Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome

Authors: YANG, QINNAN - University Of Nebraska; VAN HAUTE, MALLORY - University Of Nebraska; KORTH, NATE - University Of Nebraska; Sattler, Scott; Toy, John; SCHNABLE, JAMES - University Of Nebraska; BENSON, ANDREW - University Of Nebraska

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2022
Publication Date: 9/26/2022
Citation: Yang, Q., Van Haute, M., Korth, N., Sattler, S.E., Toy, J.J., Schnable, J.C., Benson, A.K. 2022. Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome. Nature Communications. 13:5641. https://doi.org/10.1038/s41467-022-33419-1.
DOI: https://doi.org/10.1038/s41467-022-33419-1

Interpretive Summary: The compounds within the foods humans consume have major effects on composition and function of the bacteria found within the human gut. However, studying the effects of these compounds, which vary in food crops, is challenging. Scientists in Lincoln, Nebraska developed a novel automated in vitro microbiome screening (AiMS) method to quantify how food crop components affect human gut microbes after fermentation of grain, which was used to evaluate 294 different sorghum (Sorghum bicolor) grain samples to identify genetic regions responsible for changes to bacterial composition. Ten different genetic regions were identified that affected 16 different bacterial groups. An additional set of grain samples confirmed that tannin concentrations, a cell wall component derived from the flavonoid pathway, the purple pigments of plants was responsible for the observations. Tan1 (chromosome 4) and Tan2 (chromosome 2) that encode regulators of tannin synthesis in sorghum were primarily responsible for the differences observed. This study demonstrated that plant compounds even at relatively low levels can affect the bacterial composition of human gut (microbiome), which could lead to improved human health.

Technical Abstract: Prebiotic fibers, polyphenols and other molecular components of food crops significantly affect the composition and function of the human gut microbiome and human health. The abundance of these, frequently uncharacterized, microbiome-active components vary within individual crop species. Here, we employ high throughput in vitro fermentations of pre-digested grain using a human microbiome to identify segregating genetic loci in a food crop, sorghum, that alter the composition and function of human gut microbes. Evaluating grain produced by 294 sorghum recombinant inbreds identifies 10 loci in the sorghum genome associated with variation in the abundance of microbial taxa and/or microbial metabolites. Two loci co-localize with sorghum genes regulating the biosynthesis of condensed tannins. We validate that condensed tannins stimulate the growth of microbes associated with these two loci. Our work illustrates the potential for genetic analysis to systematically discover and characterize molecular components of food crops that influence the human gut microbiome.