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ARS Home » Pacific West Area » Davis, California » Western Human Nutrition Research Center » Diet, Microbiome and Immunity Research » Research » Publications at this Location » Publication #424099
Research Project: Effect of Diet on Gut Microbiome, Gastrointestinal Health, and Immune Function

Location: Diet, Microbiome and Immunity Research

Title: Gut microbiome genes involved in plant and mucin breakdown correlate with diet and gastrointestinal inflammation in healthy United States adults

Author
item BLECKSMITH, SARAH - University Of California, Davis
item Oliver, Andrew
item Alkan, Zeynep
item Lemay, Danielle

Submitted to: Journal of Nutrition
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/28/2025
Publication Date: 9/1/2025
Citation: Blecksmith, S.E., Oliver, A.S., Alkan, Z., Lemay, D.G. 2025. Gut microbiome genes involved in plant and mucin breakdown correlate with diet and gastrointestinal inflammation in healthy United States adults. Journal of Nutrition. 155(11): 3757-3768. https://doi.org/10.1016/j.tjnut.2025.08.027.
DOI: https://doi.org/10.1016/j.tjnut.2025.08.027

Interpretive Summary: We investigated how our diet affects the gut microbes' ability to break down carbohydrates and whether this relates to health. By studying 330 healthy U.S. adults, we discovered that higher fiber intake increases the diversity and abundance of microbial genes that break down plant carbohydrates. We also developed a new measurement called Muc2Plant to assess microbes' preference for digesting dietary versus protective gut-lining carbohydrates. This metric was linked to body mass index and inflammation markers, suggesting potential dietary approaches for improving intestinal health.

Technical Abstract: Dietary carbohydrates shape the composition and function of gut microbes which may potentially influence human health, especially for infants, disease states, or extreme diets. It is not known if these diet-microbiome relationships are relevant to healthy American adults. We hypothesized that intake of dietary fiber by healthy adults would be associated with the carbohydrate active enzyme (CAZyme) capacity of their gut microbiome and that this CAZyme capacity would be correlated with GI inflammation. We analyzed CAZyme profiles from shotgun metagenomes of fecal samples in the USDA Nutritional Phenotyping Study cohort (n=330) of healthy US adults. We found that CAZyme diversity varied across participants. Plant CAZyme diversity and abundance correlated significantly with fecal pH and habitual energy-adjusted total fiber and soluble fiber intake. Between consumers of adequate and low fiber, we identified 3 differentially abundant CAZymes families and 42 differentially abundant CAZyme genes between these groups. The ratio of mucin degrading CAZymes to plant-degrading enzymes, coined here as the metric, Muc2Plant, varied across participants and differed by sex and BMI. Muc2Plant positively correlated with gastrointestinal inflammation. ML classification models were used to identify specific foods (e.g. potatoes) and microbes (e.g. Lachnospiraceae) as predictors of low Muc2Plant. These results support the relevance of diet-microbiome relationships even in healthy adults, and that reduction of Muc2Plant, via dietary and/or microbial interventions, would be a beneficial health target to prevent dysbiosis.