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Global chemical effects of the microbiome include new bile-acid conjugations
Open accessAbstract
A mosaic of cross-phylum chemical interactions occurs between all metazoans and their microbiomes. A number of molecular families that are known to be produced by the microbiome have a marked effect on the balance between health and disease 1-9. Considering the diversity of the human microbiome (which numbers over 40,000 operational taxonomic units 10), the effect of the microbiome on the chemistry of an entire animal remains underexplored. Here we use mass spectrometry informatics and data visualization approaches 11-13 to provide an assessment of the effects of the microbiome on the chemistry of an entire mammal by comparing metabolomics data from germ-free and specific-pathogen-free mice. We found that the microbiota affects the chemistry of all organs. This included the amino acid conjugations of host bile acids that were used to produce phenylalanocholic acid, tyrosocholic acid and leucocholic acid, which have not previously been characterized despite extensive research on bile-acid chemistry 14. These bile-acid conjugates were also found in humans, and were enriched in patients with inflammatory bowel disease or cystic fibrosis. These compounds agonized the farnesoid X receptor in vitro, and mice gavaged with the compounds showed reduced expression of bile-acid synthesis genes in vivo. Further studies are required to confirm whether these compounds have a physiological role in the host, and whether they contribute to gut diseases that are associated with microbiome dysbiosis.
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“Some BBAAs activate host bile acid nuclear receptors like the farnesoid X receptor (FXR) and pregnane X receptor (PXR)1,3, but an assessment of other receptors has not been completed.”
From Bile Acids Are Substrates for Amine N-Acyl Transferase Activity by Bile Salt Hydrolase (2022) · cites this paper as [1]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“Recent studies demonstrated that bacteria, in addition to the host, have bile acid amine N-acyltransferase activity, with dozens of bacterially conjugated amino acid amidates identified1–4,6,17.”
From Bile Acids Are Substrates for Amine N-Acyl Transferase Activity by Bile Salt Hydrolase (2022) · cites this paper as [1]
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“The extensive compilation of recently identified MCBAs expands the complexity of the BSH-BA pool and reinforces BSHs as the gatekeepers of bile acid metabolism, capable of reshaping the BA landscape in the gut31,32.”
From Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut (2023) · cites this paper as [31]
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“An array of intestinal bacteria can catalyse the conjugation of BAs to a variety of amino acids through an unknown mechanism”
From Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut (2023) · cites this paper as [31]
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“Furthermore, BSH activity is complicated by the emerging data indicating that these enzymes can catalyse reconjugation to generate MCBAs capable of activating host ligand-activated receptors31,33,46,47.”
From Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut (2023) · cites this paper as [31]
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“All MCBAs were purified according to literature precedent and characterization data are consistent with reported data31,33,42,77,78.”
From Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut (2023) · cites this paper as [31]
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“Glu-CDCA, Ile-CA, Leu-CA, Phe-CA, Trp-CDCA and Tyr-CA were purified according to literature precedent and characterization data are consistent with reported data31,33.”
From Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut (2023) · cites this paper as [31]
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“Bacteria in the gastrointestinal tract produce amino acid bile acid amidates that can affect host-mediated metabolic processes1–6; however, the bacterial gene(s) responsible for their production remain unknown.”
From Bile Acids Are Substrates for Amine N-Acyl Transferase Activity by Bile Salt Hydrolase (2022) · cites this paper as [1]
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“The enzymes responsible for these conjugation reactions are unknown.”
