Method for assessing inter-individual variability in the carbohydrate utilization potential of gut microbiota ex vivo

The microbial utilization of carbohydrates produces metabolic byproducts that are associated with health benefits, such as short-chain fatty acids (SCFAs). The rapid absorption of SCFAs by intestinal epithelial cells makes them challenging to study in vivo. Culturing methods address this limitation by providing controlled conditions that allow for monitoring substrate utilization and the production of fermentation byproducts. In this paper, we describe an easily implemented, cost-effective method for screening inter-individual differences in carbohydrate degradation potential among gut microbiota from different individuals using batch cultures in 96-deep well plates. In addition to culturing methods, we describe procedures for obtaining stool samples from human volunteers, as well as for processing and storing them. We demonstrate that complete or near-complete substrate utilization is typically reached within 24 hours of culturing in buffered media in 96-deep well plates, and inter-individual differences in substrate utilization rate and SCFA production are observable by 12 hours.