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Tap J, Lejzerowicz F, Cotillard A, Pichaud M, McDonald D, Song SJ, Knight R, Veiga P, Derrien M. Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nat Commun 2023; 14:3310. [PMID: 37339957 DOI: 10.1038/s41467-023-38558-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/04/2023] [Indexed: 06/22/2023] Open
Abstract
The gut microbiome is important for human health, yet modulation requires more insight into inter-individual variation. Here, we explored latent structures of the human gut microbiome across the human lifespan, applying partitioning, pseudotime, and ordination approaches to >35,000 samples. Specifically, three major gut microbiome branches were identified, within which multiple partitions were observed in adulthood, with differential abundances of species along branches. Different compositions and metabolic functions characterized the branches' tips, reflecting ecological differences. An unsupervised network analysis from longitudinal data from 745 individuals showed that partitions exhibited connected gut microbiome states rather than over-partitioning. Stability in the Bacteroides-enriched branch was associated with specific ratios of Faecalibacterium:Bacteroides. We also showed that associations with factors (intrinsic and extrinsic) could be generic, branch- or partition-specific. Our ecological framework for cross-sectional and longitudinal data allows a better understanding of overall variation in the human gut microbiome and disentangles factors associated with specific configurations.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Section for Aquatic Biology and Toxicology, University of Oslo, Oslo, Norway
| | | | | | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Patrick Veiga
- Danone Nutricia Research, Gif-sur-Yvette, France
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | - Muriel Derrien
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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2
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Oyarzun I, Le Nevé B, Yañez F, Xie Z, Pichaud M, Serrano-Gómez G, Roca J, Veiga P, Azpiroz F, Tap J, Manichanh C. Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet. Comput Struct Biotechnol J 2022; 20:1632-1641. [PMID: 35465165 PMCID: PMC9014321 DOI: 10.1016/j.csbj.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022] Open
Abstract
Healthy plant-based diets rich in fermentable residues may induce gas-related symptoms, possibly mediated by the gut microbiota. We previously showed that consumption of a fermented milk product (FMP) containing Bifidobacterium animalis subsp. lactis CNCM I-2494 and lactic acid bacteria improved gastrointestinal (GI) comfort in response to a flatulogenic dietary challenge in healthy individuals. To study the effects of the FMP on gut microbiota activity from those participants, we conducted a metatranscriptomic analysis of fecal samples (n = 262), which were collected during the ingestion of a habitual diet and two series of a 3-day high-residue challenge diet, before and following 28-days of FMP consumption. Most of the FMP species were detected or found enriched upon consumption of the product. FMP mitigated the effect of a flatulogenic diet on gas-related symptoms in several ways. First, FMP consumption was associated with the depletion of gas-producing bacteria and increased hydrogen to methane conversion. It also led to the upregulation of activities such as replication and downregulation of functions related to motility and chemotaxis. Furthermore, upon FMP intake, metabolic activities such as carbohydrate metabolism, attributed to B. animalis and S. thermophilus, were enriched; these activities were coincidentally found to be negatively associated with several GI symptoms. Finally, a more connected microbial ecosystem or mutualistic relationship among microbes was found in responders to the FMP intervention. Taken together, these findings suggest that consumption of the FMP improved the tolerance of a flatulogenic diet through active interactions with the resident gut microbiota.
