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Gut Microbes. 2018 Dec 27:1-23. doi: 10.1080/19490976.2018.1549420. [Epub ahead of print]

In vitro and in vivo characterization of Clostridium scindens bile acid transformations.

Author information

a Environmental Microbiology Laboratory , École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne , Switzerland.
b Institute for Infectious Diseases, University of Bern , Bern , Switzerland.
c Institute of Chemical Sciences and Engineering , École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne , Switzerland.
d Laboratory for Biological Geochemistry , École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne , Switzerland.
e Center for Advanced Surface Analysis , Université de Lausanne , Lausanne , Switzerland.


The human gut hosts trillions of microorganisms that exert a profound influence on human biology. Gut bacteria communicate with their host by secreting small molecules that can signal to distant organs in the body. Bile acids are one class of these signaling molecules, synthesized by the host and chemically transformed by the gut microbiota. Among bile acid metabolizers, bile acid 7-dehydroxylating bacteria are commensals of particular importance as they carry out the 7-dehydroxylation of liver-derived primary bile acids to 7-dehydroxylated bile acids. The latter represents a major fraction of the secondary bile acid pool. The microbiology of this group of gut microorganisms is understudied and warrants more attention. Here, we detail the bile acid transformations carried out by the 7-dehydroxylating bacterium Clostridium scindens in vitro and in vivo. In vitro, C. scindens exhibits not only 7α-dehydroxylating capabilities but also, the ability to oxidize other hydroxyl groups and reduce ketone groups in primary and secondary bile acids. This study revealed 12-oxolithocholic acid as a major transient product in the 7α-dehydroxylation of cholic acid. Furthermore, the in vivo study included complementing a gnotobiotic mouse line (devoid of the ability to 7-dehydroxylate bile acids) with C. scindens and investigating its colonization dynamics and bile acid transformations. Using NanoSIMS (Nanoscale Secondary Ion Mass Spectrometry), we demonstrate that the large intestine constitutes a niche for C. scindens, where it efficiently 7-dehydroxylates cholic acid to deoxycholic acid. Overall, this work reveals a novel transient species during 7-dehydroxylation as well as provides direct evidence for the colonization and growth of 7-dehydroxylating bacteria in the large intestine.


12-oxo bile acids; 7α-dehydroxylation pathway; Bile salts; clostridium; commensal bacteria; deoxycholic acid (DCA); gut ecology; intestinal colonization; lithocholic acid (LCA); stable isotopes

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