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Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T, Kehrmann J. Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices. Cell Rep Med 2024; 5:101426. [PMID: 38366600 PMCID: PMC10982974 DOI: 10.1016/j.xcrm.2024.101426] [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] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.
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Affiliation(s)
- Kun D Huang
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - Till-Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Romulo de Oliveira
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata Bielecka
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, Trento, Italy; Department of Medicine and Life Sciences, University Pompeu Fabra, Barcelona, Spain
| | - Isabel Ruf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Stefan Esser
- Department of Dermatology and Venerology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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2
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Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Valles-Colomer M, Johnson KVA, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN, Moeller AH. Microbial transmission in the social microbiome and host health and disease. Cell 2024; 187:17-43. [PMID: 38181740 PMCID: PMC10958648 DOI: 10.1016/j.cell.2023.12.014] [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: 07/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.
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Affiliation(s)
- Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Cameron J A McInroy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Siobhán Harty
- Independent, Tandy Court, Spitalfields, Dublin, Ireland
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK; Department of Computing, University of Turku, Turku, Finland
| | - Neil G O Ibata
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mireia Valles-Colomer
- Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain; Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Katerina V-A Johnson
- Institute of Psychology, Leiden University, Leiden, the Netherlands; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joseph Henrich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Francesca S Gazzaniga
- Molecular Pathology Unit, Cancer Center, Massachusetts General Hospital Research Institute, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry, University of British Columbia, Vancouver, BC, Canada
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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3
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Valles-Colomer M, Manghi P, Cumbo F, Masetti G, Armanini F, Asnicar F, Blanco-Miguez A, Pinto F, Punčochář M, Garaventa A, Amoroso L, Ponzoni M, Corrias MV, Segata N. Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding. EBioMedicine 2024; 99:104917. [PMID: 38104504 PMCID: PMC10731604 DOI: 10.1016/j.ebiom.2023.104917] [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: 07/12/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Neuroblastoma is the most frequent extracranial solid tumour in children, accounting for ∼15% of deaths due to cancer in childhood. The most common clinical presentation are abdominal tumours. An altered gut microbiome composition has been linked to multiple cancer types, and reported in murine models of neuroblastoma. Whether children with neuroblastoma display alterations in gut microbiome composition remains unexplored. METHODS We assessed gut microbiome composition by shotgun metagenomic profiling in an observational cross-sectional study on 288 individuals, consisting of patients with a diagnosis of neuroblastoma at disease onset (N = 63), healthy controls matching the patients on the main covariates of microbiome composition (N = 94), healthy siblings of the patients (N = 13), mothers of patients (N = 59), and mothers of the controls (N = 59). We examined taxonomic and functional microbiome composition and mother-infant strain transmission patterns. FINDINGS Patients with neuroblastoma displayed alterations in gut microbiome composition characterised by reduced microbiome richness, decreased relative abundances of 18 species (including Phocaeicola dorei and Bifidobacterium bifidum), enriched protein fermentation and reduced carbohydrate fermentation potential. Using machine learning, we could successfully discriminate patients from controls (AUC = 82%). Healthy siblings did not display such alterations but resembled the healthy control group. No significant differences in maternal microbiome composition nor mother-to-offspring transmission were detected. INTERPRETATION Patients with neuroblastoma display alterations in taxonomic and functional gut microbiome composition, which cannot be traced to differential maternal seeding. Follow-up research should include investigating potential causal links. FUNDING Italian Ministry of Health Ricerca Corrente and Ricerca Finalizzata 5 per mille (to MPonzoni); Fondazione Italiana Neuroblastoma (to MPonzoni); European Research Council (ERC-StG project MetaPG-716575 and ERC-CoG microTOUCH-101045015 to NS); the European H2020 program ONCOBIOME-825410 project (to NS); the National Cancer Institute of the National Institutes of Health 1U01CA230551 (to NS); the Premio Internazionale Lombardia e Ricerca 2019 (to NS); the MIUR Progetti di Ricerca di Rilevante Interesse Nazionale (PRIN) Bando 2017 Grant 2017J3E2W2 (to NS); EMBO ALTF 593-2020 and Knowledge Generation Project from the Spanish Ministry of Science and Innovation (PID2022-139328OA-I00) (to MV-C).
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Affiliation(s)
- Mireia Valles-Colomer
- Department CIBIO, University of Trento, Trento, Italy; MELIS Department, Pompeu Fabra University, Barcelona, Spain.
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | | | | | | | | | | | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
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4
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Blanco-Míguez A, Gálvez EJC, Pasolli E, De Filippis F, Amend L, Huang KD, Manghi P, Lesker TR, Riedel T, Cova L, Punčochář M, Thomas AM, Valles-Colomer M, Schober I, Hitch TCA, Clavel T, Berry SE, Davies R, Wolf J, Spector TD, Overmann J, Tett A, Ercolini D, Segata N, Strowig T. Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions. Cell Host Microbe 2023; 31:1804-1819.e9. [PMID: 37883976 PMCID: PMC10635906 DOI: 10.1016/j.chom.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based on a meta-analysis, we found reproducible associations between members of ScC and the male sex and positive correlations with lower visceral fat and favorable markers of cardiometabolic health. Our work uncovers genomic diversity within ScC, facilitating a better characterization of the human microbiome.