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Affiliation(s)
- Iñigo Oyarzun
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Francisca Yañez
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Zixuan Xie
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | | | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | | | - Fernando Azpiroz
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
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3
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Zhang S, Morgan XC, Dogan B, Martin FP, Strickler SR, Oka A, Herzog J, Liu B, Dowd SE, Huttenhower C, Pichaud M, Dogan EI, Satsangi J, Longman R, Yantiss R, Mueller LA, Scherl E, Sartor RB, Simpson KW. Mucosal metabolites fuel the growth and virulence of E. coli linked to Crohn's disease. JCI Insight 2022; 7:157013. [PMID: 35413017 PMCID: PMC9220930 DOI: 10.1172/jci.insight.157013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
Elucidating how resident enteric bacteria interact with their hosts to promote health or inflammation is of central importance to diarrheal and inflammatory bowel diseases across species. Here, we integrated the microbial and chemical microenvironment of a patient’s ileal mucosa with their clinical phenotype and genotype to identify factors favoring the growth and virulence of adherent and invasive E. coli (AIEC) linked to Crohn’s disease. We determined that the ileal niche of AIEC was characterized by inflammation, dysbiosis, coculture of Enterococcus, and oxidative stress. We discovered that mucosal metabolites supported general growth of ileal E. coli, with a selective effect of ethanolamine on AIEC that was augmented by cometabolism of ileitis-associated amino acids and glutathione and by symbiosis-associated fucose. This metabolic plasticity was facilitated by the eut and pdu microcompartments, amino acid metabolism, γ-glutamyl-cycle, and pleiotropic stress responses. We linked metabolism to virulence and found that ethanolamine and glutamine enhanced AIEC motility, infectivity, and proinflammatory responses in vitro. We connected use of ethanolamine to intestinal inflammation and L-fuculose phosphate aldolase (fucA) to symbiosis in AIEC monoassociated IL10–/– mice. Collectively, we established that AIEC were pathoadapted to utilize mucosal metabolites associated with health and inflammation for growth and virulence, enabling the transition from symbiont to pathogen in a susceptible host.
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Affiliation(s)
- Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Francois-Pierre Martin
- Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | - Susan R Strickler
- Plant Research, Boyce Thompson Institute, Ithaca, United States of America
| | - Akihiko Oka
- Department of Internal Medicine II, Shimane University Faculty of Medicine, Izumo, Japan
| | - Jeremy Herzog
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Bo Liu
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Scot E Dowd
- MR DNA: Molecular Research LP, Shallowater, United States of America
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | | | - Esra I Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Randy Longman
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - Rhonda Yantiss
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - Lukas A Mueller
- Plant Research, Boyce Thompson Institute, Ithaca, United States of America
| | - Ellen Scherl
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medical College, Cornell University, New York, United States of America
| | - R Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Kenneth W Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, United States of America
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Ke X, You K, Pichaud M, Haiser HJ, Graham DB, Vlamakis H, Porter JA, Xavier RJ. Gut bacterial metabolites modulate endoplasmic reticulum stress. Genome Biol 2021; 22:292. [PMID: 34654459 PMCID: PMC8518294 DOI: 10.1186/s13059-021-02496-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 08/07/2020] [Accepted: 09/10/2021] [Indexed: 12/26/2022] Open
Abstract
Background The endoplasmic reticulum (ER) is a membranous organelle that maintains proteostasis and cellular homeostasis, controlling the fine balance between health and disease. Dysregulation of the ER stress response has been implicated in intestinal inflammation associated with inflammatory bowel disease (IBD), a chronic condition characterized by changes to the mucosa and alteration of the gut microbiota. While the microbiota and microbially derived metabolites have also been implicated in ER stress, examples of this connection remain limited to a few observations from pathogenic bacteria. Furthermore, the mechanisms underlying the effects of bacterial metabolites on ER stress signaling have not been well established. Results Utilizing an XBP1s-GFP knock-in reporter colorectal epithelial cell line, we screened 399 microbiome-related metabolites for ER stress pathway modulation. We find both ER stress response inducers (acylated dipeptide aldehydes and bisindole methane derivatives) and suppressors (soraphen A) and characterize their activities on ER stress gene transcription and translation. We further demonstrate that these molecules modulate the ER stress pathway through protease inhibition or lipid metabolism interference. Conclusions Our study identified novel links between classes of gut microbe-derived metabolites and the ER stress response, suggesting the potential for these metabolites to contribute to gut ER homeostasis and providing insight into the molecular mechanisms by which gut microbes impact intestinal epithelial cell homeostasis. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02496-8.
