Bile Salts and Bacterial Bile Salt Hydrolase Activity Differentially Influence Escherichia coli Colonization and FXR Signaling in Colorectal Cancer Organoids

Bile salts are key regulators of host-microbe interactions and epithelial signaling in the intestine. Gut bacteria can deconjugate primary bile salts, which can be leveraged to engineer targeted therapies through bile salt hydrolase (BSH) activity. However, the interplay between bile salt signaling, microbial metabolism, and tumor-associated colonization remains poorly understood. Here, we establish an in vitro colon organoid platform to dissect bile salt-driven epithelial-microbe dynamics at cellular resolution. Using this system, we found that bile salts markedly modulated colonization of native Escherichia coli (EcAZ-2) and a BSH-expressing strain (EcAZ-2LsBSH) in healthy versus tumor murine organoids. Under bile salt exposure, EcAZ-2LsBSH preferentially colonized tumor organoids, though overall colonization was lower than that of the non-BSH strain. Beyond effects on bacterial colonization, bile salts also directly activated host signaling pathways. In presence of bile salts, EcAZ-2LsBSH significantly enhanced activation of bile acid receptors such as farnesoid X receptor (FXR) by 2-fold in healthy organoids. These findings reveal a mechanistic bridge between in vivo microbial function and bile salt interactions, offering potential microbiota and bile acid targeted therapeutic strategies.