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Affiliation(s)
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kun D Huang
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Till-Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Linda Cova
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | | | | | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Technical University of Braunschweig, Braunschweig, Germany
| | - Adrian Tett
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Wien, Austria
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
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5
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Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Punčochář M, Valles-Colomer M, Tett A, Giordano F, Davies R, Wolf J, Berry SE, Spector TD, Franzosa EA, Pasolli E, Asnicar F, Huttenhower C, Segata N. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol 2023; 41:1633-1644. [PMID: 36823356 PMCID: PMC10635831 DOI: 10.1038/s41587-023-01688-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 109.0] [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: 06/07/2022] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.
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Affiliation(s)
| | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Lauren J McIver
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kelsey N Thompson
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | | | - William A Nickols
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Elisa Piperni
- Department CIBIO, University of Trento, Trento, Italy
- IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | | | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | | | | | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Eric A Franzosa
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | | | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- IEO, European Institute of Oncology IRCCS, Milan, Italy.
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6
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Porcari S, Benech N, Valles-Colomer M, Segata N, Gasbarrini A, Cammarota G, Sokol H, Ianiro G. Key determinants of success in fecal microbiota transplantation: From microbiome to clinic. Cell Host Microbe 2023; 31:712-733. [PMID: 37167953 DOI: 10.1016/j.chom.2023.03.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Fecal microbiota transplantation (FMT) has achieved satisfactory results in preventing the recurrence of Clostridioides difficile infection, but these positive outcomes have only been partially replicated in other diseases. Several factors influence FMT success, including those related to donors and recipients (including diversity and specific composition of the gut microbiome, immune system, and host genetics) as well as to working protocols (fecal amount and number of infusions, route of delivery, and adjuvant treatments). Moreover, initial evidence suggests that the clinical success of FMT may be related to the degree of donor microbial engraftment. The application of cutting-edge technologies for microbiome assessment, along with changes in the current vision of fecal transplants, are expected to improve FMT protocols and outcomes. Here, we review the key determinants of FMT success and insights and strategies that will enable a close integration of lab-based and clinical approaches for increasing FMT success.
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Affiliation(s)
- Serena Porcari
- Department of Medical and Surgical Sciences, Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Nicolas Benech
- Hospices Civils de Lyon, Lyon, France; Université Claude Bernard Lyon 1, Lyon, France; Tumor Escape Resistance and Immunity Department, Cancer Research Center of Lyon (CRCL), Inserm U1052, CNRS UMR 5286, Lyon, France; French Fecal Transplant Group (GFTF), France
| | | | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Antonio Gasbarrini
- Department of Medical and Surgical Sciences, Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Cammarota
- Department of Medical and Surgical Sciences, Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Harry Sokol
- French Fecal Transplant Group (GFTF), France; Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France; Paris Centre for Microbiome Medicine FHU, Paris, France; INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | - Gianluca Ianiro
- Department of Medical and Surgical Sciences, Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy.
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7
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Manghi P, Blanco-Míguez A, Manara S, NabiNejad A, Cumbo F, Beghini F, Armanini F, Golzato D, Huang KD, Thomas AM, Piccinno G, Punčochář M, Zolfo M, Lesker TR, Bredon M, Planchais J, Glodt J, Valles-Colomer M, Koren O, Pasolli E, Asnicar F, Strowig T, Sokol H, Segata N. MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice. Cell Rep 2023; 42:112464. [PMID: 37141097 DOI: 10.1016/j.celrep.2023.112464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/10/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.
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Affiliation(s)
- Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | - Amir NabiNejad
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marius Bredon
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012 Paris, France; Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Julien Planchais
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | - Jeremy Glodt
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | | | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | | | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012 Paris, France; Paris Centre for Microbiome Medicine (PaCeMM) FHU, Paris, France; INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy.
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8
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Manara S, Selma-Royo M, Huang KD, Asnicar F, Armanini F, Blanco-Miguez A, Cumbo F, Golzato D, Manghi P, Pinto F, Valles-Colomer M, Amoroso L, Corrias MV, Ponzoni M, Raffaetà R, Cabrera-Rubio R, Olcina M, Pasolli E, Collado MC, Segata N. Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population. Curr Biol 2023; 33:1939-1950.e4. [PMID: 37116481 DOI: 10.1016/j.cub.2023.04.011] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 02/28/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023]
Abstract
The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns.
