Bile acids are crucial for the uptake of dietary lipids and can shape the gut-microbiome composition. This latter function is associated with the toxicity of bile acids and can be modulated by bile acid modifying bacteria such as Eggerthella lenta, but the molecular details of the interaction of bacteria depending on bile acid modifications are not well understood. In order to unravel the molecular response to bile acids and their metabolites, we cultivated eight strains from a human intestinal microbiome model alone and in co-culture with Eggerthella lenta in the presence of cholic acid (CA) and deoxycholic acid (DCA). We observed growth inhibition of particularly gram-positive strains such as Clostridium ramosum and the gram-variable Anaerostipes cacae by CA and DCA stress. C. ramosum was alleviated through co-culturing with Eggerthella lenta. We approached effects on the membrane by zeta potential and genotoxic and metabolic effects by (meta)proteomic and metabolomic analyses. Co-culturing with Eggerthella lenta decreased both CA and DCA by the formation of oxidized and epimerized bile acids. Eggerthella lenta also produces microbial bile salt conjugates in a co-cultured species-specific manner. This study highlights how the interaction with other bacteria can influence the functionality of bacteria.

Department of General Visceral and Transplant Surgery University Hospital Aachen 52074 Aachen Germany

Department of Surgery NUTRIM School of Nutrition and Translational Research in Metabolism Maastricht University 6229 Maastricht The Netherlands

Functional Microbiome Research Group Institute of Medical Microbiology RWTH University Hospital 52074 Aachen Germany

German Centre for Integrative Biodiversity Research Halle Jena Leipzig Puschstraße 4 04103 Leipzig Germany

Helmholtz Centre for Environmental Research UFZ GmbH Department of Environmental Microbiology 04318 Leipzig Germany

Helmholtz Centre for Environmental Research UFZ GmbH Department of Molecular Systems Biology 04318 Leipzig Germany

Institute of Biochemistry Faculty of Biosciences Pharmacy and Psychology University of Leipzig 04103 Leipzig Germany

Institute of Medical Biochemistry and Laboratory Diagnostics 1st Faculty of Medicine and General University Hospital Prague Charles University Kateřinská 32 12108 Prague Czech Republic

Zobrazit více v PubMed

Wu H.J., Wu E. The Role of Gut Microbiota in Immune Homeostasis and Autoimmunity. Gut Microbes. 2012;3:4–14. doi: 10.4161/gmic.19320. PubMed DOI PMC

Magnúsdóttir S., Ravcheev D., De Crécy-Lagard V., Thiele I. Systematic Genome Assessment of B-Vitamin Biosynthesis Suggests Cooperation among Gut Microbes. Front. Genet. 2015;6:148. doi: 10.3389/fgene.2015.00148. PubMed DOI PMC

Koh A., De Vadder F., Kovatcheva-Datchary P., Bäckhed F. From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites. Cell. 2016;165:1332–1345. doi: 10.1016/j.cell.2016.05.041. PubMed DOI

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. 2016;24:41–50. doi: 10.1016/j.cmet.2016.05.005. PubMed DOI

Inagaki T., Moschetta A., Lee Y.K., Peng L., Zhao G., Downes M., Yu R.T., Shelton J.M., Richardson J.A., Repa J.J., et al. Regulation of Antibacterial Defense in the Small Intestine by the Nuclear Bile Acid Receptor. Proc. Natl. Acad. Sci. USA. 2006;103:3920–3925. doi: 10.1073/pnas.0509592103. PubMed DOI PMC

Gomez-Ospina N., Potter C.J., Xiao R., Manickam K., Kim M.S., Kim K.H., Shneider B.L., Picarsic J.L., Jacobson T.A., Zhang J., et al. Mutations in the Nuclear Bile Acid Receptor FXR Cause Progressive Familial Intrahepatic Cholestasis. Nat. Commun. 2016;7:10713. doi: 10.1038/ncomms10713. PubMed DOI PMC

Pols T.W.H., Noriega L.G., Nomura M., Auwerx J., Schoonjans K. The Bile Acid Membrane Receptor TGR5: A Valuable Metabolic Target. Dig. Dis. 2011;29:37–44. doi: 10.1159/000324126. PubMed DOI PMC

