(P27-051-24) A Targeted Multi-Omics Platform for Characterizing Prebiotic-Probiotic Interactions

Objectives: Herein, we report a bioreactor study utilizing fecal samples from five human donors to monitor gut bacterial response to different fiber supplementations. We then used a recently developed rapid through-put UHPLC-QqQ multi-omics platform to obtain simultaneously the compositional changes of fiber and microbial SCFA profiles during the fermentation.

Methods: Commonly consumed fiber supplements were fermented with extracted fecal bacteria from five different donors in small-scale bioreactors under anaerobic conditions. Total and free monosaccharide content as well as glycosidic linkage composition was determined in the homogenized slurry samples; microbial SCFAs were analyzed from the supernatant. 16s rRNA sequencing was performed at each time point to monitor changes in microbial composition.

Results: Chosen fibers were fermented by the fecal microbiome of five healthy subjects. Monosaccharide, glycosidic linkage, and SCFA analysis were conducted to study compositional changes in the fiber and subsequent metabolic profile across donors using previously developed UHPLC-dMRM MS methods. Fecal fermentations without fiber addition were included as negative controls and to assess the contribution of background diet in the feces. Furthermore, 16s rRNA sequencing and transcriptomics were performed to monitor changes in the gut microbial community as well as changes in CAZyme expression.

The fermentation of several complex fibers produced results that varied widely between subjects. For coconut flour, the total monosaccharide analysis of the fiber revealed its composition to consist of glucose, galactose, mannose, and arabinose. The total monosaccharide concentration for glucose decreased from 0.5 mg/mL to 0.1 mg/mL for subject 1 after three days whereas other monosaccharides did not change in appreciable amounts. From these results, it was inferred that the gut microbiome from subject 1 had the enzymatic repertoire to break down the glucose components of the fiber but most of the fiber remained unconsumed.

Conclusions: A targeted, rapid-throughput multi-omics platform was developed and applied to bioreactor fermentations to probe prebiotic-probiotic interactions of commonly consumed fibers.

Funding Sources: NIH, USDA