions between bacterial pathogens and commensals in the context of human microbiomes and host biology that can lead to the development of innovative and sustainable ways of preventing and treating infectious diseases.
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Affiliation(s)
- Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; German Center for Infection Research, partner site, Tübingen, Germany
| | - Christoph Stein-Thoeringer
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; German Center for Infection Research, partner site, Tübingen, Germany; Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Ruth E Ley
- Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; Max Planck Institute for Biology, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; German Center for Infection Research, partner site, Tübingen, Germany
| | - Hannes Link
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; German Center for Infection Research, partner site, Tübingen, Germany
| | - Samuel Wagner
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; German Center for Infection Research, partner site, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; German Center for Infection Research, partner site, Tübingen, Germany.
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Dilmore AH, Kuplicki R, McDonald D, Kumar M, Estaki M, Youngblut N, Tyakht A, Ackermann G, Blach C, MahmoudianDehkordi S, Dunlop BW, Bhattacharyya S, Guinjoan S, Mandaviya P, Ley RE, Kaddaruh-Dauok R, Paulus MP, Knight R. Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression. bioRxiv 2024:2024.03.19.585820. [PMID: 38562901 PMCID: PMC10983923 DOI: 10.1101/2024.03.19.585820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
This study investigated the relationship between gut microbiota and neuropsychiatric disorders (NPDs), specifically anxiety disorder (ANXD) and/or major depressive disorder (MDD), as defined by DSM-IV or V criteria. The study also examined the influence of medication use, particularly antidepressants and/or anxiolytics, classified through the Anatomical Therapeutic Chemical (ATC) Classification System, on the gut microbiota. Both 16S rRNA gene amplicon sequencing and shallow shotgun sequencing were performed on DNA extracted from 666 fecal samples from the Tulsa-1000 and NeuroMAP CoBRE cohorts. The results highlight the significant influence of medication use; antidepressant use is associated with significant differences in gut microbiota beta diversity and has a larger effect size than NPD diagnosis. Next, specific microbes were associated with ANXD and MDD, highlighting their potential for non-pharmacological intervention. Finally, the study demonstrated the capability of Random Forest classifiers to predict diagnoses of NPD and medication use from microbial profiles, suggesting a promising direction for the use of gut microbiota as biomarkers for NPD. The findings suggest that future research on the gut microbiota's role in NPD and its interactions with pharmacological treatments are needed.
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Affiliation(s)
- Amanda Hazel Dilmore
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Rayus Kuplicki
- Laureate Institute for Brain Research, Tulsa, Oklahoma, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Megha Kumar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Alexander Tyakht
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colette Blach
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
- Department of Medicine, Duke University, Durham, North Carolina, USA
- Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA
| | | | - Boadie W. Dunlop
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Sudeepa Bhattacharyya
- Department of Biological Sciences, Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, USA
| | | | - Pooja Mandaviya
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Rima Kaddaruh-Dauok
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
- Department of Medicine, Duke University, Durham, North Carolina, USA
- Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA
| | | | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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Akbuğa-Schön T, Suzuki TA, Jakob D, Vu DL, Waters JL, Ley RE. The keystone gut species Christensenella minuta boosts gut microbial biomass and voluntary physical activity in mice. mBio 2024; 15:e0283623. [PMID: 38132571 PMCID: PMC10865807 DOI: 10.1128/mbio.02836-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023] Open
Abstract
The gut bacteria of the family Christensenellaceae are consistently associated with metabolic health, but their role in promoting host health is not fully understood. Here, we explored the effect of Christensenella minuta amendment on voluntary physical activity and the gut microbiome. We inoculated male and female germ-free mice with an obese human donor microbiota together with live or heat-killed C. minuta for 28 days and measured physical activity in respirometry cages. Compared to heat-killed, the live-C. minuta treatment resulted in reduced feed efficiency and higher levels of physical activity, with significantly greater distance traveled for males and higher levels of small movements and resting metabolic rate in females. Sex-specific effects of C. minuta treatment may be in part attributable to different housing conditions for males and females. Amendment with live C. minuta boosted gut microbial biomass in both sexes, immobilizing dietary carbon in the microbiome, and mice with high levels of C. minuta lose more energy in stool. Live C. minuta also reduced within and between-host gut microbial diversity. Overall, our results showed that C. minuta acts as a keystone species: despite low relative abundance, it has a large impact on its ecosystem, from the microbiome to host energy homeostasis.IMPORTANCEThe composition of the human gut microbiome is associated with human health. Within the human gut microbiome, the relative abundance of the bacterial family Christensenellaceae has been shown to correlate with metabolic health and a lean body type. The mechanisms underpinning this effect remain unclear. Here, we show that live C. minuta influences host physical activity and metabolic energy expenditure, accompanied by changes in murine metabolism and the gut microbial community in a sex-dependent manner in comparison to heat-killed C. minuta. Importantly, live C. minuta boosts the biomass of the microbiome in the gut, and a higher level of C. minuta is associated with greater loss of energy in stool. These observations indicate that modulation of activity levels and changes to the microbiome are ways in which the Christensenellaceae can influence host energy homeostasis and health.
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Affiliation(s)
- Tanja Akbuğa-Schön
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Dennis Jakob
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Mass Spectrometry Facility, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Dai Long Vu
- Mass Spectrometry Facility, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Jillian L. Waters
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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Walters WA, Ley C, Hastie T, Ley RE, Parsonnet J. A modified Michaelis-Menten equation estimates growth from birth to 3 years in healthy babies in the USA. BMC Med Res Methodol 2024; 24:27. [PMID: 38302887 PMCID: PMC10832211 DOI: 10.1186/s12874-024-02145-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Standard pediatric growth curves cannot be used to impute missing height or weight measurements in individual children. The Michaelis-Menten equation, used for characterizing substrate-enzyme saturation curves, has been shown to model growth in many organisms including nonhuman vertebrates. We investigated whether this equation could be used to interpolate missing growth data in children in the first three years of life and compared this interpolation to several common interpolation methods and pediatric growth models. METHODS We developed a modified Michaelis-Menten equation and compared expected to actual growth, first in a local birth cohort (N = 97) then in a large, outpatient, pediatric sample (N = 14,695). RESULTS The modified Michaelis-Menten equation showed excellent fit for both infant weight (median RMSE: boys: 0.22 kg [IQR:0.19; 90% < 0.43]; girls: 0.20 kg [IQR:0.17; 90% < 0.39]) and height (median RMSE: boys: 0.93 cm [IQR:0.53; 90% < 1.0]; girls: 0.91 cm [IQR:0.50;90% < 1.0]). Growth data were modeled accurately with as few as four values from routine well-baby visits in year 1 and seven values in years 1-3; birth weight or length was essential for best fit. Interpolation with this equation had comparable (for weight) or lower (for height) mean RMSE compared to the best performing alternative models. CONCLUSIONS A modified Michaelis-Menten equation accurately describes growth in healthy babies aged 0-36 months, allowing interpolation of missing weight and height values in individual longitudinal measurement series. The growth pattern in healthy babies in resource-rich environments mirrors an enzymatic saturation curve.
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Affiliation(s)
- William A Walters
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Catherine Ley
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5170, USA.
| | - Trevor Hastie
- Departments of Statistics and of Biomedical Data Sciences, Stanford University, Stanford, CA, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Julie Parsonnet
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305-5170, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
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de la Cuesta-Zuluaga J, Huus KE, Youngblut ND, Escobar JS, Ley RE. Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy. Gut Microbes 2023; 15:2246634. [PMID: 37680093 PMCID: PMC10486298 DOI: 10.1080/19490976.2023.2246634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023] Open
Abstract
Obesity (OB) and cardiometabolic disease are major public health issues linked to changes in the gut microbiome. OB and poor cardiometabolic health status (CHS) are often comorbid, which hinders efforts to identify components of the microbiome uniquely linked to either one. Here, we used a deeply phenotyped cohort of 408 adults from Colombia, including subjects with OB, unhealthy CHS, or both, to validate previously reported features of gut microbiome function and diversity independently correlated with OB or CHS using fecal metagenomes. OB was defined by body mass index, waist circumference, and body fat; CHS as healthy or unhealthy according to blood biochemistry and anthropometric data. We found that OB, more so than metabolic status, drove associations with gut microbiome structure and functions. The microbiome of obese individuals with and without co-existing unhealthy CHS was characterized by reduced metagenomic diversity, reduced fermentative potential and elevated capacity to respond to oxidative stress and produce bacterial antigens. Disease-linked features were correlated with increased host blood pressure and inflammatory markers, and were mainly contributed by members of the family Enterobacteriaceae. Our results link OB with a microbiome able to tolerate an inflammatory and oxygenated gut state, and suggest that OB is the main driver of microbiome functional differences when poor CHS is a comorbidity.
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Affiliation(s)
| | - Kelsey E. Huus
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Juan S. Escobar
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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Daniel N, Wu GD, Walters W, Compher C, Ni J, Delaroque C, Albenberg L, Ley RE, Patterson AD, Lewis JD, Gewirtz AT, Chassaing B. Human Intestinal Microbiome Determines Individualized Inflammatory Response to Dietary Emulsifier Carboxymethylcellulose Consumption. Cell Mol Gastroenterol Hepatol 2023; 17:315-318. [PMID: 37931789 PMCID: PMC10829520 DOI: 10.1016/j.jcmgh.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Affiliation(s)
- Noëmie Daniel
- INSERM U1016, Team "Mucosal Microbiota in Chronic Inflammatory Diseases", CNRS UMR 8104, Université de Paris, Paris, France
| | - Gary D Wu
- Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Charlene Compher
- Biobehavioral Health Sciences Department, School of Nursing, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Josephine Ni
- Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Clara Delaroque
- INSERM U1016, Team "Mucosal Microbiota in Chronic Inflammatory Diseases", CNRS UMR 8104, Université de Paris, Paris, France
| | - Lindsey Albenberg
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andrew D Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, State College, Pennsylvania
| | - James D Lewis
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew T Gewirtz
- Institute for Biomedical Sciences, Center for Inflammation, Immunity and Infection, Digestive Disease Research Group, Georgia State University, Atlanta, Georgia
| | - Benoit Chassaing
- INSERM U1016, Team "Mucosal Microbiota in Chronic Inflammatory Diseases", CNRS UMR 8104, Université de Paris, Paris, France.
