Bile acids play key roles in nutrient uptake, inflammation, signaling, and microbiome composition. While previous bile acid analyses have primarily focused on profiling 5 canonical primary and secondary bile acids and their glycine and taurine bile acid-amino acid (BA-AA) conjugates, recent studies suggest that many other microbial conjugated BA-AAs (or MCBAs) exist. MCBAs are produced by the gut microbiota and serve as biomarkers providing information about early disease onset and gut health. Here we analyzed 8 core bile acids synthetically conjugated with 22 proteogenic and non-proteogenic amino acids totaling 176 MCBAs to make an MCBA library, and applied this library to evaluate two model systems.

Since many of the conjugates were isomeric and only 42 different m/z values resulted from the 176 MCBAs, a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) was used for their separation. Their molecular characteristics were then used to create an in-house extended bile acid library for a combined total of 182 unique compounds. Additionally, ~250 rare bile acid extracts were also assessed to provide an additional resource for bile acid profiling and identification. This library was then applied to healthy mice dosed with antibiotics and humans having fecal microbiota transplantation (FMT) to assess MCBA presence and changes in the gut before and after each perturbation.

To assess the occurrence and diagnostic utility of MCBAs from the gut microbiota in a model system analogous to previous studies,7 cecal contents were collected from C57BL/6J mice before and after being dosed with cefoperazone, a cephalosporin-based antibiotic (abbreviated Abx). Sampling was performed prior to antibiotics (pre-Abx) and at four time points (weeks 1-4) following antibiotic dosing (post-Abx) for 4 mice per group. Twenty-two fecal samples from a longitudinal study of 6 human patients pre- and post-FMT (fecal microbiota transplant), collected at timepoints 2 weeks, 2 months, and 6 months post-FMT, were extracted for bile acid analysis.