Bile acids play key roles in gut metabolism, cell signaling, and microbiome composition. While the liver is responsible for the production of primary bile acids, microbes in the gut modify these compounds into myriad forms that greatly increase their diversity and biological function. Since the early 1960s, microbes have been known to transform human bile acids in four distinct ways: deconjugation of the amino acids glycine or taurine, and dehydroxylation, dehydrogenation, and epimerization of the cholesterol core. Alterations in the chemistry of these secondary bile acids have been linked to several diseases, such as cirrhosis, inflammatory bowel disease, and cancer. In addition to the previously known transformations, a recent study has shown that members of our gut microbiota are also able to conjugate amino acids to bile acids, representing a new set of “microbially conjugated bile acids.” This new finding greatly influences the diversity of bile acids in the mammalian gut, but the effects on host physiology and microbial dynamics are mostly unknown. This review focuses on recent discoveries investigating microbial mechanisms of human bile acids and explores the chemical diversity that may exist in bile acid structures in light of the new discovery of microbial conjugations.

Periprosthetic joint infections (PJIs) are a devastating complication that occurs in 2% of patients following joint replacement. These infections are costly and difficult to treat, often requiring multiple corrective surgeries and prolonged antimicrobial treatments. The Gram-positive bacterium Staphylococcus aureus is one of the most common causes of PJIs, and it is often resistant to a number of commonly used antimicrobials. This tolerance can be partially attributed to the ability of S. aureus to form biofilms. Biofilms associated with the surface of indwelling medical devices have been observed on components removed during chronic infection, however, the development and localization of biofilms during PJIs remains unclear. Prior studies have demonstrated that synovial fluid, in the joint cavity, promotes the development of bacterial aggregates with many biofilm-like properties, including antibiotic resistance. We anticipate these aggregates have an important role in biofilm formation and antibiotic tolerance during PJIs. Therefore, we sought to determine specifically how synovial fluid promotes aggregate formation and the impact of this process on surface attachment. Using flow cytometry and microscopy, we quantified the aggregation of various clinical S. aureus strains following exposure to purified synovial fluid components. We determined that fibrinogen and fibronectin promoted bacterial aggregation, while cell free DNA, serum albumin, and hyaluronic acid had minimal effect. To determine how synovial fluid mediated aggregation affects surface attachment, we utilized microscopy to measure bacterial attachment. Surprisingly, we found that synovial fluid significantly impeded bacterial surface attachment to a variety of materials. We conclude from this study that fibrinogen and fibronectin in synovial fluid have a crucial role in promoting bacterial aggregation and inhibiting surface adhesion during PJI. Collectively, we propose that synovial fluid may have conflicting protective roles for the host by preventing adhesion to surfaces, but by promoting bacterial aggregation is also contributing to the development of antibiotic tolerance.

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Bile acids (BAs) are steroid detergents in bile that contribute to the absorption of fats and fat-soluble vitamins while shaping the gut microbiome due to their antimicrobial properties. Recently, a novel mechanism of BA metabolism by the gut microbiota was identified involving conjugation with various amino acids. Here, we show this unique biochemistry is mediated by bile salt hydrolase acting as an aminoacyltransferase or transpeptidase (BSH/T). Clostridium perfringens BSH/T rapidly performed acyl-transfer when provided various amino acids and taurocholate, glycocholate or cholate, with an optimum at approximately pH 5.3. Amino acids selected for incorporation by CpBSH/T were pH-dependent and broad in range, though proline and aspartic acid conjugates were not observed. BA conjugation was widespread among gut bacteria but showed unique amino acid preferences depending on the organism. Members of the family Lachnospiraceae had closely related BSH/T amino acid sequences and exhibited similar amino acid conjugation profiles, while horizontal gene transfer of bsh in some species increased conjugation diversity. Tertiary structure mapping of BSH/T from different gut bacteria implicates active site structure in amino acid selectivity. The products of BSH/T aminoacyltransferase activity were potent antimicrobials but this depended on the amino acid conjugated, with phenylalanine and leucine-conjugates acting as the best inhibitors of other gut commensals and known pathogens. This inhibitory property translated in vivo, as oral gavage of mice with different microbially conjugated bile acids altered the cecal and fecal microbiomes. This study shows that transpeptidase activity of BSH/T is a widespread and common property of the enzyme that greatly diversifies the bile acid pool, with the potential to shape the human microbiome.

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