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Affiliation(s)
- Serena Manara
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Marta Selma-Royo
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy; Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain
| | - Kun D Huang
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Francesco Asnicar
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Federica Armanini
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Aitor Blanco-Miguez
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Fabio Cumbo
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Davide Golzato
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Paolo Manghi
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Federica Pinto
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Mireia Valles-Colomer
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Loredana Amoroso
- Oncology Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Roberta Raffaetà
- Ca' Foscari University Venice, Department of Philosophy and Cultural Heritage and NICHE, Malcanton Marcorà, Dorsoduro 3484/D, 30123 Venice, Italy
| | - Raul Cabrera-Rubio
- Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain
| | - Mari Olcina
- Department of Preventive Medicine and Public Health, Faculty of Pharmacy, Universitat de València, Av. Vicent Andrés Estellés s/n, Burjassot, Valencia 46100, Spain
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Naples, Italy.
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain.
| | - Nicola Segata
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy.
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9
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Valles-Colomer M, Menni C, Berry SE, Valdes AM, Spector TD, Segata N. Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective. Nat Med 2023; 29:551-561. [PMID: 36932240 DOI: 10.1038/s41591-023-02260-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/16/2023] [Indexed: 03/19/2023]
Abstract
Cardiometabolic diseases have become a leading cause of morbidity and mortality globally. They have been tightly linked to microbiome taxonomic and functional composition, with diet possibly mediating some of the associations described. Both the microbiome and diet are modifiable, which opens the way for novel therapeutic strategies. High-throughput omics techniques applied on microbiome samples (meta-omics) hold the unprecedented potential to shed light on the intricate links between diet, the microbiome, the metabolome and cardiometabolic health, with a top-down approach. However, effective integration of complementary meta-omic techniques is an open challenge and their application on large cohorts is still limited. Here we review meta-omics techniques and discuss their potential in this context, highlighting recent large-scale efforts and the novel insights they provided. Finally, we look to the next decade of meta-omics research and discuss various translational and clinical pathways to improving cardiometabolic health.
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Affiliation(s)
- Mireia Valles-Colomer
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Cristina Menni
- Department of Twin Research, King's College London, London, UK
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Ana M Valdes
- School of Medicine, University of Nottingham, Nottingham, UK
- Nottingham National Institute for Health Research Biomedical Research Centre, Nottingham, UK
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- European Institute of Oncology, Scientific Institute for Research, Hospitalization and Healthcare, Milan, Italy.
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10
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Valles-Colomer M, Blanco-Míguez A, Manghi P, Asnicar F, Dubois L, Golzato D, Armanini F, Cumbo F, Huang KD, Manara S, Masetti G, Pinto F, Piperni E, Punčochář M, Ricci L, Zolfo M, Farrant O, Goncalves A, Selma-Royo M, Binetti AG, Becerra JE, Han B, Lusingu J, Amuasi J, Amoroso L, Visconti A, Steves CM, Falchi M, Filosi M, Tett A, Last A, Xu Q, Qin N, Qin H, May J, Eibach D, Corrias MV, Ponzoni M, Pasolli E, Spector TD, Domenici E, Collado MC, Segata N. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 2023; 614:125-135. [PMID: 36653448 PMCID: PMC9892008 DOI: 10.1038/s41586-022-05620-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/02/2022] [Indexed: 01/19/2023]
Abstract
The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.
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Affiliation(s)
| | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Kun D Huang
- Department CIBIO, University of Trento, Trento, Italy
| | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Elisa Piperni
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | | | - Liviana Ricci
- Department CIBIO, University of Trento, Trento, Italy
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Olivia Farrant
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Goncalves
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Marta Selma-Royo
- Department CIBIO, University of Trento, Trento, Italy
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Ana G Binetti
- Instituto de Lactología Industrial (CONICET-UNL), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Jimmy E Becerra
- Grupo de Investigación Alimentación y Comportamiento Humano, Universidad Metropolitana, Barranquilla, Colombia
| | - Bei Han
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - John Lusingu
- National Institute for Medical Research, Tanga Medical Research Centre, Tanga, Tanzania
| | - John Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire M Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anna Last
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Qian Xu
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Realbio Genomics Institute, Shanghai, China
| | - Nan Qin
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Realbio Genomics Institute, Shanghai, China
| | - Huanlong Qin
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples 'Federico II', Portici, Italy
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Enrico Domenici
- Department CIBIO, University of Trento, Trento, Italy
- Centre for Computational and Systems Biology (COSBI), Microsoft Research Foundation, Rovereto, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
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11
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Malan-Müller S, Valles-Colomer M, Palomo T, Leza JC. The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles. Gut Microbes 2023; 15:2162306. [PMID: 36651663 PMCID: PMC9851210 DOI: 10.1080/19490976.2022.2162306] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
The prevalence of anxiety and depression soared following the COVID-19 pandemic. To effectively treat these conditions, a comprehensive understanding of all etiological factors is needed. This study investigated fecal microbial features associated with mental health outcomes (symptoms of anxiety, depression, or posttraumatic stress disorder (PTSD)) in a Spanish cohort in the aftermath of the COVID-19 pandemic. Microbial communities from stool samples were profiled in 198 individuals who completed validated, self-report questionnaires. 16S ribosomal RNA gene V3-4 amplicon sequencing was performed. Microbial diversity and community structure were analyzed, together with relative taxonomic abundance. In our cohort of N=198, 17.17% reported depressive symptoms, 37.37% state anxiety symptoms, 40.90% trait anxiety symptoms, and 8.08% PTSD symptoms, with high levels of comorbidity. Individuals with trait anxiety had lower Simpson's diversity. Fusicatenibacter saccharivorans was reduced in individuals with comorbid PTSD + depression + state and trait anxiety symptoms, whilst an expansion of Proteobacteria and depletion of Synergistetes phyla were noted in individuals with depressive symptoms. The relative abundance of Anaerostipes was positively correlated with childhood trauma, and higher levels of Turicibacter sanguinis and lower levels of Lentisphaerae were found in individuals who experienced life-threatening traumas. COVID-19 infection and vaccination influenced the overall microbial composition and were associated with distinct relative taxonomic abundance profiles. These findings will help lay the foundation for future studies to identify microbial role players in symptoms of anxiety, depression, and PTSD and provide future therapeutic targets to improve mental health outcomes.
