Microbial metabolic reprogramming regulates intraspecific competition of Enterobacteriaceae in the inflamed gut

Imbalance in beneficial and harmful bacteria underlies gastrointestinal diseases, such as inflammatory bowel disease. Here, we demonstrated that certain E. coli strains, specifically adherent-invasive E. coli (AIEC), utilize a serine metabolism pathway to outcompete other E. coli strains in the inflamed gut. In contrast, amino acid metabolism has a minimal effect on their competitive fitness in the healthy gut. The availability of luminal serine used for the competition of E. coli is largely dependent on dietary intake, as the inflammation-induced blooms of AIEC are significantly blunted when amino acids, particularly serine, are removed from the diet. Thus, intestinal inflammation regulates the intraspecific competition between Enterobacteriaceae by eliciting their metabolic reprogramming. GF mice were mono-colonized with AIEC LF82 for 1 week. E. coli mono-colonized mice were then treated with 1.5% DSS for 5 days. Cecal content was harvested and microbial gene expression was analyzed by RNA-seq (N=4).