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

By Jason Lloyd-Price, Cesar Arze, Ashwin N. Ananthakrishnan, M. Schirmer, J. Ávila-Pacheco, Tiffany W. Poon, E. Andrews, N. Ajami, Kevin S. Bonham, Colin J. Brislawn and 48 more. Nature, 2019

2,600 citations recorded by the source corpus.

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. The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

Subfields: Genetics, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/46e5a001b843e545298ac0a9194b377743d48a15

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Citations in the corpus

MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data (2023, positive): “Metabolomics is increasingly used in recent microbiome studies to connect microbial community compositions and phenotypes at the le v el of altered metabolic processes ( 1 , 2 , 29 ).”
Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome (2019, background): “A recently published study of 132 IBD patients provided the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases, demonstrating that the gut microbiome and the molecular functional profile in terms of transcriptome and metabolome, and the host immune”
MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics (2020, methodology): “Finally, the IBD data was first processed using the optimized parameters, followed by batch correction based on QC samples.”
Multivariable association discovery in population-scale meta-omics studies (2021, methodology): “, as has been done in the original HMP2 study for cross-measurement correlation analysis [39]).”
Interaction between microbiota and immunity in health and disease (2020, background): “These include a reduced bacterial diversity and marked shifts in abundance of certain bacterial taxa, including decreased abundance of Bacteroides, Firmicutes, Clostridia, Lactobacillus, Ruminococcaceae and increased abundance of Gammaproteobacteria and Enterobacteriaceae,(149,150), coupled with alt”
Short chain fatty acids and its producing organisms: An overlooked therapy for IBD? (2021, background): “Recently a multi-omics study of the gut microbial ecosystem in IBD showed that SCFAs were generally reduced in dysbiotic patients [74].”