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Elucidating how resident enteric bacteria interact with their hosts to promote health or inflammation is of central importance to diarrheal and inflammatory bowel diseases across species. Here, we integrate the microbial and chemical microenvironment of a patient's ileal mucosa with their clinical phenotype and genotype to identify factors favoring the growth and virulence of Adherent and Invasive E. coli (AIEC) linked to Crohn's disease. We determine that the ileal niche of AIEC is characterized by inflammation, dysbiosis, coculture of Enterococcus and oxidative stress. We discover that mucosal metabolites support general growth of ileal E. coli, with a selective effect of ethanolamine on AIEC that is augmented by co-metabolism of ileitis-associated amino acids and glutathione, and symbiosis-associated fucose. This metabolic plasticity is facilitated by the eut and pdu microcompartments, amino acid metabolism, γ-glutamyl-cycle and pleotropic stress responses. We link metabolism to virulence, finding that ethanolamine and glutamine enhance AIEC motility, infectivity and pro-inflammatory responses in vitro. We connect use of ethanolamine to intestinal inflammation, and L-fuculose phosphate aldolase (fucA) to symbiosis in AIEC mono-associated IL10-/- mice. Collectively, we establish that AIEC are pathoadapted to utilize mucosal metabolites associated with health and inflammation for growth and virulence, enabling the transition from symbiont to pathogen in a susceptible host.

Original publication




Journal article


JCI Insight

Publication Date



Amino acid metabolism, Inflammation, Inflammatory bowel disease, Microbiology