Albalak A., Zeidel M.L., Zucker S.D., Jackson A.A., Donovan J.M. Effects of Submicellar Bile Salt Concentrations on Biological Membrane Permeability to Low Molecular Weight Non-Ionic Solutes. Biochemistry. 1996;35:7936–7945. doi: 10.1021/bi960497i. PubMed DOI

Islam K.B.M.S., Fukiya S., Hagio M., Fujii N., Ishizuka S., Ooka T., Ogura Y., Hayashi T., Yokota A. Bile Acid Is a Host Factor That Regulates the Composition of the Cecal Microbiota in Rats. Gastroenterology. 2011;141:1773–1781. doi: 10.1053/j.gastro.2011.07.046. PubMed DOI

Kakiyama G., Pandak W.M., Gillevet P.M., Hylemon P.B., Heuman D.M., Daita K., Takei H., Muto A., Nittono H., Ridlon J.M., et al. Modulation of the Fecal Bile Acid Profile by Gut Microbiota in Cirrhosis. J. Hepatol. 2013;58:949–955. doi: 10.1016/j.jhep.2013.01.003. PubMed DOI PMC

Ridlon J.M., Kang D.J., Hylemon P.B., Bajaj J.S. Bile Acids and the Gut Microbiome. Curr. Opin. Gastroenterol. 2014;30:332–338. doi: 10.1097/MOG.0000000000000057. PubMed DOI PMC

Chiang J.Y.L. Bile Acid Metabolism and Signaling. Compr. Physiol. 2013;3:1191–1212. doi: 10.1002/cphy.c120023. PubMed DOI PMC

van Best N., Rolle-Kampczyk U., Schaap F.G., Basic M., Olde Damink S.W.M., Bleich A., Savelkoul P.H.M., von Bergen M., Penders J., Hornef M.W. Bile Acids Drive the Newborn’s Gut Microbiota Maturation. Nat. Commun. 2020;11:3692. doi: 10.1038/s41467-020-17183-8. PubMed DOI PMC

Haange S.B., Jehmlich N., Krügel U., Hintschich C., Wehrmann D., Hankir M., Seyfried F., Froment J., Hübschmann T., Müller S., et al. Gastric Bypass Surgery in a Rat Model Alters the Community Structure and Functional Composition of the Intestinal Microbiota Independently of Weight Loss. Microbiome. 2020;8:13. doi: 10.1186/s40168-020-0788-1. PubMed DOI PMC

Van Velkinburgh J.C., Gunn J.S. PhoP-PhoQ-Regulated Loci Are Required for Enhanced Bile Resistance in Salmonella spp. Infect. Immun. 1999;67:1614–1622. doi: 10.1128/IAI.67.4.1614-1622.1999. PubMed DOI PMC

Urdaneta V., Casadesús J. Interactions between Bacteria and Bile Salts in the Gastrointestinal and Hepatobiliary Tracts. Front. Med. 2017;4:163. doi: 10.3389/fmed.2017.00163. PubMed DOI PMC

Tian Y., Gui W., Koo I., Smith P.B., Allman E.L., Nichols R.G., Rimal B., Cai J., Liu Q., Patterson A.D. The Microbiome Modulating Activity of Bile Acids. Gut Microbes. 2020;11:979–996. doi: 10.1080/19490976.2020.1732268. PubMed DOI PMC

Schubert K., Olde Damink S.W.M., von Bergen M., Schaap F.G. Interactions between Bile Salts, Gut Microbiota, and Hepatic Innate Immunity. Immunol. Rev. 2017;279:23–35. doi: 10.1111/imr.12579. PubMed DOI

Di Ciaula A., Garruti G., Baccetto R.L., Molina-Molina E., Bonfrate L., Wang D.Q.H., Portincasa P. Bile Acid Physiology. Ann. Hepatol. 2017;16:s4–s14. doi: 10.5604/01.3001.0010.5493. PubMed DOI

