Cited by 597Steroid Chemistry and BiochemistryMicrobial Natural Products and BiosynthesisMicrobial Metabolic Engineering and Bioproduction

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A metabolic pathway for bile acid dehydroxylation by the gut microbiome

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Funabashi, Masanori, Grove, Tyler L., Wang, Min, Varma, Yug, McFadden, Molly E., Brown, Laura C., Guo, Chunjun, Higginbottom, Steven, Almo, Steven C., Fischbach, Michael A.·2020·Nature

DOI 10.1038/s41586-020-2396-4PMC PMC7319900

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Abstract

The gut microbiota synthesize hundreds of molecules, many of which influence host physiology. Among the most abundant metabolites are the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA), which accumulate at concentrations of around 500 μM and are known to block the growth of Clostridium difficile 1, promote hepatocellular carcinoma 2 and modulate host metabolism via the G-protein-coupled receptor TGR5 (ref. 3). More broadly, DCA, LCA and their derivatives are major components of the recirculating pool of bile acids 4; the size and composition of this pool are a target of therapies for primary biliary cholangitis and nonalcoholic steatohepatitis. Nonetheless, despite the clear impact of DCA and LCA on host physiology, an incomplete knowledge of their biosynthetic genes and a lack of genetic tools to enable modification of their native microbial producers limit our ability to modulate secondary bile acid levels in the host. Here we complete the pathway to DCA and LCA by assigning and characterizing enzymes for each of the steps in its reductive arm, revealing a strategy in which the A-B rings of the steroid core are transiently converted into an electron acceptor for two reductive steps carried out by Fe-S flavoenzymes. Using anaerobic in vitro reconstitution, we establish that a set of six enzymes is necessary and sufficient for the eight-step conversion of cholic acid to DCA. We then engineer the pathway into Clostridium sporogenes, conferring production of DCA and LCA on a nonproducing commensal and demonstrating that a microbiome-derived pathway can be expressed and controlled heterologously. These data establish a complete pathway to two central components of the bile acid pool.

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Authors: Funabashi, M., Grove, T. L., Wang, M., Varma, Y., McFadden, M. E., Brown, L. C., Guo, C., Higginbottom, S., Almo, S. C., & Fischbach, M. A.
Affiliations: Daiichi Sankyo RD Novare (Japan) (JP)
Albert Einstein College of Medicine (US)
Stanford University (US)
Indiana University Bloomington (US)
Stanford Medicine (US)
Chan Zuckerberg Biohub San Francisco (US)
Corresponding author: Almo, Steven C.
Fischbach, Michael A.
ORCID: Grove, Tyler L.
Wang, Min
McFadden, Molly E.
Brown, Laura C.
Higginbottom, Steven
Almo, Steven C.
Fischbach, Michael A.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2020-06-17
Volume: 582
Issue: 7813
Pages: 566-570
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/s41586-020-2396-4
PMC: PMC7319900
OpenAlex: W3036012425
Cited by: 590
References: 46
Citations by year: 2026: 125 · 2025: 108 · 2024: 123 · 2023: 89 · 2022: 78 · 2021: 53 · 2020: 13
FWCI: 18.90
Type: journal article
Language: en
Open access: green
doi.org
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature (publishedVersion)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: Howard Hughes Medical Institute
Price Family Foundation
National Institutes of Health (1dp2hd101401-01, GM093342, DK113598, DK110174, GM094662)
National Heart, Lung, and Blood Institute (P01HL147823)
National Institute of General Medical Sciences (U54GM093342, U54GM094662, P01GM118303)
National Institute of Diabetes and Digestive and Kidney Diseases (R01DK110174, DP1DK113598, R01DK101674)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (DP2 HD101401)
Topics: Physical Sciences › Chemistry › Organic Chemistry › Steroid Chemistry and Biochemistry
Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Microbial Natural Products and Biosynthesis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords: secondary bile acids, deoxycholic acid, lithocholic acid, gut microbiota, reductive dehydroxylation, cholic acid, Clostridium sporogenes, heterologous pathway expression, germ-free mice, primary biliary cirrhosis, nonalcoholic steatohepatitis, TGR5
MeSH terms: Gastrointestinal Microbiome, Animals, Bile Acids and Salts, Clostridium, Deoxycholic Acid, Hydroxylation, Lithocholic Acid, Male, Operon, Symbiosis, Mice, Metabolic Networks and Pathways, Metabolic Engineering

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A metabolic pathway for bile acid dehydroxylation by the gut microbiome

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