A microbiota-derived bile acid modulates biofilm formation by the probiotic strain Escherichia coli Nissle 1917

Bacteria that colonize the human gut must withstand a variety of stressors, including detergent-like compounds known as bile acids. Here, we investigated how bile acids found in the human cecum and colon impact the behavior of the probiotic strain Escherichia coli Nissle 1917 (EcN). We found that lithocholic acid (LCA), which is a microbiota-derived secondary bile acid, promotes the formation of a distinctive surface-coating biofilm by EcN, including on an organoid-derived model of the human colonic epithelium. Mechanistic investigations, including RNA-sequencing, revealed that LCA upregulates the production of several components of flagella, which are essential for LCA-induced biofilm formation and form part of the biofilm extracellular matrix. Overall design: Wildtype (plasmid-cured) E. coli Nissle was grown to log phase anaerobically in YCFA media at 37C, then treated with 1% DMSO (solvent control), 100 µM lithocholic acid, or 100 µM chenodeoxycholic acid for different periods of time (15, 30, 90, 180 minutes) prior to RNA extraction.