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Affiliation(s)
- Stefanie Malan-Müller
- Department of Pharmacology and Toxicology, Faculty of Medicine, University Complutense Madrid (UCM), Madrid, Spain
- Biomedical Network Research Center of Mental Health (CIBERSAM), Institute of Health Carlos III, Madrid, Spain
- Neurochemistry Research Institute UCM, Hospital 12 de Octubre Research Institute (Imas12), Madrid, Spain
| | - Mireia Valles-Colomer
- Department of Cellular Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Tomás Palomo
- Biomedical Network Research Center of Mental Health (CIBERSAM), Institute of Health Carlos III, Madrid, Spain
- Neurochemistry Research Institute UCM, Hospital 12 de Octubre Research Institute (Imas12), Madrid, Spain
| | - Juan C. Leza
- Department of Pharmacology and Toxicology, Faculty of Medicine, University Complutense Madrid (UCM), Madrid, Spain
- Biomedical Network Research Center of Mental Health (CIBERSAM), Institute of Health Carlos III, Madrid, Spain
- Neurochemistry Research Institute UCM, Hospital 12 de Octubre Research Institute (Imas12), Madrid, Spain
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12
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Ianiro G, Punčochář M, Karcher N, Porcari S, Armanini F, Asnicar F, Beghini F, Blanco-Míguez A, Cumbo F, Manghi P, Pinto F, Masucci L, Quaranta G, De Giorgi S, Sciumè GD, Bibbò S, Del Chierico F, Putignani L, Sanguinetti M, Gasbarrini A, Valles-Colomer M, Cammarota G, Segata N. Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases. Nat Med 2022; 28:1913-1923. [PMID: 36109637 PMCID: PMC9499858 DOI: 10.1038/s41591-022-01964-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 07/21/2022] [Indexed: 12/15/2022]
Abstract
AbstractFecal microbiota transplantation (FMT) is highly effective against recurrent Clostridioides difficile infection and is considered a promising treatment for other microbiome-related disorders, but a comprehensive understanding of microbial engraftment dynamics is lacking, which prevents informed applications of this therapeutic approach. Here, we performed an integrated shotgun metagenomic systematic meta-analysis of new and publicly available stool microbiomes collected from 226 triads of donors, pre-FMT recipients and post-FMT recipients across eight different disease types. By leveraging improved metagenomic strain-profiling to infer strain sharing, we found that recipients with higher donor strain engraftment were more likely to experience clinical success after FMT (P = 0.017) when evaluated across studies. Considering all cohorts, increased engraftment was noted in individuals receiving FMT from multiple routes (for example, both via capsules and colonoscopy during the same treatment) as well as in antibiotic-treated recipients with infectious diseases compared with antibiotic-naïve patients with noncommunicable diseases. Bacteroidetes and Actinobacteria species (including Bifidobacteria) displayed higher engraftment than Firmicutes except for six under-characterized Firmicutes species. Cross-dataset machine learning predicted the presence or absence of species in the post-FMT recipient at 0.77 average AUROC in leave-one-dataset-out evaluation, and highlighted the relevance of microbial abundance, prevalence and taxonomy to infer post-FMT species presence. By exploring the dynamics of microbiome engraftment after FMT and their association with clinical variables, our study uncovered species-specific engraftment patterns and presented machine learning models able to predict donors that might optimize post-FMT specific microbiome characteristics for disease-targeted FMT protocols.
