期刊
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021
卷 75, 期 -, 页码 199-222出版社
ANNUAL REVIEWS
DOI: 10.1146/annurev-micro-060221-012134
关键词
personalized medicine; constraint-based reconstruction and analysis; metabolic modeling; gut microbiome; metabolomics
类别
资金
- European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [757922]
- National Institute on Aging [1RF1AG058942-01, 1U19AG063744-01]
- EMBO short-term fellowship [8720]
Microbial community modeling through COBRA provides a complementary approach to meta-omics analyses, linking microbial composition and function changes to disease etiology. It helps stratify patients and controls, identify host pathways affected by the microbiome, and propose novel interventions for diseases.
The human microbiome plays an important role in human health and disease. Meta-omics analyses provide indispensable data for linking changes in microbiome composition and function to disease etiology. Yet, the lack of a mechanistic understanding of, e.g., microbiome-metabolome links hampers the translation of these findings into effective, novel therapeutics. Here, we propose metabolic modeling of microbial communities through constraint-based reconstruction and analysis (COBRA) as a complementary approach to meta-omics analyses. First, we highlight the importance of microbial metabolism in cardiometabolic diseases, inflammatory bowel disease, colorectal cancer, Alzheimer disease, and Parkinson disease. Next, we demonstrate that microbial community modeling can stratify patients and controls, mechanistically link microbes with fecal metabolites altered in disease, and identify host pathways affected by the microbiome. Finally, we outline our vision for COBRA modeling combined with meta-omics analyses and multivariate statistical analyses to inform and guide clinical trials, yield testable hypotheses, and ultimately propose novel dietary and therapeutic interventions.
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