Li T., Chiang J.Y.L. Bile Acid Signaling in Metabolic Disease and Drug Therapy. Pharmacol. Rev. 2014;66:948–983. doi: 10.1124/pr.113.008201. PubMed DOI PMC

Begley M., Gahan C.G.M., Hill C. The Interaction between Bacteria and Bile. FEMS Microbiol. Rev. 2005;29:625–651. doi: 10.1016/j.femsre.2004.09.003. PubMed DOI

De Aguiar Vallim T.Q., Tarling E.J., Edwards P.A. Pleiotropic Roles of Bile Acids in Metabolism. Cell Metab. 2013;17:657–669. doi: 10.1016/j.cmet.2013.03.013. PubMed DOI PMC

Trefflich I., Marschall H.U., Di Giuseppe R., Ståhlman M., Michalsen A., Lampen A., Abraham K., Weikert C. Associations between Dietary Patterns and Bile Acids—Results from a Cross-Sectional Study in Vegans and Omnivores. Nutrients. 2020;12:47. doi: 10.3390/nu12010047. PubMed DOI PMC

Keating N., Mroz M.S., Scharl M.M., Marsh C., Ferguson G., Hofmann A.F., Keely S.J. Physiological Concentrations of Bile Acids Down-Regulate Agonist Induced Secretion in Colonic Epithelial Cells. J. Cell Mol. Med. 2009;13:2293–2303. doi: 10.1111/j.1582-4934.2009.00838.x. PubMed DOI PMC

Devlin A.S., Fischbach M.A. A Biosynthetic Pathway for a Prominent Class of Microbiota-Derived Bile Acids. Nat. Chem. Biol. 2015;11:685–690. doi: 10.1038/nchembio.1864. PubMed DOI PMC

Ridlon J.M., Harris S.C., Bhowmik S., Kang D.J., Hylemon P.B. Consequences of Bile Salt Biotransformations by Intestinal Bacteria. Gut Microbes. 2016;7:22–39. doi: 10.1080/19490976.2015.1127483. PubMed DOI PMC

Ay Ü., Leníček M., Classen A., Olde Damink S.W.M., Bolm C., Schaap F.G. New Kids on the Block: Bile Salt Conjugates of Microbial Origin. Metabolites. 2022;12:176. doi: 10.3390/metabo12020176. PubMed DOI PMC

Tanaka H., Doesburg K., Iwasaki T., Mierau I. Screening of Lactic Acid Bacteria for Bile Salt Hydrolase Activity. J. Dairy Sci. 1999;82:2530–2535. doi: 10.3168/jds.S0022-0302(99)75506-2. PubMed DOI

Vital M., Rud T., Rath S., Pieper D.H., Schlüter D. Diversity of Bacteria Exhibiting Bile Acid-Inducible 7α-Dehydroxylation Genes in the Human Gut. Comput. Struct. Biotechnol. J. 2019;17:1016–1019. doi: 10.1016/j.csbj.2019.07.012. PubMed DOI PMC

Marion S., Studer N., Desharnais L., Menin L., Escrig S., Meibom A., Hapfelmeier S., Bernier-Latmani R. In Vitro and in Vivo Characterization of Clostridium Scindens Bile Acid Transformations. Gut Microbes. 2019;10:481–503. doi: 10.1080/19490976.2018.1549420. PubMed DOI PMC

Wells J.E., Berr F., Thomas L.A., Dowling R.H., Hylemon P.B. Isolation and Characterization of Cholic Acid 7α-Dehydroxylating Fecal Bacteria from Cholesterol Gallstone Patients. J. Hepatol. 2000;32:4–10. doi: 10.1016/S0168-8278(00)80183-X. PubMed DOI

Harris S.C., Devendran S., Méndez- García C., Mythen S.M., Wright C.L., Fields C.J., Hernandez A.G., Cann I., Hylemon P.B., Ridlon J.M. Bile Acid Oxidation by Eggerthella Lenta Strains C592 and DSM 2243 T. Gut Microbes. 2018;9:523–539. doi: 10.1080/19490976.2018.1458180. PubMed DOI PMC

