Dynamic interactions between microbes and host are essential to stimulate the immune system, maintain intestinal homeostasis, and prevent pathogen colonization. In recent decades lactic acid bacteria (LAB) have received attention due to their probiotic potential and their impact on gut microbiota and host health. This paper aims to review the main molecular mechanisms by which bile acids (BA) modify the composition of the intestinal microbiota and bacterial viability, with special emphasis on the effect on LAB. The results discussed here suggest that the BA disorganize the structure of the bacterial cell wall, modify their surface properties, their adhesion capacity and compromise the integrity of the membranes, with loss of essential ions and nutrients. They then enter the cell interior, at rates that depend on their hydrobicity. There, they dissociate, causing intracellular acidification and dissipation of membrane potential. This leads to a deficiency in the biological energy needed for critical processes, leading to cell death at high concentrations. In addition, BA causes alteration and oxidation of proteins and nucleic acids. The extent of damage caused by BA is influenced by their structure, physicochemical properties—particularly hydrophobicity—and concentration. The response of LAB depends on both their intrinsic and adaptive mechanisms. Advancing research on these interactions represents a new frontier, enabling the development of strategies to modulate intestinal microbiota composition, ultimately benefiting human health.
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