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Affiliation(s)
- Xiaobo Ke
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Novartis Institute for Biomedical Research Inc., Cambridge, MA, 02139, USA
| | - Kwontae You
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Matthieu Pichaud
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Novartis Institute for Biomedical Research Inc., Cambridge, MA, 02139, USA
| | - Henry J Haiser
- Novartis Institute for Biomedical Research Inc., Cambridge, MA, 02139, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard School of Medicine, Boston, Massachusetts, 02114, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jeffrey A Porter
- Novartis Institute for Biomedical Research Inc., Cambridge, MA, 02139, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard School of Medicine, Boston, Massachusetts, 02114, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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5
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Brown EM, Arellano-Santoyo H, Temple ER, Costliow ZA, Pichaud M, Hall AB, Liu K, Durney MA, Gu X, Plichta DR, Clish CA, Porter JA, Vlamakis H, Xavier RJ. Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors. Cell Host Microbe 2021; 29:1351-1365.e11. [PMID: 34403684 DOI: 10.1016/j.chom.2021.07.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 06/23/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022]
Abstract
Bacterial ADP-ribosyltransferases (ADPRTs) have been described as toxins involved in pathogenesis through the modification of host proteins. Here, we report that ADPRTs are not pathogen restricted but widely prevalent in the human gut microbiome and often associated with phage elements. We validated their biochemical activity in a large clinical isolate collection and further examined Bxa, a highly abundant ADPRT in Bacteroides. Bxa is expressed, secreted, and enzymatically active in Bacteroides and can ADP-ribosylate non-muscle myosin II proteins. Addition of Bxa to epithelial cells remodeled the actin cytoskeleton and induced secretion of inosine. Bxa-encoding B. stercoris can use inosine as a carbon source and colonizes the gut to significantly greater numbers than a bxa-deleted strain in germ-free and altered Schaedler flora (ASF) mice. Colonization correlated with increased inosine concentrations in the feces and tissues. Altogether, our results show that ADPRTs are abundant in the microbiome and act as bacterial fitness factors.
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Affiliation(s)
- Eric M Brown
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hugo Arellano-Santoyo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novartis Institutes for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Emily R Temple
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Matthieu Pichaud
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novartis Institutes for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - A Brantley Hall
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kai Liu
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Xiebin Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Clary A Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey A Porter
- Novartis Institutes for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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6
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Plichta DR, Somani J, Pichaud M, Wallace ZS, Fernandes AD, Perugino CA, Lähdesmäki H, Stone JH, Vlamakis H, Chung DC, Khanna D, Pillai S, Xavier RJ. Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis. Genome Med 2021; 13:35. [PMID: 33648559 PMCID: PMC7919092 DOI: 10.1186/s13073-021-00853-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/11/2021] [Indexed: 02/08/2023] Open
Abstract
Background Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in the blood as well as inflammation and fibrosis in various organs, but they have no established etiologies. Similar to other autoimmune diseases, the gut microbiome might encode disease-triggering or disease-sustaining factors. Methods The gut microbiomes from IgG4-RD and SSc patients as well as healthy individuals with no recent antibiotic treatment were studied by metagenomic sequencing of stool DNA. De novo assembly-based taxonomic and functional characterization, followed by association and accessory gene set enrichment analysis, were applied to describe microbiome changes associated with both diseases. Results Microbiomes of IgG4-RD and SSc patients distinctly separated from those of healthy controls: numerous opportunistic pathogenic Clostridium and typically oral Streptococcus species were significantly overabundant, while Alistipes, Bacteroides, and butyrate-producing species were depleted in the two diseases compared to healthy controls. Accessory gene content analysis in these species revealed an enrichment of Th17-activating Eggerthella lenta strains in IgG4-RD and SSc and a preferential colonization of a homocysteine-producing strain of Clostridium bolteae in SSc. Overabundance of the classical mevalonate pathway, hydroxyproline dehydratase, and fibronectin-binding protein in disease microbiomes reflects potential functional differences in host immune recognition and extracellular matrix utilization associated with fibrosis. Strikingly, the majority of species that were differentially abundant in IgG4-RD and SSc compared to controls showed the same directionality in both diseases. Compared with multiple sclerosis and rheumatoid arthritis, the gut microbiomes of IgG4-RD and SSc showed similar signatures; in contrast, the most differentially abundant taxa were not the facultative anaerobes consistently identified in inflammatory bowel diseases, suggesting the microbial signatures of IgG4-RD and SSc do not result from mucosal inflammation and decreased anaerobism. Conclusions These results provide an initial characterization of gut microbiome ecology in fibrosis-prone IgG4-RD and SSc and reveal microbial functions that offer insights into the pathophysiology of these rare diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00853-7.