Doden H., Sallam L.A., Devendran S., Ly L., Doden G., Daniel S.L., Alves J.M.P., Ridlon J.M. Metabolism of Oxo-Bile Acids and Characterization of Recombinant 12α- Hydroxysteroid Dehydrogenases from Bile Acid 7α-Dehydroxylating Human Gut Bacteria. Appl. Environ. Microbiol. 2018;84:e00235-18. doi: 10.1128/AEM.00235-18. PubMed DOI PMC

Macdonald I.A., Meier E.C., Mahony D.E., Costain G.A. 3α-, 7α- And 12α-Hydroxysteroid Dehydrogenase Activities from Clostridium Perfringens. Biochim. Biophys. Acta (BBA)/Lipids Lipid Metab. 1976;450:142–153. doi: 10.1016/0005-2760(76)90086-2. PubMed DOI

Lee J.Y., Arai H., Nakamura Y., Fukiya S., Wada M., Yokota A. Contribution of the 7β-Hydroxysteroid Dehydrogenase from Ruminococcus Gnavus N53 to Ursodeoxycholic Acid Formation in the Human Colon. J. Lipid Res. 2013;54:3062–3069. doi: 10.1194/jlr.M039834. PubMed DOI PMC

Quinn R.A., Melnik A.V., Vrbanac A., Fu T., Patras K.A., Christy M.P., Bodai Z., Belda-Ferre P., Tripathi A., Chung L.K., et al. Global Chemical Effects of the Microbiome Include New Bile-Acid Conjugations. Nature. 2020;579:123–129. doi: 10.1038/s41586-020-2047-9. PubMed DOI PMC

Lucas L.N., Barrett K., Kerby R.L., Zhang Q., Cattaneo L.E., Stevenson D., Rey F.E., Amador-Noguez D. Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids. mSystems. 2021;6:e00805-21. doi: 10.1128/mSystems.00805-21. PubMed DOI

Setchell K.D.R., Lawson A.M., Tanida N., Sjovall J. General Methods for the Analysis of Metabolic Profiles of Bile Acids and Related Compounds in Feces. J. Lipid Res. 1983;24:1085–1100. doi: 10.1016/S0022-2275(20)37923-2. PubMed DOI

Hyronimus B., Le Marrec C., Hadj Sassi A., Deschamps A. Acid and Bile Tolerance of Spore-Forming Lactic Acid Bacteria. Int. J. Food Microbiol. 2000;61:193–197. doi: 10.1016/S0168-1605(00)00366-4. PubMed DOI

Jacobsen C.N., Nielsen V.R., Hayford A.E., Møller P.L., Michaelsen K.F., Pærregaard A., Sandström B., Tvede M., Jakobsen M. Screening of Probiotic Activities of Forty-Seven Strains of Lactobacillus Spp. by in Vitro Techniques and Evaluation of the Colonization Ability of Five Selected Strains in Humans. Appl. Environ. Microbiol. 1999;65:4949–4956. doi: 10.1128/AEM.65.11.4949-4956.1999. PubMed DOI PMC

Becker N., Kunath J., Loh G., Blaut M. Human Intestinal Microbiota: Characterization of a Simplified and Stable Gnotobiotic Rat Model. Gut Microbes. 2011;2:25–33. doi: 10.4161/gmic.2.1.14651. PubMed DOI

Pham H.T., Arnhard K., Asad Y.J., Deng L., Felder T.K., St John-Williams L., Kaever V., Leadley M., Mitro N., Muccio S., et al. Inter-Laboratory Robustness of Next-Generation Bile Acid Study in Mice and Humans: International Ring Trial Involving 12 Laboratories. J. Appl. Lab. Med. 2016;1:129–142. doi: 10.1373/jalm.2016.020537. PubMed DOI

Kanehisa M., Sato Y., Morishima K. BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. J. Mol. Biol. 2016;428:726–731. doi: 10.1016/j.jmb.2015.11.006. PubMed DOI

Prasnicka A., Cermanova J., Hroch M., Dolezelova E., Rozkydalova L., Smutny T., Carazo A., Chladek J., Lenicek M., Nachtigal P., et al. Iron Depletion Induces Hepatic Secretion of Biliary Lipids and Glutathione in Rats. Biochim. Biophys. Acta—Mol. Cell Biol. Lipids. 2017;1862:1469–1480. doi: 10.1016/j.bbalip.2017.09.003. PubMed DOI

Dixon P. Computer Program Review VEGAN, a Package of R Functions for Community Ecology. J. Veg. Sci. 2003;14:927–930. doi: 10.1111/j.1654-1103.2003.tb02228.x. DOI

Benjamini Y., Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J. R. Stat. Soc. Ser. B (Methodol.) 1995;57:289–300.

