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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 \u003Ci>Pv\u003C/i>05 had impacts on the abundance of several \u003Ci>Lachnospiraceae\u003C/i> and \u003Ci>Ruminococcaceae\u003C/i>. 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.  ",{"alignment":66},{"alignment":60},{"id":68,"type":55,"data":69,"tunes":71},"JmMqrOSvAJ",{"text":70},"For details: ",{"alignment":72},{"alignment":60},{"id":74,"type":55,"data":75,"tunes":76},"nY0BitiPL3",{"text":47},{"alignment":77},{"alignment":60},{"id":79,"type":55,"data":80,"tunes":82},"1TwQASIwfI",{"text":81},"Mallory J. Suhr Van Haute 1,2, Qinnan Yang 1,2,3, Nate Korth 2,4, Mary M. Happ 5, Car Reen Kok 2,4,6, Chenyong Miao 5, Jennifer L. Clarke 1,2,7, Kelsey Karnik 7,8, Kent M. Eskridge 7, Carlos A. Urrea 5, David L. Hyten 2,5, James C. Schnable 2,5, Devin J. Rose 1,2,5, Andrew K. 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