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7
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Casini I, McCubbin T, Esquivel-Elizondo S, Luque GG, Evseeva D, Fink C, Beblawy S, Youngblut ND, Aristilde L, Huson DH, Dräger A, Ley RE, Marcellin E, Angenent LT, Molitor B. An integrated systems biology approach reveals differences in formate metabolism in the genus Methanothermobacter. iScience 2023; 26:108016. [PMID: 37854702 PMCID: PMC10579436 DOI: 10.1016/j.isci.2023.108016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023] Open
Abstract
Methanogenesis allows methanogenic archaea to generate cellular energy for their growth while producing methane. Thermophilic hydrogenotrophic species of the genus Methanothermobacter have been recognized as robust biocatalysts for a circular carbon economy and are already applied in power-to-gas technology with biomethanation, which is a platform to store renewable energy and utilize captured carbon dioxide. Here, we generated curated genome-scale metabolic reconstructions for three Methanothermobacter strains and investigated differences in the growth performance of these same strains in chemostat bioreactor experiments with hydrogen and carbon dioxide or formate as substrates. Using an integrated systems biology approach, we identified differences in formate anabolism between the strains and revealed that formate anabolism influences the diversion of carbon between biomass and methane. This finding, together with the omics datasets and the metabolic models we generated, can be implemented for biotechnological applications of Methanothermobacter in power-to-gas technology, and as a perspective, for value-added chemical production.
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Affiliation(s)
- Isabella Casini
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sofia Esquivel-Elizondo
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Guillermo G. Luque
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Daria Evseeva
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Christian Fink
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Sebastian Beblawy
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Daniel H. Huson
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Andreas Dräger
- Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, QLD 4072, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Largus T. Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- AG Angenent, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000 Aarhus C, Denmark
- The Novo Nordisk Foundation CO2 Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Bastian Molitor
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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Mineeva O, Danciu D, Schölkopf B, Ley RE, Rätsch G, Youngblut ND. ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning. PLoS Comput Biol 2023; 19:e1011001. [PMID: 37126495 PMCID: PMC10174551 DOI: 10.1371/journal.pcbi.1011001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 05/11/2023] [Accepted: 03/06/2023] [Indexed: 05/02/2023] Open
Abstract
The number of published metagenome assemblies is rapidly growing due to advances in sequencing technologies. However, sequencing errors, variable coverage, repetitive genomic regions, and other factors can produce misassemblies, which are challenging to detect for taxonomically novel genomic data. Assembly errors can affect all downstream analyses of the assemblies. Accuracy for the state of the art in reference-free misassembly prediction does not exceed an AUPRC of 0.57, and it is not clear how well these models generalize to real-world data. Here, we present the Residual neural network for Misassembled Contig identification (ResMiCo), a deep learning approach for reference-free identification of misassembled contigs. To develop ResMiCo, we first generated a training dataset of unprecedented size and complexity that can be used for further benchmarking and developments in the field. Through rigorous validation, we show that ResMiCo is substantially more accurate than the state of the art, and the model is robust to novel taxonomic diversity and varying assembly methods. ResMiCo estimated 7% misassembled contigs per metagenome across multiple real-world datasets. We demonstrate how ResMiCo can be used to optimize metagenome assembly hyperparameters to improve accuracy, instead of optimizing solely for contiguity. The accuracy, robustness, and ease-of-use of ResMiCo make the tool suitable for general quality control of metagenome assemblies and assembly methodology optimization.
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Affiliation(s)
- Olga Mineeva
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
- Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen, Germany
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Daniel Danciu
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Bernhard Schölkopf
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
- Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen, Germany
- ETH AI center, ETH Zürich, Zürich, Switzerland
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Gunnar Rätsch
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
- ETH AI center, ETH Zürich, Zürich, Switzerland
- Department of Biology, ETH Zürich, Zürich, Switzerland
- Medical Informatics Unit, Zürich University Hospital, Zürich, Switzerland
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
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10
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Pinto Y, Frishman S, Turjeman S, Eshel A, Nuriel-Ohayon M, Shrossel O, Ziv O, Walters W, Parsonnet J, Ley C, Johnson EL, Kumar K, Schweitzer R, Khatib S, Magzal F, Muller E, Tamir S, Tenenbaum-Gavish K, Rautava S, Salminen S, Isolauri E, Yariv O, Peled Y, Poran E, Pardo J, Chen R, Hod M, Borenstein E, Ley RE, Schwartz B, Louzoun Y, Hadar E, Koren O. Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis. Gut 2023; 72:918-928. [PMID: 36627187 PMCID: PMC10086485 DOI: 10.1136/gutjnl-2022-328406] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/26/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Gestational diabetes mellitus (GDM) is a condition in which women without diabetes are diagnosed with glucose intolerance during pregnancy, typically in the second or third trimester. Early diagnosis, along with a better understanding of its pathophysiology during the first trimester of pregnancy, may be effective in reducing incidence and associated short-term and long-term morbidities. DESIGN We comprehensively profiled the gut microbiome, metabolome, inflammatory cytokines, nutrition and clinical records of 394 women during the first trimester of pregnancy, before GDM diagnosis. We then built a model that can predict GDM onset weeks before it is typically diagnosed. Further, we demonstrated the role of the microbiome in disease using faecal microbiota transplant (FMT) of first trimester samples from pregnant women across three unique cohorts. RESULTS We found elevated levels of proinflammatory cytokines in women who later developed GDM, decreased faecal short-chain fatty acids and altered microbiome. We next confirmed that differences in GDM-associated microbial composition during the first trimester drove inflammation and insulin resistance more than 10 weeks prior to GDM diagnosis using FMT experiments. Following these observations, we used a machine learning approach to predict GDM based on first trimester clinical, microbial and inflammatory markers with high accuracy. CONCLUSION GDM onset can be identified in the first trimester of pregnancy, earlier than currently accepted. Furthermore, the gut microbiome appears to play a role in inflammation-induced GDM pathogenesis, with interleukin-6 as a potential contributor to pathogenesis. Potential GDM markers, including microbiota, can serve as targets for early diagnostics and therapeutic intervention leading to prevention.
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Affiliation(s)
- Yishay Pinto
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sigal Frishman
- Helen Schneider Hospital for Women, Rabin Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Biochemistry, School of Nutritional Sciences Food Science and Nutrition, The School of Nutritional Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sondra Turjeman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Adi Eshel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | - Oshrit Shrossel
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Oren Ziv
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tubingen, Germany
| | - Julie Parsonnet
- Department of Medicine, Stanford University, Stanford, California, USA
- Department of Epidemiology and Population Health, Stanford University, Stanford, California, USA
| | - Catherine Ley
- Department of Medicine, Stanford University, Stanford, California, USA
| | | | - Krithika Kumar
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Ron Schweitzer
- Department of Natural Compounds and Analytical Chemistry, Migal-Galilee Research Institute, Kiryat Shmona, Israel
- Analytical Chemistry Laboratory, Tel-Hai College, Upper Galilee, Israel
| | - Soliman Khatib
- Department of Natural Compounds and Analytical Chemistry, Migal-Galilee Research Institute, Kiryat Shmona, Israel
- Analytical Chemistry Laboratory, Tel-Hai College, Upper Galilee, Israel
| | - Faiga Magzal
- Laboratory of Human Health and Nutrition Sciences, Migal-Galilee Technology Center, Kiryat Shmona, Israel
- Nutritional Science Department, Tel Hai College, Upper Galilee, Israel
| | - Efrat Muller
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Snait Tamir
- Laboratory of Human Health and Nutrition Sciences, Migal-Galilee Technology Center, Kiryat Shmona, Israel
- Nutritional Science Department, Tel Hai College, Upper Galilee, Israel
| | - Kinneret Tenenbaum-Gavish
- Helen Schneider Hospital for Women, Rabin Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Samuli Rautava
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
- University of Helsinki & Helsinki University Hospital, New Children's Hospital, Pediatric Research Center, Helsinki, Finland
| | - Seppo Salminen
- Functional Foods Forum, University of Turku, Turku, Finland
| | - Erika Isolauri
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | - Or Yariv
- Clalit Health Services, Tel Aviv, Israel
| | - Yoav Peled
- Helen Schneider Hospital for Women, Rabin Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Clalit Health Services, Tel Aviv, Israel
| | - Eran Poran
- Clalit Health Services, Tel Aviv, Israel
| | - Joseph Pardo
- Helen Schneider Hospital for Women, Rabin Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Clalit Health Services, Tel Aviv, Israel
| | - Rony Chen
- Helen Schneider Hospital for Women, Rabin Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Moshe Hod
- Helen Schneider Hospital for Women, Rabin Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tubingen, Germany
| | - Betty Schwartz
- Institute of Biochemistry, School of Nutritional Sciences Food Science and Nutrition, The School of Nutritional Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Eran Hadar
- Helen Schneider Hospital for Women, Rabin Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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11
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Walters WA, Granados AC, Ley C, Federman S, Stryke D, Santos Y, Haggerty T, Sotomayor-Gonzalez A, Servellita V, Ley RE, Parsonnet J, Chiu CY. Longitudinal comparison of the developing gut virome in infants and their mothers. Cell Host Microbe 2023; 31:187-198.e3. [PMID: 36758519 PMCID: PMC9950819 DOI: 10.1016/j.chom.2023.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/15/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023]
Abstract
The human gut virome and its early life development are poorly understood. Prior studies have captured single-point assessments with the evolution of the infant virome remaining largely unexplored. We performed viral metagenomic sequencing on stool samples collected longitudinally from a cohort of 53 infants from age 2 weeks to 3 years (80.7 billion reads), and from their mothers (9.8 billion reads) to examine and compare viromes. The asymptomatic infant virome consisted of bacteriophages, nonhuman dietary/environmental viruses, and human-host viruses, predominantly picornaviruses. In contrast, human-host viruses were largely absent from the maternal virome. Previously undescribed, sequence-divergent vertebrate viruses were detected in the maternal but not infant virome. As infants aged, the phage component evolved to resemble the maternal virome, but by age 3, the human-host component remained dissimilar from the maternal virome. Thus, early life virome development is determined predominantly by dietary, infectious, and environmental factors rather than direct maternal acquisition.
