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Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Nature (London), 2019-05, Vol.569 (7758), p.655-662 [Peer Reviewed Journal]

COPYRIGHT 2019 Nature Publishing Group ;Copyright Nature Publishing Group May 30, 2019 ;The Author(s) 2019 ;ISSN: 0028-0836 ;ISSN: 1476-4687 ;EISSN: 1476-4687 ;DOI: 10.1038/s41586-019-1237-9 ;PMID: 31142855

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Title:
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
Author: Lloyd-Price, Jason ; Arze, Cesar ; Ananthakrishnan, Ashwin N ; Schirmer, Melanie ; Avila-Pacheco, Julian ; Poon, Tiffany W ; Andrews, Elizabeth ; Ajami, Nadim J ; Bonham, Kevin S ; Brislawn, Colin J ; Casero, David ; Courtney, Holly ; Gonzalez, Antonio ; Graeber, Thomas G ; Hall, A Brantley ; Lake, Kathleen ; Landers, Carol J ; Mallick, Himel ; Plichta, Damian R ; Prasad, Mahadev ; Rahnavard, Gholamali ; Sauk, Jenny ; Shungin, Dmitry ; Vázquez-Baeza, Yoshiki ; White, 3rd, Richard A ; Braun, Jonathan ; Denson, Lee A ; Jansson, Janet K ; Knight, Rob ; Kugathasan, Subra ; McGovern, Dermot P B ; Petrosino, Joseph F ; Stappenbeck, Thaddeus S ; Winter, Harland S ; Clish, Clary B ; Franzosa, Eric A ; Vlamakis, Hera ; Xavier, Ramnik J ; Huttenhower, Curtis
Subjects: 60 APPLIED LIFE SCIENCES ; Anaerobes ; Animals ; Antibodies ; Bile acids ; Biological activity ; Biopsy ; Crohn's disease ; Crohns disease ; Diagnosis ; Dysbacteriosis ; Fatty acids ; Fungi - pathogenicity ; Gastrointestinal Microbiome - genetics ; Gastrointestinal Microbiome - immunology ; Genetic aspects ; Genetic research ; Genomics ; Health ; Hospitals ; Humans ; Hypothesis testing ; IBD ; Immunology ; Inflammatory bowel disease ; Inflammatory bowel diseases ; Inflammatory Bowel Diseases - immunology ; Inflammatory Bowel Diseases - microbiology ; Inflammatory Bowel Diseases - therapy ; Inflammatory Bowel Diseases - virology ; Intestinal microflora ; Intestine ; Metabolites ; Microbial activity ; microbiome ; Microbiomes ; Microbiota (Symbiotic organisms) ; Microorganisms ; multiomics ; Phylogeny ; Serology ; Species Specificity ; Taxonomy ; Temporal variability ; Transcriptome ; Ulcerative colitis ; Viruses - pathogenicity
Is Part Of: Nature (London), 2019-05, Vol.569 (7758), p.655-662
Description: Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases.
Publisher: England: Nature Publishing Group
Language: English
Identifier: ISSN: 0028-0836
ISSN: 1476-4687
EISSN: 1476-4687
DOI: 10.1038/s41586-019-1237-9
PMID: 31142855
Source: ProQuest One Psychology
MEDLINE
ProQuest Central

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Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

COPYRIGHT 2019 Nature Publishing Group ;Copyright Nature Publishing Group May 30, 2019 ;The Author(s) 2019 ;ISSN: 0028-0836 ;ISSN: 1476-4687 ;EISSN: 1476-4687 ;DOI: 10.1038/s41586-019-1237-9 ;PMID: 31142855

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