Discovery of bioactive microbial gene products in inflammatory bowel disease.

Bacterial Proteins / analysis Chronic Disease Gastrointestinal Microbiome / genetics Genes, Microbial Humans Inflammatory Bowel Diseases / microbiology Metagenomics Proteomics Reproducibility of Results Transcriptome

Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
06 2022
Historique:
received: 16 10 2020
accepted: 15 03 2022
pubmed: 26 5 2022
medline: 25 6 2022
entrez: 25 5 2022
Statut: ppublish

Résumé

Microbial communities and their associated bioactive compounds

Identifiants

DOI: 10.1038/s41586-022-04648-7 PMID: 35614211 PMC: PMC9913614
pubmed: 35614211
doi: 10.1038/s41586-022-04648-7
pii: 10.1038/s41586-022-04648-7
pmc: PMC9913614
mid: NIHMS1866902
doi:

Substances chimiques

Bacterial Proteins 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

754-760

Subventions

Organisme : NIDDK NIH HHS
ID : P30 DK043351
Pays : United States
Organisme : NCCIH NIH HHS
ID : R01 AT009708
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK127171
Pays : United States
Organisme : NIDDK NIH HHS
ID : R24 DK110499
Pays : United States

Informations de copyright

© 2022. The Author(s), under exclusive licence to Springer Nature Limited.