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Affiliation(s)
- William A Walters
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Catherine Ley
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yale Santos
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Thomas Haggerty
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Julie Parsonnet
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA; Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
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12
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Clasen SJ, Bell MEW, Borbón A, Lee DH, Henseler ZM, de la Cuesta-Zuluaga J, Parys K, Zou J, Wang Y, Altmannova V, Youngblut ND, Weir JR, Gewirtz AT, Belkhadir Y, Ley RE. Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. Sci Immunol 2023; 8:eabq7001. [PMID: 36608151 DOI: 10.1126/sciimmunol.abq7001] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Flagellin, the protein subunit of the bacterial flagellum, stimulates the innate immune receptor Toll-like receptor 5 (TLR5) after pattern recognition or evades TLR5 through lack of recognition. This binary response fails to explain the weak agonism of flagellins from commensal bacteria, raising the question of how TLR5 response is tuned. Here, we screened abundant flagellins present in metagenomes from human gut for both TLR5 recognition and activation and uncovered a class of flagellin-TLR5 interaction termed silent recognition. Silent flagellins were weak TLR5 agonists despite pattern recognition. Receptor activity was tuned by a TLR5-flagellin interaction distal to the site of pattern recognition that was present in Salmonella flagellin but absent in silent flagellins. This interaction enabled flagellin binding to preformed TLR5 dimers and increased TLR5 signaling by several orders of magnitude. Silent recognition by TLR5 occurred in human organoids and mice, and silent flagellin proteins were present in human stool. These flagellins were produced primarily by the abundant gut bacteria Lachnospiraceae and were enriched in nonindustrialized populations. Our findings provide a mechanism for the innate immune system to tolerate commensal-derived flagellins while remaining vigilant to the presence of flagellins produced by pathogens.
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Affiliation(s)
- Sara J Clasen
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Michael E W Bell
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Andrea Borbón
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Du-Hwa Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Zachariah M Henseler
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | | | - Katarzyna Parys
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Jun Zou
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Yanling Wang
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Veronika Altmannova
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, Tübingen 72076, Germany
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - John R Weir
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, Tübingen 72076, Germany
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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13
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Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 2023; 613:639-649. [PMID: 36697862 DOI: 10.1038/s41586-022-05546-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/09/2022] [Indexed: 01/26/2023]
Abstract
Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.
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Affiliation(s)
- Katherine M Kennedy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Marcus C de Goffau
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- Wellcome Sanger Institute, Cambridge, UK
| | - Maria Elisa Perez-Muñoz
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Marie-Claire Arrieta
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thorsten Braun
- Department of Obstetrics and Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frederic D Bushman
- Department of Microbiology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joel Dore
- Université Paris-Saclay, INRAE, MetaGenoPolis, AgroParisTech, MICALIS, Jouy-en-Josas, France
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA
- UC Davis Genome Center, University of California, Davis, Davis, CA, USA
| | - Michal A Elovitz
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephanie C Ganal-Vonarburg
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michael G Gänzle
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, MA, USA
- Department of Medicine and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lindsay J Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Chair of Intestinal Microbiome, ZIEL-Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Curtis Huttenhower
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liza Konnikova
- Departments of Pediatrics and Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Andrew J Macpherson
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ruth C Massey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Hannover Braunschweig site, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Trevor D Lawley
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Liam O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jeroen Raes
- VIB Center for Microbiology, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eran Segal
- Weizmann Institute of Science, Rehovot, Israel
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
- European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Deborah M Sloboda
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, Ontario, Canada
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Harry Sokol
- Gastroenterology Department, AP-HP, Saint Antoine Hospital, Centre de Recherche Saint-Antoine, CRSA, INSERM and Sorbonne Université, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Moran Yassour
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jens Walter
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
- Department of Medicine, University College Cork, Cork, Ireland.
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14
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Suzuki TA, Fitzstevens JL, Schmidt VT, Enav H, Huus KE, Ngwese MM, Grießhammer A, Pfleiderer A, Adegbite BR, Zinsou JF, Esen M, Velavan TP, Adegnika AA, Song LH, Spector TD, Muehlbauer AL, Marchi N, Kang H, Maier L, Blekhman R, Ségurel L, Ko G, Youngblut ND, Kremsner P, Ley RE. Codiversification of gut microbiota with humans. Science 2022; 377:1328-1332. [PMID: 36108023 PMCID: PMC10777373 DOI: 10.1126/science.abm7759] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.
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Affiliation(s)
- Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - J. Liam Fitzstevens
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Victor T. Schmidt
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Kelsey E. Huus
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Mirabeau Mbong Ngwese
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Anne Grießhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Anne Pfleiderer
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Bayode R. Adegbite
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Jeannot F. Zinsou
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Meral Esen
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Thirumalaisamy P. Velavan
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Vietnamese German Center for Medical Research, Hanoi, Vietnam
| | - Ayola A. Adegnika
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research, Tübingen, Germany
- Fondation pour la Recherche Scientifique, Cotonou, Bénin
| | - Le Huu Song
- Vietnamese German Center for Medical Research, Hanoi, Vietnam
- 108 Military Central Hospital, Hanoi, Vietnam
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Nina Marchi
- Eco-anthropologie, Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Hyena Kang
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Laure Ségurel
- Eco-anthropologie, Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Paris, France
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, Villeurbanne, France
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Peter Kremsner
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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15
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Abstract
At birth, neonates provide a vast habitat awaiting microbial colonization. Microbiome assembly is a complex process involving microbial seeding and succession driven by ecological forces and subject to environmental conditions. These successional events not only significantly affect the ecology and function of the microbiome, but also impact host health. While the establishment of the infant microbiome has been a point of interest for decades, an integrated view focusing on strain level colonization has been lacking until recently. Technological and computational advancements enabling strain-level analyses of the infant microbiome have demonstrated the immense complexity of this system and allowed for an improved understanding of how strains of the same species spread, colonize, evolve, and affect the host. Here, we review the current knowledge of the establishment and maturation of the infant gut microbiome with particular emphasis on newer discoveries achieved through strain-centric analyses.
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Affiliation(s)
- Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
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16
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Chassaing B, Compher C, Bonhomme B, Liu Q, Tian Y, Walters W, Nessel L, Delaroque C, Hao F, Gershuni V, Chau L, Ni J, Bewtra M, Albenberg L, Bretin A, McKeever L, Ley RE, Patterson AD, Wu GD, Gewirtz AT, Lewis JD. Randomized Controlled-Feeding Study of Dietary Emulsifier Carboxymethylcellulose Reveals Detrimental Impacts on the Gut Microbiota and Metabolome. Gastroenterology 2022; 162:743-756. [PMID: 34774538 PMCID: PMC9639366 DOI: 10.1053/j.gastro.2021.11.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Epidemiologic and murine studies suggest that dietary emulsifiers promote development of diseases associated with microbiota dysbiosis. Although the detrimental impact of these compounds on the intestinal microbiota and intestinal health have been demonstrated in animal and in vitro models, impact of these food additives in healthy humans remains poorly characterized. METHODS To examine this notion in humans, we performed a double-blind controlled-feeding study of the ubiquitous synthetic emulsifier carboxymethylcellulose (CMC) in which healthy adults consumed only emulsifier-free diets (n = 9) or an identical diet enriched with 15 g per day of CMC (n = 7) for 11 days. RESULTS Relative to control subjects, CMC consumption modestly increased postprandial abdominal discomfort and perturbed gut microbiota composition in a way that reduced its diversity. Moreover, CMC-fed subjects exhibited changes in the fecal metabolome, particularly reductions in short-chain fatty acids and free amino acids. Furthermore, we identified 2 subjects consuming CMC who exhibited increased microbiota encroachment into the normally sterile inner mucus layer, a central feature of gut inflammation, as well as stark alterations in microbiota composition. CONCLUSIONS These results support the notion that the broad use of CMC in processed foods may be contributing to increased prevalence of an array of chronic inflammatory diseases by altering the gut microbiome and metabolome (ClinicalTrials.gov, number NCT03440229).
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Affiliation(s)
- Benoit Chassaing
- INSERM U1016, team "Mucosal microbiota in chronic inflammatory diseases,'' CNRS UMR 8104, Université de Paris, Paris, France.
| | - Charlene Compher
- School of Nursing, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Brittaney Bonhomme
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Qing Liu
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Yuan Tian
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Lisa Nessel
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Clara Delaroque
- INSERM U1016, team “Mucosal microbiota in chronic inflammatory diseases,” CNRS UMR 8104, Université de Paris, Paris, France
| | - Fuhua Hao
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Victoria Gershuni
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lillian Chau
- Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Josephine Ni
- Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Meenakshi Bewtra
- Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lindsey Albenberg
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alexis Bretin
- Institute for Biomedical Sciences, Center for Inflammation, Immunity and Infection, Digestive Disease Research Group, Georgia State University, Atlanta, Georgia
| | - Liam McKeever
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andrew D. Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Gary D. Wu
- Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew T. Gewirtz
- Institute for Biomedical Sciences, Center for Inflammation, Immunity and Infection, Digestive Disease Research Group, Georgia State University, Atlanta, Georgia
| | - James D. Lewis
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,Division of Gastroenterology and Hepatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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17
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Marsh JW, Ley RE. Microbiome engineering: Taming the untractable. Cell 2022; 185:416-418. [DOI: 10.1016/j.cell.2021.12.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/30/2022]
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18
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Youngblut ND, de la Cuesta-Zuluaga J, Ley RE. Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes. Environ Microbiol 2022; 24:3966-3984. [PMID: 35049120 DOI: 10.1111/1462-2920.15910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/15/2022] [Indexed: 11/29/2022]
Abstract
Tree-based diversity measures incorporate phylogenetic or functional relatedness into comparisons of microbial communities. This can improve the identification of explanatory factors compared to tree-agnostic diversity measures. However, applying tree-based diversity measures to metagenome data is more challenging than for single-locus sequencing (e.g., 16S rRNA gene). Utilizing the Genome Taxonomy Database (GTDB) for species-level metagenome profiling allows for functional diversity measures based on genomic content or traits inferred from it. Still, it is unclear how metagenome-based assessments of microbiome diversity benefit from incorporating phylogeny or function into measures of diversity. We assessed this by measuring phylogeny-based, function-based, and tree-agnostic diversity measures from a large, global collection of human gut metagenomes composed of 30 studies and 2943 samples. We found tree-based measures to explain phenotypic variation (e.g., westernization, disease status, and gender) better or equivalent to tree-agnostic measures. Ecophylogenetic and functional diversity measures provided unique insight into how microbiome diversity was partitioned by phenotype. Tree-based measures greatly improved machine learning model performance for predicting westernization, disease status, and gender, relative to models trained solely on tree-agnostic measures. Our findings illustrate the usefulness of tree- and function-based measures for metagenomic assessments of microbial diversity, which is a fundamental component of microbiome science. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Jacobo de la Cuesta-Zuluaga
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
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19
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Di Rienzi SC, Johnson EL, Waters JL, Kennedy EA, Jacobson J, Lawrence P, Wang DH, Worgall TS, Brenna JT, Ley RE. The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil. J Nutr Biochem 2021; 97:108808. [PMID: 34186211 PMCID: PMC8585862 DOI: 10.1016/j.jnutbio.2021.108808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
Studies in mice using germfree animals as controls for microbial colonization have shown that the gut microbiome mediates diet-induced obesity. Such studies use diets rich in saturated fat, however, Western diets in the United States America are enriched in soybean oil, composed of unsaturated fatty acids, either linoleic or oleic acid. Here, we addressed whether the microbiome is a variable in fat metabolism in mice on a soybean oil diet. We used conventionally-raised, low-germ, and germfree mice fed for 10 weeks diets either high or low in high-linoleic-acid soybean oil as the sole source of fat. Conventional and germfree mice gained relative fat weight and all mice consumed more calories on the high fat vs. low fat soybean oil diet. Plasma fatty acid levels were generally dependent on diet, with microbial colonization status affecting iso-C18:0, C20:3n-6, C14:0, and C15:0 levels. Colonization status, but not diet, impacted levels of liver sphingolipids including ceramides, sphingomyelins, and sphinganine. Our results confirm that absorbed fatty acids are mainly a reflection of the diet and that microbial colonization influences liver sphingolipid pools regardless of diet.