From Bile Acids Are Substrates for Amine N-Acyl Transferase Activity by Bile Salt Hydrolase (2022) · cites this paper as [1]
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Cites
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Sumner, L. W., Amberg, A., Barrett, D., Beale, M. H., Beger, R., Daykin, C. A., Fan, T. W.-M., Fiehn, O., Goodacre, R., Griffin, J. L., et al. (2007) · Metabolomics · doi:10.1007/s11306-007-0082-2 · Cited by 5,368
Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3597 · Cited by 4,629
Self-citationMulti-omics of the gut microbial ecosystem in inflammatory bowel diseases
Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1237-9 · Cited by 3,143
Self-citationIntestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism
Wahlstrom, A. M., Sayin, S. I., Marschall, H., & Bäckhed, F. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.05.005 · Cited by 2,969
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
Wikoff, W. R., Anfora, A. T., Liu, J., Schultz, P. G., Lesley, S. A., Peters, E. C., & Siuzdak, G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812874106 · Cited by 2,677
Sayin, S. I., Wahlström, A., Felin, J., Jäntti, S., Marschall, H.-U., Bamberg, K., Angelin, B., Hyötyläinen, T., Orešič, M., & Bäckhed, F. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.01.003 · Cited by 2,331
Gut microbiome–mediated bile acid metabolism regulates liver cancer via NKT cells
Ma, C., Han, M., Heinrich, B., Fu, Q., Zhang, Q., Sandhu, M., Agdashian, D., Terabe, M., Berzofsky, J. A., Fako, V., et al. (2018) · Science · doi:10.1126/science.aan5931 · Cited by 1,508
Bile acids and the gut microbiome
Ridlon, J. M., Kang, D. J., Hylemon, P. B., & Bajaj, J. S. (2014) · Current Opinion in Gastroenterology · doi:10.1097/mog.0000000000000057 · Cited by 1,329
Pyrosequencing study of fecal microflora of autistic and control children
Finegold, S. M., Dowd, S. E., Gontcharova, V., Liu, C., Henley, K. E., Wolcott, R. D., Youn, E., Summanen, P. H., Granpeesheh, D., Dixon, D., et al. (2010) · Anaerobe · doi:10.1016/j.anaerobe.2010.06.008 · Cited by 977
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Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
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Self-citationGut-liver axis: Pathophysiological concepts and clinical implications
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Cullin, N., Azevedo Antunes, C., Straussman, R., Stein-Thoeringer, C. K., & Elinav, E. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.08.006 · Cited by 578
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Self-citationBile acids and their receptors in metabolic disorders
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Woelfel, S., Silva, M. S., & Stecher, B. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.05.002 · Cited by 151
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Lercher, A., Baazim, H., & Bergthaler, A. (2020) · Immunity · doi:10.1016/j.immuni.2020.08.012 · Cited by 144
Strategies to access biosynthetic novelty in bacterial genomes for drug discovery
Hemmerling, F., & Piel, J. (2022) · Nature Reviews Drug Discovery · doi:10.1038/s41573-022-00414-6 · Cited by 140
T Cell Responses to the Microbiota
Ivanov, I. I., Tuganbaev, T., Skelly, A. N., & Honda, K. (2022) · Annual Review of Immunology · doi:10.1146/annurev-immunol-101320-011829 · Cited by 133
Gut bacterial extracellular vesicles: important players in regulating intestinal microenvironment
Liang, X. H., Dai, N., Sheng, K., Lu, H., Wang, J., Chen, L., & Wang, Y. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2134689 · Cited by 128
Gut commensal Christensenella minuta modulates host metabolism via acylated secondary bile acids