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13
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Xu Q, Wu C, Zhu Q, Gao R, Lu J, Valles-Colomer M, Zhu J, Yin F, Huang L, Ding L, Zhang X, Zhang Y, Xiong X, Bi M, Chen X, Zhu Y, Liu L, Liu Y, Chen Y, Fan J, Sun Y, Wang J, Cao Z, Fan C, Ehrlich SD, Segata N, Qin N, Qin H. Author Correction: Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors. Nat Aging 2022; 2:680. [PMID: 37253873 DOI: 10.1038/s43587-022-00258-0] [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: 06/01/2023]
Affiliation(s)
- Qian Xu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunyan Wu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qi Zhu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Renyuan Gao
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianquan Lu
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | | | - Jian Zhu
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Fang Yin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Linsheng Huang
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lulu Ding
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Xiaohui Zhang
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yonghui Zhang
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Xiao Xiong
- Realbio Genomics Institute, Shanghai, China
| | | | - Xiang Chen
- Realbio Genomics Institute, Shanghai, China
| | - Yefei Zhu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lin Liu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yongqiang Liu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yongshen Chen
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Jian Fan
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Yan Sun
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Jun Wang
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Zhan Cao
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunsun Fan
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - S Dusko Ehrlich
- MGP MetaGenoPolis, INRAE, Université Paris-Saclay, Jouy en Josas, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Nan Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
- Realbio Genomics Institute, Shanghai, China.
| | - Huanlong Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
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14
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Xu Q, Wu C, Zhu Q, Gao R, Lu J, Valles-Colomer M, Zhu J, Yin F, Huang L, Ding L, Zhang X, Zhang Y, Xiong X, Bi M, Chen X, Zhu Y, Liu L, Liu Y, Chen Y, Fan J, Sun Y, Wang J, Cao Z, Fan C, Ehrlich SD, Segata N, Qin N, Qin H. Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors. Nat Aging 2022; 2:438-452. [PMID: 37118062 DOI: 10.1038/s43587-022-00193-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/16/2022] [Indexed: 04/30/2023]
Abstract
A better understanding of the biological and environmental variables that contribute to exceptional longevity has the potential to inform the treatment of geriatric diseases and help achieve healthy aging. Here, we compared the gut microbiome and blood metabolome of extremely long-lived individuals (94-105 years old) to that of their children (50-79 years old) in 116 Han Chinese families. We found extensive metagenomic and metabolomic remodeling in advanced age and observed a generational divergence in the correlations with socioeconomic factors. An analysis of quantitative trait loci revealed that genetic associations with metagenomic and metabolomic features were largely generation-specific, but we also found 131 plasma metabolic quantitative trait loci associations that were cross-generational with the genetic variants concentrated in six loci. These included associations between FADS1/2 and arachidonate, PTPA and succinylcarnitine and FLVCR1 and choline. Our characterization of the extensive metagenomic and metabolomic remodeling that occurs in people reaching extreme ages may offer new targets for aging-related interventions.
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Affiliation(s)
- Qian Xu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunyan Wu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qi Zhu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Renyuan Gao
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianquan Lu
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | | | - Jian Zhu
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Fang Yin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Linsheng Huang
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lulu Ding
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Xiaohui Zhang
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yonghui Zhang
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Xiao Xiong
- Realbio Genomics Institute, Shanghai, China
| | | | - Xiang Chen
- Realbio Genomics Institute, Shanghai, China
| | - Yefei Zhu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lin Liu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yongqiang Liu
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yongshen Chen
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Jian Fan
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Yan Sun
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Jun Wang
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Zhan Cao
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunsun Fan
- Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - S Dusko Ehrlich
- MGP MetaGenoPolis, INRAE, Université Paris-Saclay, Jouy en Josas, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Nan Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
- Realbio Genomics Institute, Shanghai, China.
| | - Huanlong Qin
- Institute of Intestinal Diseases, Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
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15
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Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G. Variation and transmission of the human gut microbiota across multiple familial generations. Nat Microbiol 2022; 7:87-96. [PMID: 34969979 PMCID: PMC8727295 DOI: 10.1038/s41564-021-01021-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 07/06/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022]
Abstract
Although the composition and functional potential of the human gut microbiota evolve over the lifespan, kinship has been identified as a key covariate of microbial community diversification. However, to date, sharing of microbiota features within families has mostly been assessed between parents and their direct offspring. Here we investigate the potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (n = 102) spanning 3 to 5 generations over the same female bloodline. We observe microbiome community composition associated with kinship, with seven low abundant genera displaying familial distribution patterns. While kinship and current cohabitation emerge as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother-daughter pairs, decreasing with increasing daughter's age and being higher among cohabiting pairs than those living apart. Although rare, we detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.
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Affiliation(s)
- Mireia Valles-Colomer
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department for Integrative Biology, University of Trento, Trento, Italy
| | - Rodrigo Bacigalupe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Shinya Suzuki
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Youssef Darzi
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Raul Y Tito
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Nicola Segata
- European Institute of Oncology Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
- Department for Integrative Biology, University of Trento, Trento, Italy
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium.
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium.