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Affiliation(s)
- Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | | | - Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elizabeth A Kennedy
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Juliet Jacobson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Peter Lawrence
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Dong Hao Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Tilla S Worgall
- Department of Pathology and Cell Biology and Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - J Thomas Brenna
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA; Dell Pediatric Research Institute, Dell Medical School, University of Texas at Austin, Austin, Texas, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA; Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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20
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Youngblut ND, Reischer GH, Dauser S, Maisch S, Walzer C, Stalder G, Farnleitner AH, Ley RE. Vertebrate host phylogeny influences gut archaeal diversity. Nat Microbiol 2021; 6:1443-1454. [PMID: 34702978 PMCID: PMC8556154 DOI: 10.1038/s41564-021-00980-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 09/16/2021] [Indexed: 01/04/2023]
Abstract
Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea-host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea-Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea-vertebrate associations.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Vienna, Austria.,ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria
| | - Silke Dauser
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sophie Maisch
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Chris Walzer
- Wildlife Conservation Society, Bronx, NY, USA.,Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Andreas H Farnleitner
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Vienna, Austria.,ICC Interuniversity Cooperation Centre Water & Health, Vienna, Austria.,Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, Krems an der Donau, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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21
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Abstract
The intestinal microbiome influences host health, and its responsiveness to diet and disease is increasingly well studied. However, our understanding of the factors driving microbiome variation remain limited. Temperature is a core factor that controls microbial growth, but its impact on the microbiome remains to be fully explored. Although commonly assumed to be a constant 37°C, normal body temperatures vary across the animal kingdom, while individual body temperature is affected by multiple factors, including circadian rhythm, age, environmental temperature stress, and immune activation. Changes in body temperature via hypo- and hyperthermia have been shown to influence the gut microbiota in a variety of animals, with consistent effects on community diversity and stability. It is known that temperature directly modulates the growth and virulence of gastrointestinal pathogens; however, the effect of temperature on gut commensals is not well studied. Further, body temperature can influence other host factors, such as appetite and immunity, with indirect effects on the microbiome. In this minireview, we discuss the evidence linking body temperature and the intestinal microbiome and their implications for microbiome function during hypothermia, heat stress, and fever.
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Affiliation(s)
- Kelsey E. Huus
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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22
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Youngblut ND, Ley RE. Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets. PeerJ 2021; 9:e12198. [PMID: 34616633 PMCID: PMC8450008 DOI: 10.7717/peerj.12198] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/31/2021] [Indexed: 11/20/2022] Open
Abstract
Mapping metagenome reads to reference databases is the standard approach for assessing microbial taxonomic and functional diversity from metagenomic data. However, public reference databases often lack recently generated genomic data such as metagenome-assembled genomes (MAGs), which can limit the sensitivity of read-mapping approaches. We previously developed the Struo pipeline in order to provide a straight-forward method for constructing custom databases; however, the pipeline does not scale well enough to cope with the ever-increasing number of publicly available microbial genomes. Moreover, the pipeline does not allow for efficient database updating as new data are generated. To address these issues, we developed Struo2, which is >3.5 fold faster than Struo at database generation and can also efficiently update existing databases. We also provide custom Kraken2, Bracken, and HUMAnN3 databases that can be easily updated with new genomes and/or individual gene sequences. Efficient database updating, coupled with our pre-generated databases, enables “assembly-enhanced” profiling, which increases database comprehensiveness via inclusion of native genomic content. Inclusion of newly generated genomic content can greatly increase database comprehensiveness, especially for understudied biomes, which will enable more accurate assessments of microbiome diversity.
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Affiliation(s)
- Nicholas D Youngblut
- Microbiome Science, Max Planck Institute for Developmental Biology, Tuebingen, Baden Wurttemberg, Germany
| | - Ruth E Ley
- Microbiome Science, Max Planck Institute for Developmental Biology, Tuebingen, Baden Wurttemberg, Germany
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23
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Liu X, Sutter JL, de la Cuesta-Zuluaga J, Waters JL, Youngblut ND, Ley RE. Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis. Int J Syst Evol Microbiol 2021; 71:004774. [PMID: 33881979 PMCID: PMC8289216 DOI: 10.1099/ijsem.0.004774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/08/2021] [Indexed: 12/12/2022] Open
Abstract
The genera Catabacter (family 'Catabacteraceae') and Christensenella (family Christensenellaceae) are close relatives within the phylum Firmicutes. Members of these genera are strictly anaerobic, non-spore-forming and short straight rods with diverse phenotypes. Phylogenetic analysis of 16S rRNA genes suggest that Catabacter splits Christensenella into a polyphyletic clade. In an effort to ensure that family/genus names represent monophyletic clades, we performed a whole-genome based analysis of the genomes available for the cultured representatives of these genera: four species of Christensenella and two strains of Catabacter hongkongensis. A concatenated alignment of 135 shared protein sequences of single-copy core genes present in the included strains indicates that C. hongkongensis is indeed nested within the Christensenella clade. Based on their evolutionary relationship, we propose the transfer of Catabacter hongkongensis to the genus Christensenella as Christensenella hongkongensis comb. nov.
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Affiliation(s)
- Xiaoying Liu
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Jessica L. Sutter
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Jacobo de la Cuesta-Zuluaga
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Jillian L. Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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24
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Abstract
As human populations spread across the world, they adapted genetically to local conditions. So too did the resident microorganism communities that everyone carries with them. However, the collective influence of the diverse and dynamic community of resident microbes on host evolution is poorly understood. The taxonomic composition of the microbiota varies among individuals and displays a range of sometimes redundant functions that modify the physicochemical environment of the host and may alter selection pressures. Here we review known human traits and genes for which the microbiota may have contributed or responded to changes in host diet, climate, or pathogen exposure. Integrating host–microbiota interactions in human adaptation could offer new approaches to improve our understanding of human health and evolution.
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Affiliation(s)
- Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
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25
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Mineeva O, Rojas-Carulla M, Ley RE, Schölkopf B, Youngblut ND. DeepMAsED: evaluating the quality of metagenomic assemblies. Bioinformatics 2020; 36:3011-3017. [PMID: 32096824 DOI: 10.1093/bioinformatics/btaa124] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/19/2020] [Accepted: 02/18/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Methodological advances in metagenome assembly are rapidly increasing in the number of published metagenome assemblies. However, identifying misassemblies is challenging due to a lack of closely related reference genomes that can act as pseudo ground truth. Existing reference-free methods are no longer maintained, can make strong assumptions that may not hold across a diversity of research projects, and have not been validated on large-scale metagenome assemblies. RESULTS We present DeepMAsED, a deep learning approach for identifying misassembled contigs without the need for reference genomes. Moreover, we provide an in silico pipeline for generating large-scale, realistic metagenome assemblies for comprehensive model training and testing. DeepMAsED accuracy substantially exceeds the state-of-the-art when applied to large and complex metagenome assemblies. Our model estimates a 1% contig misassembly rate in two recent large-scale metagenome assembly publications. CONCLUSIONS DeepMAsED accurately identifies misassemblies in metagenome-assembled contigs from a broad diversity of bacteria and archaea without the need for reference genomes or strong modeling assumptions. Running DeepMAsED is straight-forward, as well as is model re-training with our dataset generation pipeline. Therefore, DeepMAsED is a flexible misassembly classifier that can be applied to a wide range of metagenome assembly projects. AVAILABILITY AND IMPLEMENTATION DeepMAsED is available from GitHub at https://github.com/leylabmpi/DeepMAsED. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Olga Mineeva
- Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen 72076, Germany.,Department of Computer Science, ETH Zürich, Zürich 8092, Switzerland
| | - Mateo Rojas-Carulla
- Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen 72076, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Bernhard Schölkopf
- Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Tübingen 72076, Germany
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
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26
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de la Cuesta-Zuluaga J, Ley RE, Youngblut ND. Struo: a pipeline for building custom databases for common metagenome profilers. Bioinformatics 2020; 36:2314-2315. [PMID: 31778148 DOI: 10.1093/bioinformatics/btz899] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/18/2019] [Accepted: 11/26/2019] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Taxonomic and functional information from microbial communities can be efficiently obtained by metagenome profiling, which requires databases of genes and genomes to which sequence reads are mapped. However, the databases that accompany metagenome profilers are not updated at a pace that matches the increase in available microbial genomes, and unifying database content across metagenome profiling tools can be cumbersome. To address this, we developed Struo, a modular pipeline that automatizes the acquisition of genomes from public repositories and the construction of custom databases for multiple metagenome profilers. The use of custom databases that broadly represent the known microbial diversity by incorporating novel genomes results in a substantial increase in mappability of reads in synthetic and real metagenome datasets. AVAILABILITY AND IMPLEMENTATION Source code available for download at https://github.com/leylabmpi/Struo. Custom genome taxonomy database databases available at http://ftp.tue.mpg.de/ebio/projects/struo/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ruth E Ley
- Department of Microbiome Science. Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Nicholas D Youngblut
- Department of Microbiome Science. Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
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Walters WA, Reyes F, Soto GM, Reynolds ND, Fraser JA, Aviles R, Tribble DR, Irvin AP, Kelley-Loughnane N, Gutierrez RL, Riddle MS, Ley RE, Goodson MS, Simons MP. Epidemiology and associated microbiota changes in deployed military personnel at high risk of traveler's diarrhea. PLoS One 2020; 15:e0236703. [PMID: 32785284 PMCID: PMC7423091 DOI: 10.1371/journal.pone.0236703] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
Travelers’ diarrhea (TD) is the most prevalent illness encountered by deployed military personnel and has a major impact on military operations, from reduced job performance to lost duty days. Frequently, the etiology of TD is unknown and, with underreporting of cases, it is difficult to accurately assess its impact. An increasing number of ailments include an altered or aberrant gut microbiome. To better understand the relationships between long-term deployments and TD, we studied military personnel during two nine-month deployment cycles in 2015–2016 to Honduras. To collect data on the prevalence of diarrhea and impact on duty, a total of 1173 personnel completed questionnaires at the end of their deployment. 56.7% reported reduced performance and 21.1% reported lost duty days. We conducted a passive surveillance study of all cases of diarrhea reporting to the medical unit with 152 total cases and a similar pattern of etiology. Enteroaggregative E. coli (EAEC, 52/152), enterotoxigenic E. coli (ETEC, 50/152), and enteropathogenic E. coli (EPEC, 35/152) were the most prevalent pathogens detected. An active longitudinal surveillance of 67 subjects also identified diarrheagenic E. coli as the primary etiology (7/16 EPEC, 7/16 EAEC, and 6/16 ETEC). Eleven subjects were recruited into a nested longitudinal substudy to examine gut microbiome changes associated with deployment. A 16S rRNA amplicon survey of fecal samples showed differentially abundant baseline taxa for subjects who contracted TD versus those who did not, as well as detection of taxa positively associated with self-reported gastrointestinal distress. Disrupted microbiota was also qualitatively observable for weeks preceding and following the incidents of TD. These findings illustrate the complex etiology of diarrhea amongst military personnel in deployed settings and its impacts on job performance. Potential factors of resistance or susceptibility can provide a foundation for future clinical trials to evaluate prevention and treatment strategies.