Wickham H. Ggplot2. Wiley Interdiscip. Rev. Comput. Stat. 2011;3:180–185. doi: 10.1002/wics.147. DOI

Hamilton J.P., Xie G., Raufman J.P., Hogan S., Griffin T.L., Packard C.A., Chatfield D.A., Hagey L.R., Steinbach J.H., Hofmann A.F. Human Cecal Bile Acids: Concentration and Spectrum. Am. J. Physiol.—Gastrointest. Liver Physiol. 2007;293:256–263. doi: 10.1152/ajpgi.00027.2007. PubMed DOI

Schwiertz A., Hold G.L., Duncan S.H., Gruhl B., Collins M.D., Lawson P.A., Flint H.J., Blaut M. Anaerostipes Caccae Gen. Nov., Sp. Nov., a New Saccharolytic, Acetate-Utilising, Butyrate-Producing Bacterium from Human Faeces. Syst. Appl. Microbiol. 2002;25:46–51. doi: 10.1078/0723-2020-00096. PubMed DOI

Tokumasu F., Ostera G.R., Amaratunga C., Fairhurst R.M. Modifications in Erythrocyte Membrane Zeta Potential by Plasmodium Falciparum Infection. Exp. Parasitol. 2012;131:245–251. doi: 10.1016/j.exppara.2012.03.005. PubMed DOI PMC

Baumgarten T., Sperling S., Seifert J., von Bergen M., Steiniger F., Wick L.Y., Heipieper H.J. Membrane Vesicle Formation as a Multiple-Stress Response Mechanism Enhances Pseudomonas Putida DOT-T1E Cell Surface Hydrophobicity and Biofilm Formation. Appl. Environ. Microbiol. 2012;78:6217–6224. doi: 10.1128/AEM.01525-12. PubMed DOI PMC

Baumgarten T., Vazquez J., Bastisch C., Veron W., Feuilloley M.G.J., Nietzsche S., Wick L.Y., Heipieper H.J. Alkanols and Chlorophenols Cause Different Physiological Adaptive Responses on the Level of Cell Surface Properties and Membrane Vesicle Formation in Pseudomonas Putida DOT-T1E. Appl. Microbiol. Biotechnol. 2012;93:837–845. doi: 10.1007/s00253-011-3442-9. PubMed DOI

Arakha M., Saleem M., Mallick B.C., Jha S. The Effects of Interfacial Potential on Antimicrobial Propensity of ZnO Nanoparticle. Sci. Rep. 2015;5:9578. doi: 10.1038/srep09578. PubMed DOI PMC

Oh J.K., Yegin Y., Yang F., Zhang M., Li J., Huang S., Verkhoturov S.V., Schweikert E.A., Perez-Lewis K., Scholar E.A., et al. The Influence of Surface Chemistry on the Kinetics and Thermodynamics of Bacterial Adhesion. Sci. Rep. 2018;8:17247. doi: 10.1038/s41598-018-35343-1. PubMed DOI PMC

Haiser H.J., Gootenberg D.B., Chatman K., Sirasani G., Balskus E.P., Turnbaugh P.J. Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella Lenta. Science. 2013;341:295–298. doi: 10.1126/science.1235872. PubMed DOI PMC

Hayakawa S., Fujiwara T. Microbiological Degradation of Bile Acids. Further Degradation of a Cholic Acid Metabolite Containing the Hexahydroindane Nucleus by Corynebacterium Equi. Biochem. J. 1977;162:387–397. doi: 10.1042/bj1620387. PubMed DOI PMC