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
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16
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Belkhou C, Tadeo RT, Bacigalupe R, Valles-Colomer M, Chaffron S, Joossens M, Obregon A, Marín Reyes L, Trujillo O, Huys GRB, Raes J. Treponema peruense sp. nov., a commensal spirochaete isolated from human faeces. Int J Syst Evol Microbiol 2021; 71. [PMID: 34672919 PMCID: PMC8604162 DOI: 10.1099/ijsem.0.005050] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A Gram-stain-negative, obligatory anaerobic spirochaete (RCC2812T) was isolated from a faecal sample obtained from an individual residing in a remote Amazonian community in Peru. The bacterium showed highest 16S rRNA gene sequence similarity to the pig intestinal spirochete Treponema succinifaciens (89.48 %). Average nucleotide identity values between strain RCC2812T and all available Treponema genomes from validated type strains were all <73 %, thus clearly lower than the species delineation threshold. The DNA G+C content of RCC2812T was 41.24 mol%. Phenotypic characterization using the API-ZYM and API 20A systems confirmed the divergent position of this bacterium within the genus Treponema. Strain RCC2812T could be differentiated from the phylogenetically most closely related T. succinifaciens by the presence of alkaline phosphatase and α -glucosidase activities. Unlike T. succinifaciens, strain RCC2812T grew equally well with or without serum. Strain RCC2812T is the first commensal Treponema isolated from the human faecal microbiota of remote populations, and based on the collected data represents a novel Treponema species for which the name Treponema peruense sp. nov. is proposed. The type strain is RCC2812T (=LMG 31794T=CIP 111910T).
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Affiliation(s)
- Claire Belkhou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Raul Tito Tadeo
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Rodrigo Bacigalupe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Mireia Valles-Colomer
- Centre for Integrative Biology (CIBIO), Università degli Studi di Trento (UNITN), Trento, Italy
| | | | - Marie Joossens
- Department of Biochemistry and microbiology, Universiteit Gent, Gent, Belgium
| | - Alexandra Obregon
- Department of Genetic Counseling, College of Health Professions, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Luis Marín Reyes
- Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru
| | - Omar Trujillo
- Centro Nacional de Salud Intercultural, Instituto Nacional de Salud, Lima, Peru
| | - Geert R B Huys
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
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17
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Karcher N, Nigro E, Punčochář M, Blanco-Míguez A, Ciciani M, Manghi P, Zolfo M, Cumbo F, Manara S, Golzato D, Cereseto A, Arumugam M, Bui TPN, Tytgat HLP, Valles-Colomer M, de Vos WM, Segata N. Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Genome Biol 2021; 22:209. [PMID: 34261503 PMCID: PMC8278651 DOI: 10.1186/s13059-021-02427-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored. RESULTS We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon. CONCLUSIONS We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria.
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Affiliation(s)
| | - Eleonora Nigro
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Anna Cereseto
- Department CIBIO, University of Trento, Trento, Italy
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thi Phuong Nam Bui
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Current address: Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- IEO, European Institute of Oncology IRCCS, Milan, Italy.
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18
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Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 2021; 10:65088. [PMID: 33944776 PMCID: PMC8096432 DOI: 10.7554/elife.65088] [Citation(s) in RCA: 651] [Impact Index Per Article: 217.0] [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: 11/22/2020] [Accepted: 04/21/2021] [Indexed: 02/06/2023] Open
Abstract
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.
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Affiliation(s)
| | - Lauren J McIver
- Harvard T.H. Chan School of Public Health, Boston, United States
| | | | | | | | - Sagun Maharjan
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Ana Mailyan
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Matthias Scholz
- Department of Food Quality and Nutrition, Research and Innovation Center, Edmund Mach Foundation, San Michele all'Adige, Italy
| | | | | | - George Weingart
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Yancong Zhang
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Eric A Franzosa
- Harvard T.H. Chan School of Public Health, Boston, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.,IEO, European Institute of Oncology IRCCS, Milan, Italy
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19
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Schiweck C, Valles-Colomer M, Arolt V, Müller N, Raes J, Wijkhuijs A, Claes S, Drexhage H, Vrieze E. Depression and suicidality: A link to premature T helper cell aging and increased Th17 cells. Brain Behav Immun 2020; 87:603-609. [PMID: 32061905 DOI: 10.1016/j.bbi.2020.02.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/16/2019] [Accepted: 02/11/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Previous research has demonstrated a strong link between immune system abnormalities and Major Depressive Disorder (MDD). High suicide risk is a major complication of MDD and has recently been linked to strong (neuro-)immune alterations, but little is known on the link between circulating immune cell composition and suicidal risk status. METHODS Here, we assessed percentages of circulating peripheral blood mononuclear cells with focus on T helper cell subsets (memory T helper cells, Th1, Th2, Th17 and T regulatory cells) in a large and well-matched cohort of 153 patients diagnosed with MDD and 153 age and sex matched controls. We explored the association of these cell populations with suicide risk while accounting for age, sex, BMI, depression severity and childhood trauma. RESULTS Patients with MDD had reduced percentages of NK cells, and higher percentages of B and T cells in line with current literature. Further exploration of T-cells revealed a robustly elevated number of memory T helper cells, regardless of age group. Patients at high risk for suicide had the highest memory T helper cells and additionally showed a robust increase of Th17 cells compared to other suicide risk groups. CONCLUSIONS The higher abundance of memory T helper cells points towards premature aging of the immune system in MDD patients, even during young adulthood. Patients at high risk for suicide show the clearest immune abnormalities and may represent a clinically relevant subtype of depression.