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Affiliation(s)
| | | | - Giselle M. Soto
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6),Callao, Lima, Peru
| | - Nathanael D. Reynolds
- Infectious Diseases Directorate, U.S. Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Jamie A. Fraser
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States of America
| | | | - David R. Tribble
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Adam P. Irvin
- 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, OH, United States of America
| | - Nancy Kelley-Loughnane
- 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, OH, United States of America
| | - Ramiro L. Gutierrez
- Infectious Diseases Directorate, U.S. Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Mark S. Riddle
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Ruth E. Ley
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Michael S. Goodson
- 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, OH, United States of America
- * E-mail:
| | - Mark P. Simons
- Infectious Diseases Directorate, U.S. Naval Medical Research Center, Silver Spring, MD, United States of America
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Johnson EL, Heaver SL, Waters JL, Kim BI, Bretin A, Goodman AL, Gewirtz AT, Worgall TS, Ley RE. Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels. Nat Commun 2020; 11:2471. [PMID: 32424203 PMCID: PMC7235224 DOI: 10.1038/s41467-020-16274-w] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
Gut microbes are linked to host metabolism, but specific mechanisms remain to be uncovered. Ceramides, a type of sphingolipid (SL), have been implicated in the development of a range of metabolic disorders from insulin resistance (IR) to hepatic steatosis. SLs are obtained from the diet and generated by de novo synthesis in mammalian tissues. Another potential, but unexplored, source of mammalian SLs is production by Bacteroidetes, the dominant phylum of the gut microbiome. Genomes of Bacteroides spp. and their relatives encode serine palmitoyltransfease (SPT), allowing them to produce SLs. Here, we explore the contribution of SL-production by gut Bacteroides to host SL homeostasis. In human cell culture, bacterial SLs are processed by host SL-metabolic pathways. In mouse models, Bacteroides-derived lipids transfer to host epithelial tissue and the hepatic portal vein. Administration of B. thetaiotaomicron to mice, but not an SPT-deficient strain, reduces de novo SL production and increases liver ceramides. These results indicate that gut-derived bacterial SLs affect host lipid metabolism.
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Affiliation(s)
- Elizabeth L Johnson
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Stacey L Heaver
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Benjamin I Kim
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Alexis Bretin
- Center for Inflammation, Immunity, and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, 30303, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity, and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, 30303, USA
| | - Tilla S Worgall
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.
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Abstract
Iron is essential for both the host and its resident microbes, resulting in competition under iron-deficient conditions. However, the molecular details underlying this competition are not fully understood. In this issue, Das et al. (2019) describe how a common gut commensal disrupts the host iron regulatory pathway to prevent uptake when iron is scarce.
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Affiliation(s)
- Sara J Clasen
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
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Tran HQ, Ley RE, Gewirtz AT, Chassaing B. Flagellin-elicited adaptive immunity suppresses flagellated microbiota and vaccinates against chronic inflammatory diseases. Nat Commun 2019; 10:5650. [PMID: 31827095 PMCID: PMC6906489 DOI: 10.1038/s41467-019-13538-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/05/2019] [Indexed: 12/22/2022] Open
Abstract
Alterations in gut microbiota composition are associated with metabolic syndrome and chronic inflammatory diseases such as inflammatory bowel disease. One feature of inflammation-associated gut microbiotas is enrichment of motile bacteria, which can facilitate microbiota encroachment into the mucosa and activate pro-inflammatory gene expression. Here, we set out to investigate whether elicitation of mucosal anti-flagellin antibodies by direct administration of purified flagellin might serve as a general vaccine against subsequent development of chronic gut inflammation. We show, in mice, that repeated injection of flagellin elicits increases in fecal anti-flagellin IgA and alterations in microbiota composition, reduces fecal flagellin concentration, prevents microbiota encroachment, protects against IL-10 deficiency-induced colitis, and ameliorates diet-induced obesity. Flagellin's impact on the microbiota is B-lymphocyte dependent and, in humans, obese subjects exhibit increased levels of fecal flagellin and reduced levels of fecal flagellin-specific IgA, relative to normal weight subjects. Thus, administration of flagellin, and perhaps other pathobiont antigens, may confer some protection against chronic inflammatory diseases.
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Affiliation(s)
- Hao Q Tran
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Benoit Chassaing
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
- Neuroscience Institute, Georgia State University, Atlanta, GA, USA.
- INSERM, U1016, team "Mucosal microbiota in chronic inflammatory diseases", Paris, France.
- Université de Paris, Paris, France.
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Janzon A, Goodrich JK, Koren O, Waters JL, Ley RE. Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut. mSystems 2019; 4:e00612-19. [PMID: 31771976 PMCID: PMC6880043 DOI: 10.1128/msystems.00612-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Interactions between the gut microbiome and immunoglobulin A (IgA) in the gut during infancy are important for future health. IgM and IgG are also present in the gut; however, their interactions with the microbiome in the developing infant remain to be characterized. Using stool samples sampled 15 times in infancy from 32 healthy subjects at 4 locations in 3 countries, we characterized patterns of microbiome development in relation to fecal levels of IgA, IgG, and IgM. For 8 infants from a single location, we used fluorescence-activated cell sorting of microbial cells from stool by Ig-coating status over 18 months. We used 16S rRNA gene profiling on full and sorted microbiomes to assess patterns of antibody coating in relation to age and other factors. All antibodies decreased in concentration with age but were augmented by breastmilk feeding regardless of infant age. Levels of IgA correlated with relative abundances of operational taxonomic units (OTUs) belonging to the Bifidobacteria and Enterobacteriaceae, which dominated the early microbiome, and IgG levels correlated with Haemophilus The diversity of Ig-coated microbiota was influenced by breastfeeding and age. IgA and IgM coated the same microbiota, which reflected the overall diversity of the microbiome, while IgG targeted a different subset. Blautia generally evaded antibody coating, while members of the Bifidobacteria and Enterobacteriaceae were high in IgA/M. IgA/M displayed similar dynamics, generally coating the microbiome proportionally, and were influenced by breastfeeding status. IgG only coated a small fraction of the commensal microbiota and differed from the proportion targeted by IgA and IgM.IMPORTANCE Antibodies are secreted into the gut and attach to roughly half of the trillions of bacterial cells present. When babies are born, the breastmilk supplies these antibodies until the baby's own immune system takes over this task after a few weeks. The vast majority of these antibodies are IgA, but two other types, IgG and IgM, are also present in the gut. Here, we ask if these three different antibody types target different types of bacteria in the infant gut as the infant develops from birth to 18 months old and how patterns of antibody coating of bacteria change with age. In this study of healthy infant samples over time, we found that IgA and IgM coat the same bacteria, which are generally representative of the diversity present, with a few exceptions that were more or less antibody coated than expected. IgG coated a separate suite of bacteria. These results provide a better understanding of how these antibodies interact with the developing infant gut microbiome.
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Affiliation(s)
- Anders Janzon
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Julia K Goodrich
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Omry Koren
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Poole AC, Goodrich JK, Youngblut ND, Luque GG, Ruaud A, Sutter JL, Waters JL, Shi Q, El-Hadidi M, Johnson LM, Bar HY, Huson DH, Booth JG, Ley RE. Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes. Cell Host Microbe 2019; 25:553-564.e7. [PMID: 30974084 DOI: 10.1016/j.chom.2019.03.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/10/2018] [Accepted: 03/01/2019] [Indexed: 12/20/2022]
Abstract
Host genetic variation influences microbiome composition. While studies have focused on associations between the gut microbiome and specific alleles, gene copy number (CN) also varies. We relate microbiome diversity to CN variation of the AMY1 locus, which encodes salivary amylase, facilitating starch digestion. After imputing AMY1-CN for ∼1,000 subjects, we identified taxa differentiating fecal microbiomes of high and low AMY1-CN hosts. In a month-long diet intervention study, we show that diet standardization drove gut microbiome convergence, and AMY1-CN correlated with oral and gut microbiome composition and function. The microbiomes of low-AMY1-CN subjects had enhanced capacity to break down complex carbohydrates. High-AMY1-CN subjects had higher levels of salivary Porphyromonas; their gut microbiota had increased abundance of resistant starch-degrading microbes, produced higher levels of short-chain fatty acids, and drove higher adiposity when transferred to germ-free mice. This study establishes AMY1-CN as a genetic factor associated with microbiome composition and function.
