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

作者：J. Lloyd-Price, Cesar Arze, A. Ananthakrishnan, M. Schirmer, J. Ávila-Pacheco, Tiffany W. Poon, Elizabeth Andrews, N. Ajami, K. Bonham, Colin J. Brislawn, David Casero, H. Courtney, Antonio Gonzalez, T. Graeber, A. B. Hall, Kathleen Lake, C. Landers, Himel Mallick, D. Plichta, Mahadev Prasad, Gholamali Rahnavard, J. Sauk, D. Shungin, Y. Vázquez-Baeza, R. White, Jason Kevin Amy Courtney Jess L. Hamed Lauren J. Christo Bishai Bullock Deik Dennis Kaplan Khalili McIver M, J. Bishai, K. Bullock, A. Deik, C. Dennis, Jess L. Kaplan, H. Khalili, L. McIver, C. Moran, L. Nguyen, K. Pierce, Randall Schwager, Alexandra Sirota-Madi, B. Stevens, W. Tan, J. ten Hoeve, G. Weingart, R. Wilson, V. Yajnik, J. Braun, L. Denson, J. Jansson, R. Knight, S. Kugathasan, D. McGovern, J. Petrosino, T. Stappenbeck, H. Winter, C. Clish, E. Franzosa, H. Vlamakis, R. Xavier, C. Huttenhower · 发表于：Nature · 年份：2019 · DOI：10.1038/s41586-019-1237-9 · 被引用次数：2713 · 研究领域：Medicine、Biology

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 M...