These diseases, the most prevalent forms of which are Crohn’s disease (CD) and ulcerative colitis (UC), are characterized by debilitating and chronic relapsing and remitting inflammation of the gastrointestinal tract (for CD) or the colon (in UC). Inflammatory bowel diseases (IBD) affect more than 3.5 million people, and their incidence is increasing worldwide 1. The study’s infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi’omics Database ( ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. 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. Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. 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). Individual contributing factors have been the focus of extensive research. Crohn’s disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide.
Nature volume 569, pages 655–662 ( 2019) Cite this article Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases