Complete genome-derived metabolic interactions reveal impact of gut ecology on human health

Abstract Metabolic interactions govern gut microbiome assembly, yet functional rules remain obscured by genomic incompleteness and fragmentation. Here, we leverage 1,150 complete genomes to construct genome-scale metabolic models, demonstrating that draft genomes introduce systemic artifacts missing critical transport functions. We observe that metabolic interactions are intrinsically driven by genomic traits and niche specialization rather than random association. We stratifies strains into four ecological groups, including active players, resource predators, utilizers, and contributors, each of which exhibits distinct metabolite exchange/competition signatures. This functional architecture is strongly coupled to secondary metabolism. Applying this framework to inflammatory bowel disease revealed distinct temporal dynamics of ecological groups across disease subtypes, where group-specific dysbiosis predicted clinical phenotypes better than whole community profiles. Furthermore, integrating metabolic and co-occurrence networks to identify keystone for classifiers as features significantly improved disease diagnosis. Our study provides novel insights into gut metabolic interaction landscape, bridging the gap between genomic potential and clinical utility for precision microbiome therapeutics. Competing Interest Statement Yiyi Zhong is the head of the research and development department of BGI Precision Nutrition. Zhang Haifeng is the general manager of BGI Precision Nutrition. Liang Xiao and Yuanqiang Zou are part-time microbial scientists at BGI Precision Nutrition. BGI Precision Nutrition is a company engaged in the production and sale of probiotic products, which may lead to potential conflicts of interest.