Global chemical effects of the microbiome include new bile-acid conjugations

Global chemical effects of the microbiome include new bile-acid conjugations


  • 1.

    Ridlon, J. M., Kang, D. J., Hylemon, P. B. & Bajaj, J. S. Bile acids and the gut microbiome. Curr. Opin. Gastroenterol. 30, 332–338 (2014).

  • 2.

    Gilbert, J. A. et al. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 535, 94–103 (2016).

  • 3.

    Wikoff, W. R. et al. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl Acad. Sci. USA 106, 3698–3703 (2009).

  • 4.

    Marcobal, A. et al. Metabolome progression during early gut microbial colonization of gnotobiotic mice. Sci. Rep. 5, 11589 (2015).

  • 5.

    Miller, T. L. & Wolin, M. J. Pathways of acetate, propionate, and butyrate formation by the human fecal microbial flora. Appl. Environ. Microbiol. 62, 1589–1592 (1996).

  • 6.

    Gillner, M., Bergman, J., Cambillau, C., Fernström, B. & Gustafsson, J. A. Interactions of indoles with specific binding sites for 2,3,7,8-tetrachlorodibenzo-p-dioxin in rat liver. Mol. Pharmacol. 28, 357–363 (1985).

  • 7.

    Martin, F.-P. J. et al. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol. Syst. Biol. 3, 112 (2007).

  • 8.

    Moriya, T., Satomi, Y., Murata, S., Sawada, H. & Kobayashi, H. Effect of gut microbiota on host whole metabolome. Metabolomics 13, 101 (2017).

  • 9.

    Swann, J. R. et al. Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc. Natl Acad. Sci. USA 108 (Suppl 1), 4523–4530 (2011).

  • 10.

    Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).

  • 11.

    Wang, M. et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat. Biotechnol. 34, 828–837 (2016).

  • 12.

    Watrous, J. et al. Mass spectral molecular networking of living microbial colonies. Proc. Natl Acad. Sci. USA 109, E1743–E1752 (2012).

  • 13.

    Protsyuk, I. et al. 3D molecular cartography using LC-MS facilitated by Optimus and ’ili software. Nat. Protocols 13, 134–154 (2018).

  • 14.

    Hofmann, A. F. & Hagey, L. R. Key discoveries in bile acid chemistry and biology and their clinical applications: history of the last eight decades. J. Lipid Res. 55, 1553–1595 (2014).

  • 15.

    Yang, J. Y. et al. Molecular networking as a dereplication strategy. J. Nat. Prod. 76, 1686–1699 (2013).

  • 16.

    Sumner, L. W. et al. Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics 3, 211–221 (2007).

  • 17.

    Hartmann, A. C. et al. Meta-mass shift chemical profiling of metabolomes from coral reefs. Proc. Natl Acad. Sci. USA 114, 11685–11690 (2017).

  • 18.

    Hirano, S. & Masuda, N. Characterization of NADP-dependent 7β-hydroxysteroid dehydrogenases from Peptostreptococcus productus and Eubacterium aerofaciens. Appl. Environ. Microbiol. 43, 1057–1063 (1982).

  • 19.

    Wahlström, A., Sayin, S. I., Marschall, H.-U. & Bäckhed, F. Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metab. 24, 41–50 (2016).

  • 20.

    Huijghebaert, S. M. & Hofmann, A. F. Influence of the amino acid moiety on deconjugation of bile acid amidates by cholylglycine hydrolase or human fecal cultures. J. Lipid Res. 27, 742–752 (1986).

  • 21.

    Myher, J. J., Marai, L., Kuksis, A., Yousef, I. M. & Fisher, M. M. Identification of ornithine and arginine conjugates of cholic acid by mass spectrometry. Can. J. Biochem. 53, 583–590 (1975).

  • 22.

    Peric-Golia, L. & Jones, R. S. Ornithocholanic acids and cholelithiasis in man. Science 142, 245–246 (1963).

  • 23.

    Gordon, B. A., Kuksis, A. & Beveridge, J. M. R. Separation of bile acid conjugates by ion exchange chromatography. Can. J. Biochem. Physiol. 41, 77–89 (1963).

  • 24.

    Yousef, I. M. & Fisher, M. M. Bile acid metabolism in mammals. VIII. Biliary secretion of cholylarginine by the isolated perfused rat liver. Can. J. Physiol. Pharmacol. 53, 880–887 (1975).

  • 25.

    Tamari, M., Ogawa, M. & Kametaka, M. A new bile acid conjugate, ciliatocholic acid, from bovine gall bladder bile. J. Biochem. 80, 371–377 (1976).

  • 26.

    Hagey, L. R., Schteingart, C. D., Rossi, S. S., Ton-Nu, H. T. & Hofmann, A. F. An N-acyl glycyltaurine conjugate of deoxycholic acid in the biliary bile acids of the rabbit. J. Lipid Res. 39, 2119–2124 (1998).

  • 27.

    Nair, P. P., Solomon, R., Bankoski, J. & Plapinger, R. Bile acids in tissues: binding of lithocholic acid to protein. Lipids 13, 966–970 (1978).

  • 28.

    McDonald, D. et al. American gut: an open platform for citizen science microbiome research. mSystems 3, e00031-18 (2018).

  • 29.

    Shalapour, S. et al. Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature 551, 340–345 (2017).

  • 30.

    Manor, O. et al. Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis. Sci. Rep. 6, 22493 (2016).

  • 31.

    Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655–662 (2019).

  • 32.

    Hirano, S., Masuda, N., Oda, H. & Mukai, H. Transformation of bile acids by Clostridium perfringens. Appl. Environ. Microbiol. 42, 394–399 (1981).

  • 33.

    Winston, J. A. & Theriot, C. M. Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract. Anaerobe 41, 44–50 (2016).

  • 34.

    McDonald, J. A. K. et al. Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model. J. Microbiol. Methods 95, 167–174 (2013).

  • 35.

    Finegold, S. M. et al. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 16, 444–453 (2010).

  • 36.

    Dehoux, P. et al. Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants. BMC Genomics 17, 819 (2016).

  • 37.

    Caballero, S. et al. Cooperating commensals restore colonization resistance to vancomycin-resistant Enterococcus faecium. Cell Host Microbe 21, 592–602.e4 (2017).

  • 38.

    Sayin, S. I. et al. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab. 17, 225–235 (2013).

  • 39.

    Downes, M. et al. A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR. Mol. Cell 11, 1079–1092 (2003).

  • 40.

    Gustafsson, B. E., Gustafsson, J. A. & Sjövall, J. Intestinal and fecal sterols in germfree and conventional rats. Bile acids and steroids 172. Acta Chem. Scand. 20, 1827–1835 (1966).

  • 41.

    Midtvedt, T. Microbial bile acid transformation. Am. J. Clin. Nutr. 27, 1341–1347 (1974).

  • 42.

    Gérard, P. Metabolism of cholesterol and bile acids by the gut microbiota. Pathogens 3, 14–24 (2013).

  • 43.

    Wang, M. et al. Mass spectrometry searches using MASST. Nat. Biotechnol. 38, 23–26 (2020).


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