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Published March 2023 | Supplemental Material
Journal Article Open

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease


For decades, variability in clinical efficacy of the widely used inflammatory bowel disease (IBD) drug 5-aminosalicylic acid (5-ASA) has been attributed, in part, to its acetylation and inactivation by gut microbes. Identification of the responsible microbes and enzyme(s), however, has proved elusive. To uncover the source of this metabolism, we developed a multi-omics workflow combining gut microbiome metagenomics, metatranscriptomics and metabolomics from the longitudinal IBDMDB cohort of 132 controls and patients with IBD. This associated 12 previously uncharacterized microbial acetyltransferases with 5-ASA inactivation, belonging to two protein superfamilies: thiolases and acyl-CoA N-acyltransferases. In vitro characterization of representatives from both families confirmed the ability of these enzymes to acetylate 5-ASA. A cross-sectional analysis within the discovery cohort and subsequent prospective validation within the independent SPARC IBD cohort (n = 208) found three of these microbial thiolases and one acyl-CoA N-acyltransferase to be epidemiologically associated with an increased risk of treatment failure among 5-ASA users. Together, these data address a longstanding challenge in IBD management, outline a method for the discovery of previously uncharacterized gut microbial activities and advance the possibility of microbiome-based personalized medicine.

Additional Information

© 2023 Springer Nature. We express our sincere thanks to the members of the Huttenhower laboratory for their editorial assistance. The computations in this paper were run on the FASRC Cannon cluster supported by the FAS Division of Science Research Computing Group at Harvard University or on the O2 High Performance Compute Cluster, supported by the Research Computing Group, at Harvard Medical School. See https://it.hms.harvard.edu/our-services/research-computing for more information. Funding: National Institutes of Health grant R35 CA253185 (A.T.C.); National Institutes of Health grant R24 DK110499-01A1 (C.H.); National Institutes of Health grant T32HL008633-36 (J.R.M.); National Institutes of Health grant 1K23DK125838 (L.H.N.); American College of Gastroenterology (R.S.M.); Crohn's & Colitis Foundation (R.S.M. and L.H.N.); American Gastroenterological Association (L.H.N. and W.M.); Pfizer Ulcerative Colitis Grant (A.T.C.); Stuart and Suzanne Steele MGH Research Scholarship (A.T.C.); Howard Hughes Medical Institute (E.P.B.); National Science Foundation Postdoctoral Research Fellowship in Biology grant 1907240 (N.R.G.); National Science Foundation Alan T. Waterman Award 2038059 (J.R.M.); Linde Family Foundation (S.D.P.); Novartis Institute for Biomedical Research (S.D.P.); Doris Duke Charitable Foundation (S.D.P.); National Institutes of Health grant P30 GM124165 (S.D.P.); and National Institutes of Health-ORIP HEI grant S10OD021527 (S.D.P.). Contributions. Conceptualization: R.S.M., E.P.B., A.T.C. and C.H. Methodology: R.S.M., J.R.M., Y.Z., N.G., J.A.P., H.S., C.C., S.D.P., E.F., E.P.B. and C.H. Investigation: R.S.M., J.R.M., Y.Z., A.B., N.R.G., L.H.N., W.M., S.B., T.B., K.S., L.B., A.N.A. and E.F. Visualization: R.S.M. and J.R.M. Funding acquisition: R.S.M., E.P.B., A.T.C. and C.H. Project administration: R.S.M., E.P.B., A.T.C. and C.H. Supervision: E.P.B., A.T.C. and C.H. contributed equally. Writing—original draft: R.S.M., J.R.M., A.T.C. and C.H. Writing—review and editing: R.S.M., J.R.M., Y.Z., N.R.G., A.B., L.H.N., W.M., S.B., T.B., A.N.A., J.A.P., H.S., S.D.P., E.F., E.P.B., A.T.C. and C.H. These authors contributed equally: Raaj S. Mehta, Jared R. Mayers. Data availability. All multi-omics and participant data from the HMP2 used in this analysis are available at http://IBDMDB.org. Access to PRISM data may be available after contact of rxavier@molbio.harvard.edu. The SPARC IBD data are available upon approved application to Crohn's & Colitis Foundation IBD Plexus (https://www.crohnscolitisfoundation.org/ibd-plexus). Code availability. All analysis code can be accessed at https://github.com/drraajmehta/hmp2_5asa for purposes of reproducibility. Competing interests. C.H. is a consultant to Zoe, Ltd. and is on the scientific advisory boards of Seres Therapeutics and Empress Therapeutics. A.T.C. has been an investigator on a clinical study supported by Zoe, Ltd. Other authors declare that they have no competing interests. R.S.M., J.R.M., E.P.B., A.T.C. and C.H. filed a provisional patent application (63/383,269) on 11 November 2022.

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Additional details

August 22, 2023
August 22, 2023