Références

Cohen, L. J. et al. Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature 549, 48–53 (2017).
pubmed: 28854168 pmcid: 5777231 doi: 10.1038/nature23874
Guo, C. J. et al. Discovery of reactive microbiota-derived metabolites that inhibit host proteases. Cell 168, 517–526 (2017).
pubmed: 28111075 pmcid: 5302092 doi: 10.1016/j.cell.2016.12.021
Bhattarai, Y. et al. Gut microbiota-produced tryptamine activates an epithelial G-protein-coupled receptor to increase colonic secretion. Cell Host Microbe 23, 775–785 (2018).
pubmed: 29902441 pmcid: 6055526 doi: 10.1016/j.chom.2018.05.004
Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655–662 (2019).
pubmed: 31142855 pmcid: 6650278 doi: 10.1038/s41586-019-1237-9
Galperin, M. Y. & Koonin, E. V. ‘Conserved hypothetical’ proteins: prioritization of targets for experimental study. Nucleic Acids Res. 32, 5452–5463 (2004).
pubmed: 15479782 pmcid: 524295 doi: 10.1093/nar/gkh885
Galperin, M. Y. & Koonin, E. V. From complete genome sequence to ‘complete’ understanding? Trends Biotechnol. 28, 398–406 (2010).
pubmed: 20647113 pmcid: 3065831 doi: 10.1016/j.tibtech.2010.05.006
Joice, R., Yasuda, K., Shafquat, A., Morgan, X. C. & Huttenhower, C. Determining microbial products and identifying molecular targets in the human microbiome. Cell Metab. 20, 731–741 (2014).
pubmed: 25440055 pmcid: 4254638 doi: 10.1016/j.cmet.2014.10.003
Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).
pubmed: 25337874 doi: 10.1038/nature13828
Zipperer, A. et al. Human commensals producing a novel antibiotic impair pathogen colonization. Nature 535, 511–516 (2016).
pubmed: 27466123 doi: 10.1038/nature18634
Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012).
pubmed: 23013615 pmcid: 3506950 doi: 10.1186/gb-2012-13-9-r79
Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R. & Wu, C. H. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 1282–1288 (2007).
pubmed: 17379688 doi: 10.1093/bioinformatics/btm098
Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000).
pubmed: 10802651 pmcid: 3037419 doi: 10.1038/75556
UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 43, D204–D212 (2015).
doi: 10.1093/nar/gku989
Konstantinidis, K. T. & Tiedje, J. M. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 187, 6258–6264 (2005).
pubmed: 16159757 pmcid: 1236649 doi: 10.1128/JB.187.18.6258-6264.2005
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).
pubmed: 30148503 doi: 10.1038/nbt.4229
Plaza Oñate, F. et al. MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. Bioinformatics 35, 1544–1552 (2019).
pubmed: 30252023 doi: 10.1093/bioinformatics/bty830
Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841 (2014).
pubmed: 24997786 doi: 10.1038/nbt.2942
Jandhyala, S. M. et al. Role of the normal gut microbiota. World J. Gastroenterol. 21, 8787–8803 (2015).
pubmed: 26269668 pmcid: 4528021 doi: 10.3748/wjg.v21.i29.8787
Zhang, R., Ou, H. Y. & Zhang, C. T. DEG: a database of essential genes. Nucleic Acids Res. 32, D271–D272 (2004).
pubmed: 14681410 pmcid: 308758 doi: 10.1093/nar/gkh024
Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl Acad. Sci. USA 105, 16731–16736 (2008).
pubmed: 18936492 pmcid: 2575488 doi: 10.1073/pnas.0804812105
Lopez-Siles, M., Duncan, S. H., Garcia-Gil, L. J. & Martinez-Medina, M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J. 11, 841–852 (2017).
pubmed: 28045459 pmcid: 5364359 doi: 10.1038/ismej.2016.176
Schirmer, M., Garner, A., Vlamakis, H. & Xavier, R. J. Microbial genes and pathways in inflammatory bowel disease. Nat. Rev. Microbiol. 17, 497–511 (2019).
pubmed: 31249397 pmcid: 6759048 doi: 10.1038/s41579-019-0213-6
Lewis, J. D. et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe 18, 489–500 (2015).
pubmed: 26468751 pmcid: 4633303 doi: 10.1016/j.chom.2015.09.008
Franzosa, E. A. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nature Microbiol. 4, 293–305 (2019).
doi: 10.1038/s41564-018-0306-4
Hall, A. B. et al. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med. 9, 103 (2017).
pubmed: 29183332 pmcid: 5704459 doi: 10.1186/s13073-017-0490-5
Hughes, E. R. et al. Microbial respiration and formate oxidation as metabolic signatures of inflammation-associated dysbiosis. Cell Host Microbe 21, 208–219 (2017).
pubmed: 28182951 pmcid: 5313043 doi: 10.1016/j.chom.2017.01.005
Högbom, M. & Ihalin, R. Functional and structural characteristics of bacterial proteins that bind host cytokines. Virulence 8, 1592–1601 (2017).
pubmed: 28783440 pmcid: 5810482 doi: 10.1080/21505594.2017.1363140
Wells, T. J., Tree, J. J., Ulett, G. C. & Schembri, M. A. Autotransporter proteins: novel targets at the bacterial cell surface. FEMS Microbiol. Lett. 274, 163–172 (2007).
pubmed: 17610513 doi: 10.1111/j.1574-6968.2007.00833.x
Pizarro-Cerdá, J. & Cossart, P. Bacterial adhesion and entry into host cells. Cell 124, 715–727 (2006).
pubmed: 16497583 doi: 10.1016/j.cell.2006.02.012
Palmela, C. et al. Adherent-invasive Escherichia coli in inflammatory bowel disease. Gut 67, 574–587 (2018).
pubmed: 29141957 doi: 10.1136/gutjnl-2017-314903
Xu, Q. et al. A Distinct type of pilus from the human microbiome. Cell 165, 690–703 (2016).
pubmed: 27062925 pmcid: 4842110 doi: 10.1016/j.cell.2016.03.016
Zhang, Y., Thompson, K. N., Huttenhower, C. & Franzosa, E. A. Statistical approaches for differential expression analysis in metatranscriptomics. Bioinformatics 37, i34–i41 (2021).
pubmed: 34252963 pmcid: 8275336 doi: 10.1093/bioinformatics/btab327
Starks, A. M., Froehlich, B. J., Jones, T. N. & Scott, J. R. Assembly of CS1 pili: the role of specific residues of the major pilin, CooA. J. Bacteriol. 188, 231–239 (2006).
pubmed: 16352839 pmcid: 1317577 doi: 10.1128/JB.188.1.231-239.2006
Galkin, V. E. et al. The structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism. J. Bacteriol. 195, 1360–1370 (2013).
pubmed: 23175654 pmcid: 3624524 doi: 10.1128/JB.01989-12
Vatanen, T. et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165, 842–853 (2016).
pubmed: 27133167 pmcid: 4950857 doi: 10.1016/j.cell.2016.04.007
Dalbey, R. E. & Kuhn, A. Protein traffic in Gram-negative bacteria—how exported and secreted proteins find their way. FEMS Microbiol. Rev. 36, 1023–1045 (2012).
pubmed: 22250915 doi: 10.1111/j.1574-6976.2012.00327.x
Costa, T. R. et al. Secretion systems in Gram-negative bacteria: structural and mechanistic insights. Nat. Rev. Microbiol. 13, 343–359 (2015).
pubmed: 25978706 doi: 10.1038/nrmicro3456
Shipman, J. A., Berleman, J. E. & Salyers, A. A. Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron. J. Bacteriol. 182, 5365–5372 (2000).
pubmed: 10986238 pmcid: 110978 doi: 10.1128/JB.182.19.5365-5372.2000
Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000).
pubmed: 10592235 pmcid: 102472 doi: 10.1093/nar/28.1.235
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).
pubmed: 25950237 pmcid: 5298202 doi: 10.1038/nprot.2015.053
Dong, R., Pan, S., Peng, Z., Zhang, Y. & Yang, J. mTM-align: a server for fast protein structure database search and multiple protein structure alignment. Nucleic Acids Res. 46, W380–w386 (2018).
pubmed: 29788129 pmcid: 6030909 doi: 10.1093/nar/gkx1013
Treuner-Lange, A. et al. PilY1 and minor pilins form a complex priming the type IVa pilus in Myxococcus xanthus. Nat. Commun. 11, 5054 (2020).
pubmed: 33028835 pmcid: 7541494 doi: 10.1038/s41467-020-18803-z
Co, J. Y. et al. Mucins trigger dispersal of Pseudomonas aeruginosa biofilms. NPJ Biofilms Microbiomes 4, 23 (2018).
pubmed: 30323945 pmcid: 6180003 doi: 10.1038/s41522-018-0067-0
Medema, M. H. et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39, W339–W346 (2011).
pubmed: 21672958 pmcid: 3125804 doi: 10.1093/nar/gkr466
Haroon, M. F., Thompson, L. R., Parks, D. H., Hugenholtz, P. & Stingl, U. A catalogue of 136 microbial draft genomes from Red Sea metagenomes. Sci. Data 3, 160050 (2016).
pubmed: 27377622 pmcid: 4932879 doi: 10.1038/sdata.2016.50