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Affiliation(s)
- Angela C Poole
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Julia K Goodrich
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Guillermo G Luque
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Albane Ruaud
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Jessica L Sutter
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Qiaojuan Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Mohamed El-Hadidi
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Lynn M Johnson
- Cornell Statistical Consulting Unit, Cornell University, Ithaca, NY 14853, USA
| | - Haim Y Bar
- Department of Statistics, University of Connecticut, Storrs, CT 06269, USA
| | - Daniel H Huson
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - James G Booth
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Waters JL, Ley RE. The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health. BMC Biol 2019; 17:83. [PMID: 31660948 PMCID: PMC6819567 DOI: 10.1186/s12915-019-0699-4] [Citation(s) in RCA: 335] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022] Open
Abstract
The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date. The family is also related to a healthy status in a number of other different disease contexts, including obesity and inflammatory bowel disease. In addition, Christensenellaceae is highly heritable across multiple populations, although specific human genes underlying its heritability have so far been elusive. Further research into the microbial ecology and metabolism of these bacteria should reveal mechanistic underpinnings of their host-health associations and enable their development as therapeutics.
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Affiliation(s)
- Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tuebingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tuebingen, Germany.
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Affiliation(s)
- Rob Knight
- Department of Pediatrics, University of California, Gilman Drive, La Jolla, San Diego, CA, 92093, USA. .,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, Gilman Drive, La Jolla, San Diego, CA, 92093-0436, USA. .,Department of Computer Science and Engineering, University of California, Gilman Drive, La Jolla, San Diego, CA, 92093-0404, USA. .,Department of Bioengineering, University of California, La Jolla, San Diego, CA, 92093-0412, USA.
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring, 72076, Tübingen, Germany
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat, 3000, Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Campus Gasthuisberg, Rega Instituut, Herestraat, 3000, Leuven, Belgium
| | - Elizabeth A Grice
- Department of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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de la Cuesta-Zuluaga J, Kelley ST, Chen Y, Escobar JS, Mueller NT, Ley RE, McDonald D, Huang S, Swafford AD, Knight R, Thackray VG. Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems 2019; 4:e00261-19. [PMID: 31098397 PMCID: PMC6517691 DOI: 10.1128/msystems.00261-19] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 11/22/2022] Open
Abstract
Gut microbial diversity changes throughout the human life span and is known to be associated with host sex. We investigated the association of age, sex, and gut bacterial alpha diversity in three large cohorts of adults from four geographical regions: subjects from the United States and United Kingdom in the American Gut Project (AGP) citizen-science initiative and two independent cohorts of Colombians and Chinese. In three of the four cohorts, we observed a strong positive association between age and alpha diversity in young adults that plateaued after age 40 years. We also found sex-dependent differences that were more pronounced in younger adults than in middle-aged adults, with women having higher alpha diversity than men. In contrast to the other three cohorts, no association of alpha diversity with age or sex was observed in the Chinese cohort. The association of alpha diversity with age and sex remained after adjusting for cardiometabolic parameters in the Colombian cohort and antibiotic usage in the AGP cohort. We further attempted to predict the microbiota age in individuals using a machine-learning approach for the men and women in each cohort. Consistent with our alpha-diversity-based findings, U.S. and U.K. women had a significantly higher predicted microbiota age than men, with a reduced difference being seen above age 40 years. This difference was not observed in the Colombian cohort and was observed only in middle-aged Chinese adults. Together, our results provide new insights into the influence of age and sex on the biodiversity of the human gut microbiota during adulthood while highlighting similarities and differences across diverse cohorts. IMPORTANCE Microorganisms in the human gut play a role in health and disease, and in adults higher gut biodiversity has been linked to better health. Since gut microorganisms may be pivotal in the development of microbial therapies, understanding the factors that shape gut biodiversity is of utmost interest. We performed large-scale analyses of the relationship of age and sex to gut bacterial diversity in adult cohorts from four geographic regions: the United States, the United Kingdom, Colombia, and China. In the U.S., U.K., and Colombian cohorts, bacterial biodiversity correlated positively with age in young adults but plateaued at about age 40 years, with no positive association being found in middle-aged adults. Young, but not middle-aged, adult women had higher gut bacterial diversity than men, a pattern confirmed via supervised machine learning. Interestingly, in the Chinese cohort, minimal associations were observed between gut biodiversity and age or sex. Our results highlight the patterns of adult gut biodiversity and provide a framework for future research.
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Affiliation(s)
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Yingfeng Chen
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Juan S. Escobar
- Vidarium—Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Noel T. Mueller
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Welch Center for Epidemiology, Prevention and Clinical Research, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Austin D. Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Varykina G. Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, California, USA
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Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE, Farnleitner AH. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nat Commun 2019; 10:2200. [PMID: 31097702 PMCID: PMC6522487 DOI: 10.1038/s41467-019-10191-3] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.
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Affiliation(s)
- Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany.
| | - Georg H Reischer
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, 1060, Vienna, Austria
- ICC Interuniversity Cooperation Centre Water & Health, 1160, Vienna, Austria
| | - William Walters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Nathalie Schuster
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, 1160, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, 1160, Austria
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076, Tübingen, Germany
| | - Andreas H Farnleitner
- TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, 1060, Vienna, Austria
- ICC Interuniversity Cooperation Centre Water & Health, 1160, Vienna, Austria
- Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, 3500, Krems an der Donau, Austria
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Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector TD, Bell JT, Youngblut ND, Hewson I, Reyes A, Ley RE. Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. Cell Host Microbe 2019; 25:261-272.e5. [PMID: 30763537 PMCID: PMC6411085 DOI: 10.1016/j.chom.2019.01.019] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/31/2018] [Accepted: 01/24/2019] [Indexed: 01/01/2023]
Abstract
The virome is one of the most variable components of the human gut microbiome. Within twin pairs, viromes have been shown to be similar for infants, but not for adults, indicating that as twins age and their environments and microbiomes diverge, so do their viromes. The degree to which the microbiome drives the vast virome diversity is unclear. Here, we examine the relationship between microbiome and virome diversity in 21 adult monozygotic twin pairs selected for high or low microbiome concordance. Viromes derived from virus-like particles are unique to each individual, are dominated by Caudovirales and Microviridae, and exhibit a small core that includes crAssphage. Microbiome-discordant twins display more dissimilar viromes compared to microbiome-concordant twins, and the richer the microbiomes, the richer the viromes. These patterns are driven by bacteriophages, not eukaryotic viruses. Collectively, these observations support a strong role of the microbiome in patterning for the virome.
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Affiliation(s)
- J Leonardo Moreno-Gallego
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Shao-Pei Chou
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sara C Di Rienzi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Julia K Goodrich
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Nicholas D Youngblut
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia; Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
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Alves da Silva AV, de Castro Oliveira SB, Di Rienzi SC, Brown-Steinke K, Dehan LM, Rood JK, Carreira VS, Le H, Maier EA, Betz KJ, Aihara E, Ley RE, Preidis GA, Shen L, Moore SR. Murine Methyl Donor Deficiency Impairs Early Growth in Association with Dysmorphic Small Intestinal Crypts and Reduced Gut Microbial Community Diversity. Curr Dev Nutr 2018. [PMCID: PMC6324351 DOI: 10.1093/cdn/nzy070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Folate and choline are essential methyl donor nutrients throughout the life span; however, the adverse effects of combined deficiency on early growth, intestinal epithelial morphology, and the gut microbiome remain only partially understood. Objectives We investigated the effects of dietary folate and choline deficiency on early growth, small intestinal (SI) epithelial architecture, and the gut microbiota of mice. To explore potential mechanisms for adverse effects on gut epithelial morphology, we also evaluated gene expression and DNA methylation in mouse intestinal epithelial organoids (enteroids) maintained in methyl donor–deficient (MDD) conditions. Methods Pregnant dams were administered 1 of 4 diets: 1) control diet (CD−), 2) an isocaloric MDD− diet, or 3) CD+ and 4) MDD+ formulations containing 1% succinylsulfathiazole to inhibit folate-producing gut bacteria. We weaned pups to their dams’ diet at 3 wk of age and monitored body weight and tail length pre- and postweaning. We measured serum folate, SI crypt morphology, and microbiota composition at 7 wk of age. Results Both MDD+ and MDD− diets impaired early ponderal and linear growth, lowered serum folate concentrations, and produced patchy areas of increased crypt depth throughout the SI. Succinylsulfathiazole increased crypt depth independently of diet. MDD or succinylsulfathiazole, alone or in combination, altered the gut microbiome, with decreased Bacteroidales and Clostridiales, increased Lactobacillales and Erysipelotrichaceae taxa, and decreased α-diversity indexes. Enteroids maintained in MDD media displayed dysmorphic crypt domains, altered expression of stem cell and secretory differentiation genes, and decreased DNA methylation of the glycosylation genes Beta-1,4-N-Acetyl-Galactosaminyltransferase-1 (B4galnt1) and Phosphoethanolamine/Phosphocholine-Phosphatase (Phospho1). Conclusion MDD impairs ponderal and linear growth in mice in association with dysmorphic SI crypts and reduced gut microbial diversity. In vitro methyl donor deficiency similarly induced dysmorphic crypts in mouse enteroids in conjunction with altered gene expression and DNA methylation.
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Affiliation(s)
- Antonio V Alves da Silva
- Instituto de Biomedicina, Universidade Federal do Ceará, Fortaleza, Brazil
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Stephanie B de Castro Oliveira
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sara C Di Rienzi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX
| | | | - Lauren M Dehan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Jill K Rood
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Hung Le
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Elizabeth A Maier
- Instituto de Biomedicina, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Kristina J Betz
- Instituto de Biomedicina, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Eitaro Aihara
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Geoffrey A Preidis
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine Houston, TX
| | - Lanlan Shen
- USDA Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Sean R Moore
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA
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Di Rienzi SC, Jacobson J, Kennedy EA, Bell ME, Shi Q, Waters JL, Lawrence P, Brenna JT, Britton RA, Walter J, Ley RE. Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids. eLife 2018; 7:e32581. [PMID: 29580380 PMCID: PMC5902164 DOI: 10.7554/elife.32581] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Over the past century, soybean oil (SBO) consumption in the United States increased dramatically. The main SBO fatty acid, linoleic acid (18:2), inhibits in vitro the growth of lactobacilli, beneficial members of the small intestinal microbiota. Human-associated lactobacilli have declined in prevalence in Western microbiomes, but how dietary changes may have impacted their ecology is unclear. Here, we compared the in vitro and in vivo effects of 18:2 on Lactobacillus reuteri and L. johnsonii. Directed evolution in vitro in both species led to strong 18:2 resistance with mutations in genes for lipid biosynthesis, acid stress, and the cell membrane or wall. Small-intestinal Lactobacillus populations in mice were unaffected by chronic and acute 18:2 exposure, yet harbored both 18:2- sensitive and resistant strains. This work shows that extant small intestinal lactobacilli are protected from toxic dietary components via the gut environment as well as their own capacity to evolve resistance.