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Affiliation(s)
| | - Juhi Somani
- Department of Computer Science, Aalto University, 02150, Espoo, Finland
| | | | - Zachary S Wallace
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA.,Clinical Epidemiology Program and Rheumatology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ana D Fernandes
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Cory A Perugino
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, 02150, Espoo, Finland
| | - John H Stone
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel C Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Cancer Risk Assessment, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dinesh Khanna
- University of Michigan Scleroderma Program, Ann Arbor, MI, USA
| | - Shiv Pillai
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
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7
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Plaza Oñate F, Le Chatelier E, Almeida M, Cervino ACL, Gauthier F, Magoulès F, Ehrlich SD, Pichaud M. MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. Bioinformatics 2020; 35:1544-1552. [PMID: 30252023 PMCID: PMC6499236 DOI: 10.1093/bioinformatics/bty830] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/29/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022] Open
Abstract
Motivation Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained from de novo assembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters. Results We introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses. Availability and implementation The binary is freely available for non-commercial users at www.enterome.com/downloads. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Florian Plaza Oñate
- Enterome, 94-96 Avenue Ledru Rollin, Paris, France
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
- To whom correspondence should be addressed. E-mail:
| | | | - Mathieu Almeida
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | - Franck Gauthier
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Frédéric Magoulès
- CentraleSupélec, Université Paris Saclay, 9 rue Joliot Curie, Gif-sur-Yvette, France
| | - S Dusko Ehrlich
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
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8
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Ellouze M, Pichaud M, Bonaiti C, Coroller L, Couvert O, Thuault D, Vaillant R. Modelling pH evolution and lactic acid production in the growth medium of a lactic acid bacterium: Application to set a biological TTI. Int J Food Microbiol 2008; 128:101-7. [DOI: 10.1016/j.ijfoodmicro.2008.06.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 06/17/2008] [Accepted: 06/27/2008] [Indexed: 11/27/2022]
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Abstract
Only a tiny fraction of the many hundreds of known protein complexes are also of known three-dimensional structure. The experimental difficulties surrounding structure determination of complexes make methods that are able to predict structures paramount. The challenge of predicting complex structures is daunting and raises many issues that need to be addressed. To produce the best models, new prediction methods have to somehow combine partial structures with a mixed bag of experimental data, including interactions and low-resolution electron microscopy images.
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Affiliation(s)
- Patrick Aloy
- EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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10
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Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 2004; 14:313-24. [PMID: 15193311 DOI: 10.1016/j.sbi.2004.04.006] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structures of macromolecular complexes are necessary for a mechanistic description of biochemical and cellular processes. They can be solved by experimental methods, such as X-ray crystallography, NMR spectroscopy and electron microscopy, as well as by computational protein structure prediction, docking and bioinformatics. Recent advances and applications of these methods emphasize the need for hybrid approaches that combine a variety of data to achieve better efficiency, accuracy, resolution and completeness.
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