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Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
- Source :
- Nature, vol 569, iss 7758
- Publication Year :
- 2019
- Publisher :
- eScholarship, University of California, 2019.
-
Abstract
- 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.
- Subjects :
- General Science & Technology
Inflammatory Bowel Disease
Fungi
Crohn's Disease
Inflammatory Bowel Diseases
Autoimmune Disease
Oral and gastrointestinal
Gastrointestinal Microbiome
Species Specificity
Clinical Research
Health
Viruses
Genetics
2.1 Biological and endogenous factors
IBDMDB Investigators
Animals
Humans
Aetiology
Digestive Diseases
Transcriptome
Phylogeny
Nutrition
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Nature, vol 569, iss 7758
- Accession number :
- edsair.dedup.wf.001..24589a86eab5bee252e9323e8d43de54