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Affiliation(s)
- Carmen Schiweck
- Department of Neurosciences, Psychiatry Research Group KU Leuven-University of Leuven, Leuven, Belgium.
| | - Mireia Valles-Colomer
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium
| | - Volker Arolt
- Departments of Psychiatry and Psychotherapy, Westfälische Wilhelms-Universität WWU, Münster, Germany
| | - Norbert Müller
- Departments of Psychiatry and Psychotherapy, Ludwig Maximilians-Universität LMU, Munich, Germany
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium; VIB, Center for Microbiology, Leuven, Belgium
| | | | - Stephan Claes
- Department of Neurosciences, Psychiatry Research Group KU Leuven-University of Leuven, Leuven, Belgium
| | - Hemmo Drexhage
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Elske Vrieze
- Department of Neurosciences, Psychiatry Research Group KU Leuven-University of Leuven, Leuven, Belgium
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20
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Reynders T, Devolder L, Valles-Colomer M, Van Remoortel A, Joossens M, De Keyser J, Nagels G, D'hooghe M, Raes J. Gut microbiome variation is associated to Multiple Sclerosis phenotypic subtypes. Ann Clin Transl Neurol 2020; 7:406-419. [PMID: 32162850 PMCID: PMC7187717 DOI: 10.1002/acn3.51004] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [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: 05/15/2019] [Revised: 08/02/2019] [Accepted: 08/24/2019] [Indexed: 12/24/2022] Open
Abstract
Objective Multiple sclerosis (MS) is a heterogenous, inflammatory disease of the central nervous system. Microbiota alterations in MS versus healthy controls (HC) are observed, but results are inconsistent. We studied diversity, enterotypes, and specific gut microbial taxa variation between MS and HC, and between MS subgroups. Methods Amplicon sequencing of the 16S ribosomal RNA V4 region (Illumina MiSeq) was used to evaluate alpha and beta diversity, enterotypes, and relative taxa abundances on stool samples. MS subgroups were based on phenotype, disease course modifiers, and treatment status. Results were controlled for recently identified confounders of microbiota composition. Results Ninety‐eight MS patients and 120 HC were included. Microbial richness was lower in interferon‐treated (RRMS_I, N = 24) and untreated relapsing–remitting MS during relapse (RRMS_R, N = 4) when compared to benign (BMS, N = 20; Z = −3.07, Pcorr = 0.032 and Z = −2.68, Pcorr = 0.055) and primary progressive MS (PPMS, N = 26; Z = −2.39, Pcorr = 0.062 and Z = −2.26, Pcorr = 0.071). HC (N = 120) and active untreated MS (RRMS_U, N = 24) showed intermediate microbial richness. Enterotypes were associated with clinical subgroups (N = 218, χ2 = 36.10, P = 0.002), with Bacteroides 2 enterotype being more prevalent in RRMS_I. Butyricicoccus abundance was lower in PPMS than in RRMS_U (Z = −3.00, Pcorr = 0.014) and BMS (Z = −2.56, Pcorr = 0.031), lower in RRMS_I than in BMS (Z = −2.50, Pcorr = 0.034) and RRMS_U (Z = −2.91, Pcorr = 0.013), and inversely correlated with self‐reported physical symptoms (rho = −0.400, Pcorr = 0.001) and disease severity (rho = −0.223, P = 0.027). Interpretation These results emphasize the importance of phenotypic subcategorization in MS‐microbiome research, possibly explaining previous result heterogeneity, while showing the potential for specific microbiome‐based biomarkers for disease activity and severity.
