Carbohydrate Active Enzyme Profiles of Gut Microbiomes From Low and Adequate Fiber Consumers in a Healthy U.S. Cohort

OBJECTIVES: Carbohydrate structures are incredibly diverse, but humans possess only about a dozen endogenous enzymes to break down carbohydrates in the diet. Microbial enzymes, produced by the gut microbiota, can degrade and ferment what human bodies cannot. We studied the microbial genes for enzymes that degrade carbohydrates in the microbiota of healthy adult men and women in the USDA Nutritional Phenotyping Study. Individual carbohydrate active enzyme (CAZyme) gene abundances and CAZyme family diversity metrics were compared between groups of adequate and low fiber consumers in the study. We hypothesized that the CAZyme profiles of these different fiber consumption groups would differ, with adequate fiber consumers showing higher CAZyme family diversity and a different suite of CAZyme genes than the low fiber consumers. METHODS: The USDA Nutritional Phenotyping Study is a cross-sectional observational trial designed to evaluate dietary and other factors associated with metabolic health. Participants completed dietary recalls with ASA24 and a Block 2014 Food frequency questionnaire and submitted stool samples for shotgun metagenomics and fecal pH measurements. Adequate (14g/1000kcal) and low fiber consumers (lowest quartile) were identified using both dietary instruments. DNA was extracted from fecal samples and sequenced. Shotgun metagenomes (n = 290) were analyzed and mapped to the CAZy database. DESeq2 was used to compare CAZyme gene abundances. Plant substrate CAZyme family diversity using the Chao1 and Shannon metrics were tested for association with fecal pH by regression model. RESULTS: Plant substrate CAZyme family Chao1 and Shannon diversity metrics were negatively associated with fecal pH (p = 0.0009 and p = 0.0008, respectively) but were not significantly different between the consumers of adequate (n = 47) and low fiber (n = 34). However, the abundance of 28 genes for CAZyme glycoside hydrolases differed significantly between adequate and low fiber groups. CONCLUSIONS: Taken together, the enzymatic capacity of the gut microbiome may only be partly explained by habitual or recent consumption of dietary fiber. FUNDING SOURCES: USDA ARS 2032–51,530-026–00D.