Liu, C., Du, M., Xie, L., Wang, W.-Z., Chen, B., Yun, C., Sun, X., Luo, X., Jiang, Y., Wang, K., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-023-01570-0 · Cited by 129
microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data
Zuffa, S., Schmid, R., Bauermeister, A., Gomes, P. W. P., Caraballo‐Rodríguez, A. M., Abiead, Y. E., Aron, A. T., Gentry, E. C., Zemlin, J., Meehan, M. J., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-023-01575-9 · Cited by 137
Self-citationCharacterization of interactions of dietary cholesterol with the murine and human gut microbiome
Le, H. H., Lee, M.-T., Besler, K. R., Comrie, J. M. C., & Johnson, E. L. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01195-9 · Cited by 126
Minich, J. J., Poore, G. D., Jantawongsri, K., Johnston, C., Bowie, K., Bowman, J. P., Knight, R. D., Nowak, B. F., & Allen, E. E. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.00411-20 · Cited by 123
Self-citationMetabolomic signatures of coral bleaching history
Roach, T. N. F., Dilworth, J., Christian Martin, H., Jones, A. D., Quinn, R. A., & Drury, C. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01388-7 · Cited by 121
Self-citationMaternal microbiota-derived metabolic profile in fetal murine intestine, brain and placenta
Pessa‐Morikawa, T., Husso, A., Kärkkäinen, O. K., Koistinen, V., Hanhineva, K., Iivanainen, A., & Niku, M. (2022) · BMC Microbiology · doi:10.1186/s12866-022-02457-6 · Cited by 118
Microbial Hydroxysteroid Dehydrogenases: From Alpha to Omega
Doden, H. L., & Ridlon, J. M. (2021) · Microorganisms · doi:10.3390/microorganisms9030469 · Cited by 113
Vila, A. V., Zhang, J., Liu, M., Faber, K. N., & Weersma, R. K. (2024) · Gut · doi:10.1136/gutjnl-2023-329969 · Cited by 112
Advanced analytical and informatic strategies for metabolite annotation in untargeted metabolomics
Cai, Y. A., Zhou, Z., & Zhu, Z. (2022) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2022.116903 · Cited by 109
Bile acids activated receptors in inflammatory bowel disease
Biagioli, M., Marchianò, S., Carino, A., Di Giorgio, C., Santucci, L., Distrutti, E., & Fiorucci, S. (2021) · Cells · doi:10.3390/cells10061281 · Cited by 103
Biogeography of microbial bile acid transformations along the murine gut
Marion, S., Desharnais, L., Studer, N., Dong, Y., Notter, M. D., Poudel, S., Menin, L., Janowczyk, A. R., Hettich, R. L., Hapfelmeier, S., et al. (2020) · Journal of Lipid Research · doi:10.1194/jlr.ra120001021 · Cited by 101
Physiological Role of Bile Acids Modified by the Gut Microbiome
Kiriyama, Y., & Nochi, H. (2021) · Microorganisms · doi:10.3390/microorganisms10010068 · Cited by 105
Versatile Triad Alliance: Bile Acid, Taurine and Microbiota
Duszka, K. (2022) · Cells · doi:10.3390/cells11152337 · Cited by 101
Conditioning of the immune system by the microbiome
Graham, D. B., & Xavier, R. J. (2023) · Trends in Immunology · doi:10.1016/j.it.2023.05.002 · Cited by 103
Self-citationMetabolome–Microbiome Crosstalk and Human Disease
Lee‐Sarwar, K. A., Lasky-Su, J. A., Kelly, R. S., Litonjua, A. A., & Weiss, S. T. (2020) · Metabolites · doi:10.3390/metabo10050181 · Cited by 98
The functions of gut microbiota-mediated bile acid metabolism in intestinal immunity
He, Y., Shaoyong, W., Chen, Y., Li, M., Gan, Y., Sun, L., Liu, Y., Wang, Y., & Jin, M. (2025) · Journal of Advanced Research · doi:10.1016/j.jare.2025.05.015 · Cited by 107
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Won, T. H., Arifuzzaman, M., Parkhurst, C. N., Miranda, I. C., Zhang, B., Hu, E., Kashyap, S., Letourneau, J., Jin, W., Fu, Y., et al. (2025) · Nature · doi:10.1038/s41586-024-08379-9 · Cited by 100
