There is growing interest in developing foods that predictably modulate the human gut microbiome to promote health. To this end, Yang et al. developed a system to genetically analyse seed traits in Sorghum bicolour that are associated with changes in the abundance of microbial taxa and/or metabolites in the human gut microbiome. Of the 10 genomic loci identified, two were close to genes involved in condensed tannin biosynthesis. Indeed, subsequent analyses showed that condensed tannins regulate the abundance of taxa associated with these loci and, in particular, supported and promoted growth of Faecalibacterium prausnitzii, a beneficial bacterium that is typically depleted in the gut of individuals with inflammatory bowel disease. This study provides a framework for identifying seed traits in food crops that have health-promoting effects on the gut microbiome and that can be incorporated into crop improvement schemes.