Disease-specific loss of microbial cross-feeding interactions in the human gut.
Publication Title
Nat Commun
Document Type
Article
Publication Date
10-20-2023
Keywords
Humans; Gastrointestinal Microbiome; Case-Control Studies; Microbiota; Metagenome; Crohn Disease; washington; isb
Abstract
Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging to quantify and remain poorly characterized. Here, we introduce a Metabolite Exchange Score (MES) to quantify those interactions. Using metabolic models of prokaryotic metagenome-assembled genomes from over 1600 individuals, MES allows us to identify and rank metabolic interactions that are significantly affected by a loss of cross-feeding partners in 10 out of 11 diseases. When applied to a Crohn's disease case-control study, our approach identifies a lack of species with the ability to consume hydrogen sulfide as the main distinguishing microbiome feature of disease. We propose that our conceptual framework will help prioritize in-depth analyses, experiments and clinical targets, and that targeting the restoration of microbial cross-feeding interactions is a promising mechanism-informed strategy to reconstruct a healthy gut ecosystem.
Clinical Institute
Digestive Health
Specialty/Research Institute
Gastroenterology
DOI
10.1038/s41467-023-42112-w
