Dietary Polysaccharides Modulate Interactions between Bacteroides and the Gut Microbiota: Gene-Level Mechanisms and Perspectives on Genome-Scale Metabolic Modeling for Community Simulation

Bacteroides is a major gut genus involved in polysaccharide uptake and degradation, yet the gene-level mechanisms by which dietary polysaccharides modulate interactions between Bacteroides and other gut microbes remain insufficiently integrated. This review summarizes dietary-polysaccharide-driven Bacteroides interactions from the perspectives of PULs, CAZymes, released oligosaccharides, fermentation products, and GEM-based community simulation. Emphasis is placed on how PUL–CAZyme repertoires shape substrate specificity, metabolite exchange, cross-feeding, competition, commensalism, and mutualism under different glycan conditions. The review further discusses the application of GEMs to simulate Bacteroides -centered communities, including reconstruction tool selection, static and dynamic modeling frameworks, and current limitations in representing polysaccharide structure and stepwise degradation. These advances provide a framework for linking dietary polysaccharide chemistry, microbial gene functions, community metabolism, and gut health-related outcomes.