Auteurs

Yancong Zhang (Y)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
ORCID: 0000-0002-2768-2975

Amrisha Bhosle (A)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Sena Bae (S)

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Lauren J McIver (LJ)

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Gleb Pishchany (G)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.

Emma K Accorsi (EK)

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
ORCID: 0000-0002-7443-7921

Kelsey N Thompson (KN)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
ORCID: 0000-0002-9437-9722

Cesar Arze (C)

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
ORCID: 0000-0002-3606-4183

Ya Wang (Y)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Ayshwarya Subramanian (A)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
ORCID: 0000-0002-4134-7612

Sean M Kearney (SM)

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.

April Pawluk (A)

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Damian R Plichta (DR)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
ORCID: 0000-0002-6555-2557

Ali Rahnavard (A)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
ORCID: 0000-0002-9710-0248

Afrah Shafquat (A)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Ramnik J Xavier (RJ)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.

Hera Vlamakis (H)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
ORCID: 0000-0003-1086-9191

Wendy S Garrett (WS)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
ORCID: 0000-0002-5092-0150

Andy Krueger (A)

Takeda Pharmaceutical Company, Cambridge, MA, USA.

Curtis Huttenhower (C)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. chuttenh@hsph.harvard.edu.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. chuttenh@hsph.harvard.edu.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. chuttenh@hsph.harvard.edu.
Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA. chuttenh@hsph.harvard.edu.
ORCID: 0000-0002-1110-0096

Eric A Franzosa (EA)

Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. franzosa@hsph.harvard.edu.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. franzosa@hsph.harvard.edu.
Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA. franzosa@hsph.harvard.edu.
ORCID: 0000-0002-8798-7068

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Classifications MeSH

questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines bactériennes › Discovery of bioactive microbial gene products...
questionsmedicales.fr › États, signes et symptômes pathologiques › Processus pathologiques › Caractéristiques de la maladie › Maladie chronique › Discovery of bioactive microbial gene products...
questionsmedicales.fr › Environnement et santé publique › Environnement › Écosystème › Biodiversité › Biote › Microbiote › Microbiome gastro-intestinal › Discovery of bioactive microbial gene products...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Gènes microbiens › Discovery of bioactive microbial gene products...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Discovery of bioactive microbial gene products...
questionsmedicales.fr › Maladies de l'appareil digestif › Maladies gastro-intestinales › Maladies intestinales › Maladies inflammatoires intestinales › Discovery of bioactive microbial gene products...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Métagénomique › Discovery of bioactive microbial gene products...
questionsmedicales.fr › Disciplines des sciences naturelles › Chimie › Biochimie › Protéomique › Discovery of bioactive microbial gene products...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Méthodologie en recherche épidémiologique › Reproductibilité des résultats › Discovery of bioactive microbial gene products...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › Discovery of bioactive microbial gene products...