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Affiliation(s)
- Sara C Di Rienzi
- Department of Microbiome ScienceMax Planck Institute for Developmental BiologyTübingenGermany
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Juliet Jacobson
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Elizabeth A Kennedy
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Mary E Bell
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Qiaojuan Shi
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Jillian L Waters
- Department of Microbiome ScienceMax Planck Institute for Developmental BiologyTübingenGermany
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
| | - Peter Lawrence
- Division of Nutritional SciencesCornell UniversityIthacaUnited States
| | - J Thomas Brenna
- Division of Nutritional SciencesCornell UniversityIthacaUnited States
- Dell Pediatric Research Institute, Dell Medical SchoolUniversity of Texas at AustinAustinUnited States
| | - Robert A Britton
- Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonUnited States
| | - Jens Walter
- Department of Agricultural, Food, and Nutritional ScienceUniversity of AlbertaEdmontonCanada
- Department of Biological SciencesUniversity of AlbertaEdmontonCanada
| | - Ruth E Ley
- Department of Microbiome ScienceMax Planck Institute for Developmental BiologyTübingenGermany
- Department of Molecular Biology and GeneticsCornell UniversityIthacaUnited States
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40
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Heaver SL, Johnson EL, Ley RE. Sphingolipids in host-microbial interactions. Curr Opin Microbiol 2018; 43:92-99. [PMID: 29328957 DOI: 10.1016/j.mib.2017.12.011] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 01/28/2023]
Abstract
Sphingolipids, a lipid class characterized by a long-chain amino alcohol backbone, serve vital structural and signaling roles in eukaryotes. Though eukaryotes produce sphingolipids, this capacity is phylogenetically highly restricted in Bacteria. Intriguingly, bacterial species commonly associated in high abundance with eukaryotic hosts include sphingolipid producers, such as the Bacteroidetes in the mammalian gut. To date, a role for bacterial sphingolipids in immune system maturation has been described, but their fate and impact in host physiology and metabolism remain to be elucidated. The structural conservation of bacterial sphingolipids with those produced by their mammalian hosts offer clues about which aspects of mammalian biology may be modulated by these intriguing lipids.
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Affiliation(s)
- Stacey L Heaver
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14580, USA
| | - Elizabeth L Johnson
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14580, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14580, USA.
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41
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Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, Wang K, Devescovi G, Stillman K, Monteiro F, Rangel Alvarez B, Lundberg DS, Lu TY, Lebeis S, Jin Z, McDonald M, Klein AP, Feltcher ME, Rio TG, Grant SR, Doty SL, Ley RE, Zhao B, Venturi V, Pelletier DA, Vorholt JA, Tringe SG, Woyke T, Dangl JL. Genomic features of bacterial adaptation to plants. Nat Genet 2017; 50:138-150. [PMID: 29255260 PMCID: PMC5957079 DOI: 10.1038/s41588-017-0012-9] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 11/10/2017] [Indexed: 01/10/2023]
Abstract
Plants intimately associate with diverse bacteria. Plant-associated (PA) bacteria have ostensibly evolved genes enabling adaptation to the plant environment. However, the identities of such genes are mostly unknown and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3837 bacterial genomes to identify thousands of PA gene clusters. Genomes of PA bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant associated genomes. We experimentally validated candidates from two sets of PA genes, one involved in plant colonization, the other serving in microbe-microbe competition between PA bacteria. We also identified 64 PA protein domains that potentially mimic plant domains; some are shared with PA fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides leads for efficient and sustainable agriculture through microbiome engineering.
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Affiliation(s)
- Asaf Levy
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Isai Salas Gonzalez
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Jiamin Miao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.,The Grassland College, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Kunru Wang
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA
| | - Giulia Devescovi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Freddy Monteiro
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Derek S Lundberg
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tse-Yuan Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sarah Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Zhao Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Meredith McDonald
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Andrew P Klein
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Meghan E Feltcher
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,BD Technologies and Innovation, Research Triangle Park, NC, USA
| | | | - Sarah R Grant
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Sharon L Doty
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA
| | - Ruth E Ley
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Susannah G Tringe
- DOE Joint Genome Institute, Walnut Creek, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, USA. .,Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
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Abstract
The body's microbiome, composed of microbial cells that number in the trillions, is involved in human health and disease in ways that are just starting to emerge. The microbiome is assembled at birth, develops with its host, and is greatly influenced by environmental factors such as diet and other exposures. Recently, a role for human genetic variation has emerged as also influential in accounting for interpersonal differences in microbiomes. Thus, human genes may influence health directly or by promoting a beneficial microbiome. Studies of the heritability of gut microbiotas reveal a subset of microbes whose abundances are partly genetically determined by the host. However, the use of genome-wide association studies (GWASs) to identify human genetic variants associated with microbiome phenotypes has proven challenging. Studies to date are small by GWAS standards, and cross-study comparisons are hampered by differences in analytical approaches. Nevertheless, associations between microbes or microbial genes and human genes have emerged that are consistent between human populations. Most notably, higher levels of beneficial gut bacteria called Bifidobacteria are associated with the human lactase nonpersister genotype, which typically confers lactose intolerance, in several different human populations. It is time for the microbiome to be incorporated into studies that quantify interactions among genotype, environment, and the microbiome in order to predict human disease susceptibility.
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Affiliation(s)
- Julia K Goodrich
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Emily R Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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43
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Guss JD, Horsfield MW, Fontenele FF, Sandoval TN, Luna M, Apoorva F, Lima SF, Bicalho RC, Singh A, Ley RE, van der Meulen MC, Goldring SR, Hernandez CJ. Alterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties. J Bone Miner Res 2017; 32:1343-1353. [PMID: 28244143 PMCID: PMC5466506 DOI: 10.1002/jbmr.3114] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/13/2017] [Accepted: 02/20/2017] [Indexed: 02/07/2023]
Abstract
Alterations in the gut microbiome have been associated with changes in bone mass and microstructure, but the effects of the microbiome on bone biomechanical properties are not known. Here we examined bone strength under two conditions of altered microbiota: (1) an inbred mouse strain known to develop an altered gut microbiome due to deficits in the immune system (the Toll-like receptor 5-deficient mouse [TLR5KO]); and (2) disruption of the gut microbiota (ΔMicrobiota) through chronic treatment with selected antibiotics (ampicillin and neomycin). The bone phenotypes of TLR5KO and WT (C57Bl/6) mice were examined after disruption of the microbiota from 4 weeks to 16 weeks of age as well as without treatment (n = 7 to 16/group, 39 animals total). Femur bending strength was less in ΔMicrobiota mice than in untreated animals and the reduction in strength was not fully explained by differences in bone cross-sectional geometry, implicating impaired bone tissue material properties. Small differences in whole-bone bending strength were observed between WT and TLR5KO mice after accounting for differences in bone morphology. No differences in trabecular bone volume fraction were associated with genotype or disruption of gut microbiota. Treatment altered the gut microbiota by depleting organisms from the phyla Bacteroidetes and enriching for Proteobacteria, as determined from sequencing of fecal 16S rRNA genes. Differences in splenic immune cell populations were also observed; B and T cell populations were depleted in TLR5KO mice and in ΔMicrobiota mice (p < 0.001), suggesting an association between alterations in bone tissue material properties and immune cell populations. We conclude that alterations in the gut microbiota for extended periods during growth may lead to impaired whole-bone mechanical properties in ways that are not explained by bone geometry. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Jason D Guss
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.,Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Michael W Horsfield
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA
| | - Fernanda F Fontenele
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA
| | - Taylor N Sandoval
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA
| | - Marysol Luna
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.,Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Fnu Apoorva
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA
| | - Svetlana F Lima
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Ankur Singh
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.,Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ruth E Ley
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Marjolein Ch van der Meulen
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.,Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.,Hospital for Special Surgery, New York, NY, USA
| | | | - Christopher J Hernandez
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.,Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.,Hospital for Special Surgery, New York, NY, USA
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44
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McGavigan AK, Garibay D, Henseler ZM, Chen J, Bettaieb A, Haj FG, Ley RE, Chouinard ML, Cummings BP. TGR5 contributes to glucoregulatory improvements after vertical sleeve gastrectomy in mice. Gut 2017; 66:226-234. [PMID: 26511794 PMCID: PMC5512436 DOI: 10.1136/gutjnl-2015-309871] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Vertical sleeve gastrectomy (VSG) produces high rates of type 2 diabetes remission; however, the mechanisms responsible remain incompletely defined. VSG increases circulating bile acid concentrations and bile acid signalling through TGR5 improves glucose homeostasis. Therefore, we investigated the role of TGR5 signalling in mediating the glucoregulatory benefits of VSG. DESIGN VSG or sham surgery was performed in high-fat-fed male Tgr5+/+ (wild type) and Tgr5-/- (knockout) littermates. Sham-operated mice were fed ad libitum or food restricted to match their body weight to VSG-operated mice. Body weight, food intake, energy expenditure, insulin signalling and circulating bile acid profiles were measured and oral glucose tolerance testing, islet immunohistochemistry and gut microbial profiling were performed. RESULTS VSG decreased food intake and body weight, increased energy expenditure and circulating bile acid concentrations, improved fasting glycaemia, glucose tolerance and glucose-stimulated insulin secretion, enhanced nutrient-stimulated glucagon-like peptide 1 secretion and produced favourable shifts in gut microbial populations in both genotypes. However, the body weight-independent improvements in fasting glycaemia, glucose tolerance, hepatic insulin signalling, hepatic inflammation and islet morphology after VSG were attenuated in Tgr5-/- relative to Tgr5+/+ mice. Furthermore, VSG produced metabolically favourable alterations in circulating bile acid profiles that were blunted in Tgr5-/- relative to Tgr5+/+ mice. TGR5-dependent regulation of hepatic Cyp8b1 expression may have contributed to TGR5-mediated shifts in the circulating bile acid pool after VSG. CONCLUSIONS These results suggest that TGR5 contributes to the glucoregulatory benefits of VSG surgery by promoting metabolically favourable shifts in the circulating bile acid pool.
