Genetic variation and historical breeding patterns in common bean (Phaseolus vulgaris L.) affect fermentation patterns by the human gut microbiome

Common beans, which contain diverse bioactive molecules, have not been systematically studied for their variation in how they affect the human gut microbiome. We measured taxonomic shifts and metabolite production of three human gut microbiomes cultured with 299 common bean cultivars under conditions that mimic the nutrient availability of the human colon. Common bean population structure (landrace and market class) had significant effects on microbiota diversity, composition, and metabolite production. Genome-wide association analysis identified seven multiple effect loci (MEL) where genetic variation in the common bean genome affected the microbiome. One MEL on chromosome Pv05 had impacts on the abundance of several Lachnospiraceae and Ruminococcaceae. Molecular complementation experiments suggested that variation in the biosynthesis of saponins at this MEL was the mechanism driving the variability in microbiota composition and function. This study provides innovative understanding of how genetics of common beans affects the human gut microbiome and potentially human health.