Bacterial metabolism and cooperation during colon fermentation, an in vitro approach.

The human colon, which is densely populated by bacteria belonging to the Bacteriodetes and Firmicutes, and its associated fermentation process play a role in health and disease. Although the importance of these bacteria for colon health is beyond questioning, many remain poorly characterized metabolically. Knowledge of microbial (im)balances in the colon can help selecting prebiotics and probiotics, not only to maintain or restore the optimal colon microbiota in conditions of stress, disease, or antibiotic therapy, but also to reduce, for instance, obesity risks. The present study will strengthen the relationship between prebiotics, probiotics, and the colon microbiota, focusing on less known bacterial species, their metabolites (butyrate and propionate), and crossfeeding mechanisms, through kinetic, metabolite target, and transcriptomic analyses. It aims at mapping kinetics of inulin-type fructan degradation by fermentation analysis of a range of hardly characterized colon bacteria (e.g., Faecalibacterium prausnitzii). The project sets out to reveal variations in prebiotic degradation systems among colon bacteria and the impact of such diversity on bacterial interactions in co-culture fermentations. Genome analysis and transcriptomics will identify biomarkers for and elucidate the mechanisms behind cross-feeding. In this combined approach, a valuable contribution to the exploration of the human colon ecosystem will thus be obtained.