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Affiliation(s)
- Anne K McGavigan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Darline Garibay
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Zachariah M Henseler
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Jack Chen
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ahmed Bettaieb
- Department of Nutrition, University of California, Davis, Davis, California, USA
| | - Fawaz G Haj
- Department of Nutrition, University of California, Davis, Davis, California, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Michael L Chouinard
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, USA
| | - Bethany P Cummings
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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45
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McGavigan AK, Henseler ZM, Garibay D, Butler SD, Jayasinghe S, Ley RE, Davisson RL, Cummings BP. Vertical sleeve gastrectomy reduces blood pressure and hypothalamic endoplasmic reticulum stress in mice. Dis Model Mech 2017; 10:235-243. [PMID: 28093508 PMCID: PMC5374323 DOI: 10.1242/dmm.027474] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/04/2017] [Indexed: 12/13/2022] Open
Abstract
Bariatric surgery, such as vertical sleeve gastrectomy (VSG), causes remarkable improvements in cardiometabolic health, including hypertension remission. However, the mechanisms responsible remain undefined and poorly studied. Therefore, we developed and validated the first murine model of VSG that recapitulates the blood pressure-lowering effect of VSG using gold-standard radiotelemetry technology. We used this model to investigate several potential mechanisms, including body mass, brain endoplasmic reticulum (ER) stress signaling and brain inflammatory signaling, which are all critical contributors to the pathogenesis of obesity-associated hypertension. Mice fed on a high-fat diet underwent sham or VSG surgery and radiotelemeter implantation. Sham mice were fed ad libitum or were food restricted to match their body mass to VSG-operated mice to determine the role of body mass in the ability of VSG to lower blood pressure. Blood pressure was then measured in freely moving unstressed mice by radiotelemetry. VSG decreased energy intake, body mass and fat mass. Mean arterial blood pressure (MAP) was reduced in VSG-operated mice compared with both sham-operated groups. VSG-induced reductions in MAP were accompanied by a body mass-independent decrease in hypothalamic ER stress, hypothalamic inflammation and sympathetic nervous system tone. Assessment of gut microbial populations revealed VSG-induced increases in the relative abundance of Gammaproteobacteria and Enterococcus, and decreases in Adlercreutzia. These results suggest that VSG reduces blood pressure, but this is only partly due to the reduction in body weight. VSG-induced reductions in blood pressure may be driven by a decrease in hypothalamic ER stress and inflammatory signaling, and shifts in gut microbial populations. Summary: Vertical sleeve gastrectomy in mice decreases blood pressure independent of body mass, which may be due to a decrease in hypothalamic ER stress.
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Affiliation(s)
- Anne K McGavigan
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Zachariah M Henseler
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.,Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Darline Garibay
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Scott D Butler
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Sisitha Jayasinghe
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.,Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Robin L Davisson
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.,Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Bethany P Cummings
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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46
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Bäckhed F, Ley RE, Sonnenburg JL, Gordon JI. The human intestinal microbiota and its relationship to energy balance. Scandinavian Journal of Food and Nutrition 2016. [DOI: 10.1080/17482970601066546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Fredrik Bäckhed
- Center for Genome SciencesSchool of Medicine, Washington UniversitySt LouisMissouriUSA
| | - Ruth E. Ley
- Center for Genome SciencesSchool of Medicine, Washington UniversitySt LouisMissouriUSA
| | - Justin L. Sonnenburg
- Center for Genome SciencesSchool of Medicine, Washington UniversitySt LouisMissouriUSA
| | - Jeffrey I. Gordon
- Center for Genome SciencesSchool of Medicine, Washington UniversitySt LouisMissouriUSA
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47
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Davenport ER, Goodrich JK, Bell JT, Spector TD, Ley RE, Clark AG. ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins. BMC Genomics 2016; 17:941. [PMID: 27871240 PMCID: PMC5117602 DOI: 10.1186/s12864-016-3290-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/15/2016] [Indexed: 12/30/2022] Open
Abstract
Background Host genetics is one of several factors known to shape human gut microbiome composition, however, the physiological processes underlying the heritability are largely unknown. Inter-individual differences in host factors secreted into the gut lumen may lead to variation in microbiome composition. One such factor is the ABO antigen. This molecule is not only expressed on the surface of red blood cells, but is also secreted from mucosal surfaces in individuals containing an intact FUT2 gene (secretors). Previous studies report differences in microbiome composition across ABO and secretor genotypes. However, due to methodological limitations, the specific bacterial taxa involved remain unknown. Results Here, we sought to determine the relationship of the microbiota to ABO blood group and secretor status in a large panel of 1503 individuals from a cohort of twins from the United Kingdom. Contrary to previous reports, robust associations between either ABO or secretor phenotypes and gut microbiome composition were not detected. Overall community structure, diversity, and the relative abundances of individual taxa were not significantly associated with ABO or secretor status. Additionally, joint-modeling approaches were unsuccessful in identifying combinations of taxa that were predictive of ABO or secretor status. Conclusions Despite previous reports, the taxonomic composition of the microbiota does not appear to be strongly associated with ABO or secretor status in 1503 individuals from the United Kingdom. These results highlight the importance of replicating microbiome-associated traits in large, well-powered cohorts to ensure results are robust. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3290-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emily R Davenport
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.
| | - Julia K Goodrich
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ruth E Ley
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.,Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübigen, Germany
| | - Andrew G Clark
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
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48
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Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD, Bell JT. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biol 2016; 17:189. [PMID: 27666579 PMCID: PMC5036307 DOI: 10.1186/s13059-016-1052-7] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/31/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Variation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-metabolic disease risk factor. Here, we explore links between the fecal microbiota and abdominal adiposity using body composition as measured by dual-energy X-ray absorptiometry in a large sample of twins from the TwinsUK cohort, comparing fecal 16S rRNA diversity profiles with six adiposity measures. RESULTS We profile six adiposity measures in 3666 twins and estimate their heritability, finding novel evidence for strong genetic effects underlying visceral fat and android/gynoid ratio. We confirm the association of lower diversity of the fecal microbiome with obesity and adiposity measures, and then compare the association between fecal microbial composition and the adiposity phenotypes in a discovery subsample of twins. We identify associations between the relative abundances of fecal microbial operational taxonomic units (OTUs) and abdominal adiposity measures. Most of these results involve visceral fat associations, with the strongest associations between visceral fat and Oscillospira members. Using BMI as a surrogate phenotype, we pursue replication in independent samples from three population-based cohorts including American Gut, Flemish Gut Flora Project and the extended TwinsUK cohort. Meta-analyses across the replication samples indicate that 8 OTUs replicate at a stringent threshold across all cohorts, while 49 OTUs achieve nominal significance in at least one replication sample. Heritability analysis of the adiposity-associated microbial OTUs prompted us to assess host genetic-microbe interactions at obesity-associated human candidate loci. We observe significant associations of adiposity-OTU abundances with host genetic variants in the FHIT, TDRG1 and ELAVL4 genes, suggesting a potential role for host genes to mediate the link between the fecal microbiome and obesity. CONCLUSIONS Our results provide novel insights into the role of the fecal microbiota in cardio-metabolic disease with clear potential for prevention and novel therapies.
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Affiliation(s)
- Michelle Beaumont
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Julia K Goodrich
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew A Jackson
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Idil Yet
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Emily R Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- VIB lab for Bioinformatics and (eco-)systems biology, Leuven, Belgium
| | - Justine Debelius
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Present address: Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tess Pallister
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK
| | - Jeroen Raes
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- VIB lab for Bioinformatics and (eco-)systems biology, Leuven, Belgium
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- Biofrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
- Howard Hughes Medical Institute, Boulder, CO, 80309, USA
- Present address: Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrew G Clark
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Ruth E Ley
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK.
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, 3rd Floor, South Wing, Block D, London, SE1 7EH, UK.
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49
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Affiliation(s)
- Ruth E Ley
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY (R.E.L.); the Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany (R.E.L.); and the Center for Inflammation Immunity and Infection, Georgia State University, Atlanta (A.T.G.)
| | - Andrew T Gewirtz
- From the Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY (R.E.L.); the Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany (R.E.L.); and the Center for Inflammation Immunity and Infection, Georgia State University, Atlanta (A.T.G.)
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50
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Giloteaux L, Goodrich JK, Walters WA, Levine SM, Ley RE, Hanson MR. Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome. Microbiome 2016; 4:30. [PMID: 27338587 PMCID: PMC4918027 DOI: 10.1186/s40168-016-0171-4] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/11/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Gastrointestinal disturbances are among symptoms commonly reported by individuals diagnosed with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). However, whether ME/CFS is associated with an altered microbiome has remained uncertain. Here, we profiled gut microbial diversity by sequencing 16S ribosomal ribonucleic acid (rRNA) genes from stool as well as inflammatory markers from serum for cases (n = 48) and controls (n = 39). We also examined a set of inflammatory markers in blood: C-reactive protein (CRP), intestinal fatty acid-binding protein (I-FABP), lipopolysaccharide (LPS), LPS-binding protein (LBP), and soluble CD14 (sCD14). RESULTS We observed elevated levels of some blood markers for microbial translocation in ME/CFS patients; levels of LPS, LBP, and sCD14 were elevated in ME/CFS subjects. Levels of LBP correlated with LPS and sCD14 and LPS levels correlated with sCD14. Through deep sequencing of bacterial rRNA markers, we identified differences between the gut microbiomes of healthy individuals and patients with ME/CFS. We observed that bacterial diversity was decreased in the ME/CFS specimens compared to controls, in particular, a reduction in the relative abundance and diversity of members belonging to the Firmicutes phylum. In the patient cohort, we find less diversity as well as increases in specific species often reported to be pro-inflammatory species and reduction in species frequently described as anti-inflammatory. Using a machine learning approach trained on the data obtained from 16S rRNA and inflammatory markers, individuals were classified correctly as ME/CFS with a cross-validation accuracy of 82.93 %. CONCLUSIONS Our results indicate dysbiosis of the gut microbiota in this disease and further suggest an increased incidence of microbial translocation, which may play a role in inflammatory symptoms in ME/CFS.
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Affiliation(s)
- Ludovic Giloteaux
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Julia K Goodrich
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - William A Walters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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