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Vatanen, T., Ang, Q. Y., Siegwald, L., Sarker, S. A., Roy, C. I. L., Duboux, S., Delannoy-Bruno, O., Ngom‐Bru, C., Boulangé, C. L., Stražar, M., et al. (2022) · Cell · doi:10.1016/j.cell.2022.10.011 · Cited by 95
Self-citationBittremieux, W., Schmid, R., Huber, F., van der Hooft, J. J. J., Wang, M., & Dorrestein, P. C. (2022) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.2c00153 · Cited by 98
Self-citationFu, T., Huan, T., Rahman, G., Zhi, H., Xu, Z. Z., Oh, T. G., Guo, J. P., Coulter, S., Tripathi, A., Martino, C., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112997 · Cited by 94
Self-citationGut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease
Pandey, H., Jain, D., Tang, D. W. T., Wong, S. H., & Lal, D. (2023) · Intestinal Research · doi:10.5217/ir.2023.00080 · Cited by 95
Agolino, G., Pino, A., Vaccalluzzo, A., Cristofolini, M., Solieri, L., Caggia, C., & Randazzo, C. L. (2024) · Journal of Functional Foods · doi:10.1016/j.jff.2024.106357 · Cited by 99
Annotating metabolite mass spectra with domain-inspired chemical formula transformers
Goldman, S., Wohlwend, J., Stražar, M., Haroush, G., Xavier, R. J., & Coley, C. W. (2023) · Nature Machine Intelligence · doi:10.1038/s42256-023-00708-3 · Cited by 87
Self-citationMeasuring the microbiome: Best practices for developing and benchmarking microbiomics methods
Bokulich, N. A., Ziemski, M., Robeson, M. S., & Kaehler, B. D. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.11.049 · Cited by 98
Messengers From the Gut: Gut Microbiota-Derived Metabolites on Host Regulation
Li, C., Liang, Y., & Qiao, Y. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.863407 · Cited by 88
Yadegar, A., Pakpour, S., Ibrahim, F. F., Nabavi-Rad, A., Cook, L. E., Walter, J., Seekatz, A. M., Wong, K., Monaghan, T. M., & Kao, D. H. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.03.019 · Cited by 90
Bile Acids, Their Receptors, and the Gut Microbiota
Poland, J. C., & Flynn, C. R. (2021) · Physiology · doi:10.1152/physiol.00028.2020 · Cited by 93
The Gut-Lung Axis in Cystic Fibrosis
Price, C. E., & O’Toole, G. A. (2021) · Journal of Bacteriology · doi:10.1128/jb.00311-21 · Cited by 85
Immunology of bile acids regulated receptors
Fiorucci, S., Marchianò, S., Urbani, G., Giorgio, C. D., Distrutti, E., Zampella, A., & Biagioli, M. (2024) · Progress in Lipid Research · doi:10.1016/j.plipres.2024.101291 · Cited by 88
Bile Acid Signaling in Metabolic and Inflammatory Diseases and Drug Development
Li, T., & Chiang, J. Y. L. (2024) · Pharmacological Reviews · doi:10.1124/pharmrev.124.000978 · Cited by 85
Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity
Jin, W., Xiao, L., Jeong, M., Han, S.-J., Zhang, W., Yano, H., Shi, H., Arifuzzaman, M., Lyu, M., Wang, D., et al. (2025) · Cell · doi:10.1016/j.cell.2025.02.029 · Cited by 94
Schirmer, M., Stražar, M., Ávila-Pacheco, J., Rojas‐Tapias, D. F., Brown, E., Temple, E. R., Deik, A., Bullock, K. H., Jeanfavre, S., Pierce, K. A., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2023.12.013 · Cited by 87
Self-citation
Metadata
- Authors
- 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., Downes, M., Welch, R. D., Quinn, M., Humphrey, G., Panitchpakdi, M., Weldon, K. C., Aksenov, A., da Silva, R., Avila-Pacheco, J., Clish, C., Bae, S., Mallick, H., Franzosa, E. A., Lloyd-Price, J., Bussell, R., Thron, T., Nelson, A. T., Wang, M., Leszczynski, E., Vargas, F., Gauglitz, J. M., Meehan, M. J., Gentry, E., Arthur, T. D., Komor, A. C., Poulsen, O., Boland, B. S., Chang, J. T., Sandborn, W. J., Lim, M., Garg, N., Lumeng, J. C., Xavier, R. J., Kazmierczak, B. I., Jain, R., Egan, M., Rhee, K. E., Ferguson, D., Raffatellu, M., Vlamakis, H., Haddad, G. G., Siegel, D., Huttenhower, C., Mazmanian, S. K., Evans, R. M., Nizet, V., Knight, R., & Dorrestein, P. C.