Tanaka N., Nonaka T., Tanabe T., Yoshimoto T., Tsuru D., Mitsui Y. Crystal Structures of the Binary and Ternary Complexes of 7α-Hydroxysteroid Dehydrogenase from Escherichia Coli. Biochemistry. 1996;35:7715–7730. doi: 10.1021/bi951904d. PubMed DOI

Hirano S., Masuda N. Transformation of Bile Acids by Eubacterium Lentum. Appl. Environ. Microbiol. 1981;42:912–915. doi: 10.1128/aem.42.5.912-915.1981. PubMed DOI PMC

Doden H.L., Wolf P.G., Gaskins H.R., Anantharaman K., Alves J.M.P., Ridlon J.M. Completion of the Gut Microbial Epi-Bile Acid Pathway. Gut Microbes. 2021;13:1907271. doi: 10.1080/19490976.2021.1907271. PubMed DOI PMC

Bernstein C., Bernstein H., Payne C.M., Beard S.E., Schneider J. Bile Salt Activation of Stress Response Promoters in Escherichia Coli. Curr. Microbiol. 1999;39:68–72. doi: 10.1007/s002849900420. PubMed DOI

Hagi T., Geerlings S.Y., Nijsse B., Belzer C. The Effect of Bile Acids on the Growth and Global Gene Expression Profiles in Akkermansia Muciniphila. Appl. Microbiol. Biotechnol. 2020;104:10641–10653. doi: 10.1007/s00253-020-10976-3. PubMed DOI PMC

Leverrier P., Dimova D., Pichereau V., Auffray Y., Boyaval P., Jan G. Susceptibility and Adaptive Response to Bile Salts in Propionibacterium Freudenreichii: Physiological and Proteomic Anlysis. Appl. Environ. Microbiol. 2003;69:3809–3818. doi: 10.1128/AEM.69.7.3809-3818.2003. PubMed DOI PMC

Sievers S., Metzendorf N.G., Dittmann S., Troitzsch D., Gast V., Tröger S.M., Wolff C., Zühlke D., Hirschfeld C., Schlüter R., et al. Differential View on the Bile Acid Stress Response of Clostridioides Difficile. Front. Microbiol. 2019;10:258. doi: 10.3389/fmicb.2019.00258. PubMed DOI PMC

Sutherland J.D., Macdonald I.A. The Metabolism of Primary, 7-Oxo, and 7β-Hydroxy Bile Acids by Clostridium Absonum. J. Lipid Res. 1982;23:726–732. doi: 10.1016/S0022-2275(20)38105-0. PubMed DOI

Campbell C., McKenney P.T., Konstantinovsky D., Isaeva O.I., Schizas M., Verter J., Mai C., Jin W.B., Guo C.J., Violante S., et al. Bacterial Metabolism of Bile Acids Promotes Generation of Peripheral Regulatory T Cells. Nature. 2020;581:475–479. doi: 10.1038/s41586-020-2193-0. PubMed DOI PMC

Makishima M., Lu T.T., Xie W., Whitfield G.K., Domoto H., Evans R.M., Haussler M.R., Mangelsdorf D.J. Vitamin D Receptor as an Intestinal Bile Acid Sensor. Science. 2002;296:1313–1316. doi: 10.1126/science.1070477. PubMed DOI

Heuman D.M. Quantitative Estimation of the Hydrophilic-Hydrophobic Balance of Mixed Bile Salt Solutions. J. Lipid Res. 1989;30:719–730. doi: 10.1016/S0022-2275(20)38331-0. PubMed DOI

Perez-Riverol Y., Bai J., Bandla C., García-Seisdedos D., Hewapathirana S., Kamatchinathan S., Kundu D.J., Prakash A., Frericks-Zipper A., Eisenacher M., et al. The PRIDE Database Resources in 2022: A Hub for Mass Spectrometry-Based Proteomics Evidences. Nucleic Acids Res. 2022;50:D543–D552. doi: 10.1093/nar/gkab1038. PubMed DOI PMC

Microbially conjugated bile salts found in human bile activate the bile salt receptors TGR5 and FXR