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Affiliation(s)
- Tatjana Reynders
- Department of Neurology, Universitair Ziekenhuis Antwerpen, Edegem, Belgium.,Department of Neurology, Universitair Ziekenhuis Brussel, Jette, Belgium.,Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium
| | - Lindsay Devolder
- Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium.,Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium.,Center of Microbiology, VIB, Leuven, Belgium
| | - Mireia Valles-Colomer
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium.,Center of Microbiology, VIB, Leuven, Belgium
| | | | - Marie Joossens
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium.,Center of Microbiology, VIB, Leuven, Belgium
| | - Jacques De Keyser
- Department of Neurology, Universitair Ziekenhuis Brussel, Jette, Belgium.,Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium.,National Multiple Sclerosis Center, Melsbroek, Belgium.,Department of Neurology, Universitair Medisch Centrum Groningen, Groningen, The Netherlands
| | - Guy Nagels
- Department of Neurology, Universitair Ziekenhuis Brussel, Jette, Belgium.,Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium.,National Multiple Sclerosis Center, Melsbroek, Belgium.,Faculté de Psychology et des Sciences de l'Education, Mons, Belgium
| | - Marie D'hooghe
- Department of Neurology, Universitair Ziekenhuis Brussel, Jette, Belgium.,Center for Neurosciences, Vrije Universiteit Brussel, Jette, Belgium.,National Multiple Sclerosis Center, Melsbroek, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium.,Center of Microbiology, VIB, Leuven, Belgium
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21
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Valles-Colomer M, Falony G, Darzi Y, Tigchelaar EF, Wang J, Tito RY, Schiweck C, Kurilshikov A, Joossens M, Wijmenga C, Claes S, Van Oudenhove L, Zhernakova A, Vieira-Silva S, Raes J. The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol 2019; 4:623-632. [DOI: 10.1038/s41564-018-0337-x] [Citation(s) in RCA: 784] [Impact Index Per Article: 156.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 12/05/2018] [Indexed: 11/09/2022]
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22
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Malan-Muller S, Valles-Colomer M, Raes J, Lowry CA, Seedat S, Hemmings SM. The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders. ACTA ACUST UNITED AC 2018; 22:90-107. [DOI: 10.1089/omi.2017.0077] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Stefanie Malan-Muller
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Mireia Valles-Colomer
- Department of Microbiology and Immunology, Rega Institute, KU Leuven–University of Leuven, Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven–University of Leuven, Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | - Christopher A. Lowry
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, Boulder, Colorado
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-Core), Aurora, Colorado
- Department of Psychiatry, Neurology & Physical Medicine and Rehabilitation, Anschutz School of Medicine, University of Colorado, Aurora, Colorado
- VA Rocky Mountain Mental Illness Research, Education, and Clinical Center (MIRECC), Denver, Colorado
- Center for Neuroscience, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Sian M.J. Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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23
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Valles-Colomer M, Darzi Y, Vieira-Silva S, Falony G, Raes J, Joossens M. Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines. J Crohns Colitis 2016; 10:735-46. [PMID: 26802086 DOI: 10.1093/ecco-jcc/jjw024] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 10/06/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022]
Abstract
Meta-omics [metagenomics, metatranscriptomics, and metaproteomics] are rapidly expanding our knowledge of the gut microbiota in health and disease. These technologies are increasingly used in inflammatory bowel disease [IBD] research. Yet, meta-omics data analysis, interpretation, and among-study comparison remain challenging. In this review we discuss the role these techniques are playing in IBD research, highlighting their strengths and limitations. We give guidelines on proper sample collection and preparation methods, and on performing the analyses and interpreting the results, reporting available user-friendly tools and pipelines.
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Affiliation(s)
- Mireia Valles-Colomer
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Youssef Darzi
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sara Vieira-Silva
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Marie Joossens
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium VIB, Center for the Biology of Disease, Leuven, Belgium Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. Population-level analysis of gut microbiome variation. Science 2016; 352:560-4. [PMID: 27126039 DOI: 10.1126/science.aad3503] [Citation(s) in RCA: 1393] [Impact Index Per Article: 174.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/11/2016] [Indexed: 12/14/2022]
Abstract
Fecal microbiome variation in the average, healthy population has remained under-investigated. Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (FGFP; discovery cohort; N = 1106) and the Dutch LifeLines-DEEP study (LLDeep; replication; N = 1135). Integration with global data sets (N combined = 3948) revealed a 14-genera core microbiota, but the 664 identified genera still underexplore total gut diversity. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate. Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations. Early-life events such as birth mode were not reflected in adult microbiota composition. Finally, we found that proposed disease marker genera associated to host covariates, urging inclusion of the latter in study design.
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Affiliation(s)
- Gwen Falony
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Marie Joossens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Sara Vieira-Silva
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Jun Wang
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Youssef Darzi
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Karoline Faust
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Alexander Kurilshikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. Novosibirsk State University, Novosibirsk, Russia
| | - Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands
| | - Mireia Valles-Colomer
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Doris Vandeputte
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Raul Y Tito
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Samuel Chaffron
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Leen Rymenans
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Chloë Verspecht
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Lise De Sutter
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Gipsi Lima-Mendez
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Kevin D'hoe
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Karl Jonckheere
- VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Daniel Homola
- VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Roberto Garcia
- VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Ettje F Tigchelaar
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands. Top Institute Food and Nutrition, Wageningen, Netherlands
| | - Linda Eeckhaudt
- VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands. University of Groningen, University Medical Center Groningen, Department of Pediatrics, 9700 RB Groningen, Netherlands
| | - Liesbet Henckaerts
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. KU Leuven-University Hospitals Leuven, Department of General Internal Medicine, Leuven, Belgium
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands. Top Institute Food and Nutrition, Wageningen, Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, Netherlands
| | - Jeroen Raes
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Leuven, Belgium. VIB, Center for the Biology of Disease, Leuven, Belgium. Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium.
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