- Affiliations
- University of California San Diego (US)
- Salk Institute for Biological Studies (US)
- Michigan State University (US)
- Broad Institute (US)
- Harvard University (US)
- California Institute of Technology (US)
- Georgia Institute of Technology (US)
- University of Michigan (US)
- Yale University (US)
- Corresponding author
- Dorrestein, Pieter C.
- ORCID
- Quinn, Robert A.
- Melnik, Alexey V.
- Vrbanac, Alison
- Patras, Kathryn A.
- Christy, Mitchell P.
- Bodai, Zsolt
- Tripathi, Anupriya
- Downes, Michael
- Quinn, Melissa
- Panitchpakdi, Morgan
- Weldon, Kelly C.
- Aksenov, Alexander
- Clish, Clary
- Mallick, Himel
- Franzosa, Eric A.
- Thron, Taren
- Nelson, Andrew T.
- Wang, Mingxun
- Leszczynski, Eric
- Vargas, Fernando
- Gauglitz, Julia M.
- Meehan, Michael J.
- Gentry, Emily
- Arthur, Timothy D.
- Komor, Alexis C.
- Boland, Brigid S.
- Chang, John T.
- Sandborn, William J.
- Garg, Neha
- Lumeng, Julie C.
- Xavier, Ramnik J.
- Kazmierczak, Barbara I.
- Jain, Ruchi
- Egan, Marie
- Rhee, Kyung E.
- Ferguson, David
- Raffatellu, Manuela
- Vlamakis, Hera
- Haddad, Gabriel G.
- Siegel, Dionicio
- Huttenhower, Curtis
- Mazmanian, Sarkis K.
- Evans, Ronald M.
- Nizet, Victor
- Knight, Rob
- Dorrestein, Pieter C.
- Venue
- Nature
- Published
- 2020-02-26
- Volume
- 579
- Issue
- 7797
- Pages
- 123-129
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC7252668
- OpenAlex
- W3007415664
- Cited by
- 579
- References
- 43
- Citations by year
- 2026: 79 · 2025: 99 · 2024: 124 · 2023: 73 · 2022: 99 · 2021: 64 · 2020: 40
- FWCI
- 22.39
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Crohn's and Colitis Foundation (675191, 815985)
- National Institutes of Health (1s10rr029121-01, 1r03ca211211-01, KL2TR001444, UL1TR001863)
- National Heart, Lung, and Blood Institute (R01HL105278, R01HL116235, P01HL088093)
- National Cancer Institute (CA014195, R03 CA211211, P30CA014195)
- National Institute of General Medical Sciences (R01GM107550)
- National Institute of Allergy and Infectious Diseases (R01AI126277, U01AI124316)
- National Institute of Diabetes and Digestive and Kidney Diseases (R37DK057978, T32DK007494, R01DK057978, R24DK110499, P30DK120515, P30DK043351, P30DK040561)
- National Institute of Environmental Health Sciences (P42ES010337)
- National Institute of Dental and Craniofacial Research (U54DE023798)
- U.S. National Library of Medicine (T15LM011271)
- National Center for Research Resources (S10-RR029121)
- National Center for Advancing Translational Sciences
- National Center for Complementary and Integrative Health (DP1AT010885)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD084163)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
- Keywords
- gut microbiota, bile acid conjugation, farnesoid X receptor, germ-free mice, inflammatory bowel disease, cystic fibrosis, bile acid synthesis, dysbiosis, host metabolome
- MeSH terms
- Receptor, Farnesoid X-Activated, Animals, Bile Acids and Salts, Cystic Fibrosis, Germ-Free Life, Humans, Inflammatory Bowel Diseases, Receptors, Cytoplasmic and Nuclear, Cholic Acid, Mice, Metabolomics, Microbiota
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