Abstract
Through biochemical transformation of host-derived bile acids, gut bacteria mediate host-microbe crosstalk and function at the interface of nutrition and host metabolic regulation. Bile acids play a crucial role in human health by facilitating the absorption of dietary lipophilic nutrients, interacting with hormone receptors to regulate host physiology, and shaping gut microbiota composition through antimicrobial activity. Bile acids deconjugation by bacterial bile salt hydrolase has long been recognized as the first necessary bile acid modification required before further transformations can occur. Here, we show that bile salt hydrolase activity is common among human gut bacterial isolates spanning seven major phyla. However, we observed variation in both the extent and the specificity of deconjugation of bile acids among the tested taxa. Unexpectedly, we discovered that certain strains were capable of directly dehydrogenating conjugated bile acids via hydroxysteroid dehydrogenases to produce conjugated secondary bile acids both in vitro and in vivo. These results challenge the prevailing notion that deconjugation is a prerequisite for further bile acid modifications and lay a foundation for new hypotheses regarding how bacteria act individually or in concert to diversify the bile acid pool and influence host physiology.
Data availability
Accession codes for sequenced bacterial strains have been included in Supplementary Table 1 in the Supplementary Information file. Accession codes and hyperlinks are included in the Source Data for Fig. 3. The raw data generated in this study are provided in the Source Data file. The metabolomics data generated in this study are available in the MassIVE database (gnps.ucsd.edu) under MassIVE ID MSV000100317. Source data are provided with this paper.
Code availability
All custom code can be found at: https://github.com/qijunz/Lucas_BSH_paper.
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Acknowledgements
L.N.L. was supported by the Molecular and Applied Nutrition Training Program (MANTP) NIH T32 DK 007665. L.N.L. was supported by an NIH Ruth L. Kirschstein National Research Service Award (F32 DK142449). J.M. was supported in part by the National Institutes of Health (NIH) grants HL148577 (F.E.R.), DK117850 (F.E.R) and by the Transatlantic Networks of Excellence Award from the Leducq Foundation. L.N.L. and J.M. were supported in part by the University of Wisconsin–Madison Office of the Vice Chancellor for Research with funding from the Wisconsin Alumni Research Foundation. L.E.C. was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number T32 GM135066. L.E.C. was also supported by the University of Wisconsin–Madison SciMed Graduate Research Scholars Fellowship. A.P.C. was supported by an NIH Ruth L. Kirschstein National Research Service Award (F32 GM155981).
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L.N.L., J.M., D.A.N., and F.E.R. conceived the project. R.L.K. provided gut bacterial strains and media recipes. L.E.C. performed systematic in vitro screening for BSH activity in all strains. B.G. and L.N.L. performed in vitro monoculture experiments. J.M. performed in vitro coculture experiments. J.M. generated the Δhsd mutant. L.N.L. and J.M. performed the in vivo experiment. Q.Z. wrote scripts for bioinformatic analyses. A.P.C. and H.E.B. synthesized the glyco-7-oxolithocholic acid standard and confirmed its purity. L.N.L. analyzed all data and generated figures. L.N.L., J.M., D.A.N., and F.E.R. interpreted data. D.M.S. provided guidance on LC-MS/MS methods and analyses. L.N.L. wrote the manuscript, D.A.N. substantively revised it, J.M. and F.E.R. provided feedback throughout the writing process, and all authors edited and approved the final manuscript.
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Lucas, L.N., Jillella, M., Cattaneo, L.E. et al. Investigation of bile salt hydrolase activity in human gut bacteria reveals production of conjugated secondary bile acids. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68556-4
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DOI: https://doi.org/10.1038/s41467-026-68556-4
