Almut Heinken, Arianna Basile, Johannes Hertel, Cyrille Thinnes, Ines Thiele
{"title":"Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine.","authors":"Almut Heinken, Arianna Basile, Johannes Hertel, Cyrille Thinnes, Ines Thiele","doi":"10.1146/annurev-micro-060221-012134","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":7946,"journal":{"name":"Annual review of microbiology","volume":"75 ","pages":"199-222"},"PeriodicalIF":8.5000,"publicationDate":"2021-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"23","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Annual review of microbiology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1146/annurev-micro-060221-012134","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2021/7/27 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
引用次数: 23
Abstract
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.
期刊介绍:
Annual Review of Microbiology is a Medical and Microbiology Journal and published by Annual Reviews Inc. The Annual Review of Microbiology, in publication since 1947, covers significant developments in the field of microbiology, encompassing bacteria, archaea, viruses, and unicellular eukaryotes. The current volume of this journal has been converted from gated to open access through Annual Reviews' Subscribe to Open program, with all articles published under a CC BY license. The Impact Factor of Annual Review of Microbiology is 10.242 (2024) Impact factor. The Annual Review of Microbiology Journal is Indexed with Pubmed, Scopus, UGC (University Grants Commission).