Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
Nat Rev Microbiol. 2019 Aug;17(8):497-511. doi: 10.1038/s41579-019-0213-6.
Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). Studies of treatment-naive patients have identified microbial taxa associated with disease course and treatment efficacy. To gain a mechanistic understanding of how the microbiome affects gastrointestinal health, we need to move from census to function. Bacteria, including those that adhere to epithelial cells as well as several Clostridium species, can alter differentiation of T helper 17 cells and regulatory T cells. Similarly, microbial products such as short-chain fatty acids and sphingolipids also influence immune responses. Metagenomics and culturomics have identified strains of Ruminococcus gnavus and adherent invasive Escherichia coli that are linked to IBD and gut inflammation. Integrated analysis of multiomics data, including metagenomics, metatranscriptomics and metabolomics, with measurements of host response and culturomics, have great potential in understanding the role of the microbiome in IBD. In this Review, we highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD.
肠道微生物组的紊乱与炎症性肠病（IBD）有关。对未经治疗的患者的研究已经确定了与疾病过程和治疗效果相关的微生物类群。为了从普查到功能上深入了解微生物组如何影响胃肠道健康，我们需要了解细菌，包括那些粘附在肠上皮细胞上的细菌以及几种梭菌，可改变 T 辅助 17 细胞和调节性 T 细胞的分化。同样，微生物产物，如短链脂肪酸和鞘脂类，也会影响免疫反应。宏基因组学和培养组学已经确定了与 IBD 和肠道炎症相关的罗氏真杆菌和粘附侵袭性大肠杆菌菌株。包括宏基因组学、宏转录组学和代谢组学在内的多组学数据与宿主反应和培养组学的测量的综合分析，对于理解微生物组在 IBD 中的作用具有巨大的潜力。在这篇综述中，我们强调了与 IBD 发病机制相关的肠道微生物因素的现有知识，并讨论了如何利用来自健康和疾病的大规模人群研究的多组学数据来识别与 IBD 相关的特定微生物菌株、转录变化和代谢改变。
