The inflammatory bowel diseases (IBDs), which include Crohn’s disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome—the molecular interface between host and microbiota—are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients. Metabolomic and metagenomic profiles were broadly correlated with faecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While > 50% of differentially abundant metabolite features were uncharacterized, many could be assigned putative roles through metabolomic ‘guilt by association’ (covariation with known metabolites). Differentially abundant species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between differentially abundant species and well-characterized differentially abundant metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome–metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.

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Data availability

Metagenomic sequences for the PRISM, LifeLines DEEP and NLIBD cohorts are available via SRA with BioProject number PRJNA400072. Metabolomics data (accession number PR000677) are available at the National Institutes of Health Common Fund’s Metabolomics Data Repository and Coordinating Center (supported by National Institutes of Health grant no. U01-DK097430): Metabolomics Workbench (http://www.metabolomicsworkbench.org). Tables of processed metabolite, microbial species and microbial enzyme abundance are available as Supplementary Datasets 2, 4 and 6.

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The authors are grateful to the members of the PRISM, LifeLines DEEP and NLIBD cohorts for participating in the study and providing sample material. We thank T. Poon for project management and coordination of data generation, T. Reimels for editorial assistance and A. Garner for providing helpful feedback on the manuscript. The Dutch research team was funded by: CVON IN-CONTROL (CVON2012–03 to A.Z. and J.F.); the Dutch Digestive Foundation (D16–14 to R.K.W. and A.Z.); the Netherlands Organization for Scientific Research (NWO-VIDI 864.13.013 to J.F., NWO-VIDI 016.Vidi.178.056 to A.Z., NWOOW-VIDI 016.136.308 to R.K.W.); a Spinoza Prize (SPI 92–266 to C.W.); and the European Research Council (ERC-Starting no. 715772 to A.Z. and ERC-Advanced 2012–322698 to C.W.). The Boston research team was funded by: the National Science Foundation (NSF CAREER DBI-1053486 and NSF EAGER MCB-1453942 to C.H.); the National Institutes of Health (R01HG00596 to C.H., U54DK102557 to C.H. and R.J.X., R01DK92405 to R.J.X., R24DK110499 to C.H.); the Crohn’s and Colitis Foundation of America to R.J.X. and C.H.; and the Center for Microbiome Informatics and Therapeutics (6933665 PO no. 5710004058 to R.J.X.). A.B.H. is a Merck Fellow of the Helen Hay Whitney Foundation.

Author information

Author notes

  1. These authors contributed equally: Eric A. Franzosa, Alexandra Sirota-Madi.


  1. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    • Eric A. Franzosa
    • , Alexandra Sirota-Madi
    • , Julian Avila-Pacheco
    • , Nadine Fornelos
    • , Tommi Vatanen
    • , A. Brantley Hall
    • , Himel Mallick
    • , Lauren J. McIver
    • , Justin M. Scott
    • , Kerry Pierce
    • , Amy A. Deik
    • , Kevin Bullock
    • , Clary B. Clish
    • , Hera Vlamakis
    • , Curtis Huttenhower
    •  & Ramnik J. Xavier
  2. Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA

    • Eric A. Franzosa
    • , Himel Mallick
    • , Lauren J. McIver
    •  & Curtis Huttenhower
  3. Novartis Institute for Biomedical Research Inc., Cambridge, MA, USA

    • Henry J. Haiser
    •  & Stefan Reinker
  4. Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA

    • Jenny S. Sauk
    • , Robin G. Wilson
    • , Betsy W. Stevens
    •  & Ramnik J. Xavier
  5. Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands

    • Floris Imhann
    •  & Rinse K. Weersma
  6. Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands

    • Floris Imhann
    • , Alexandra Zhernakova
    • , Jingyuan Fu
    •  & Cisca Wijmenga
  7. Novartis Institute for Biomedical Research Inc., Basel, Switzerland

    • Jeffrey A. Porter
  8. Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands

    • Jingyuan Fu
  9. Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway

    • Cisca Wijmenga
  10. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA

    • Ramnik J. Xavier


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E.A.F., A.S-M., H.V., C.H. and R.J.X. designed the research. E.A.F., A.S-M., J.A-P., N.F., T.V., H.M. and L.J.M. performed the research. H.J.H., S.R., J.S.S., R.G.W., B.W.S., F.I., A.Z., J.F., R.K.W. and C.W. contributed materials. J.A-P., J.M.S., K.P., A.A.D., K.B. and C.B.C. generated the data. E.A.F., A.S-M., J.A-P., N.F., A.B.H. and H.V. analysed the data. E.A.F., J.A.P., R.K.W., C.W., H.V., C.H. and R.J.X. provided project oversight. E.A.F., A.S-M., H.V., C.H. and R.J.X. wrote the paper.

Competing interests

F.I. received a speaker’s fee from AbbVie.

Corresponding authors

Correspondence to Curtis Huttenhower or Ramnik J. Xavier.

Supplementary information

  1. Supplementary Information

    Supplementary Figures 1–13

  2. Reporting Summary

  3. Supplementary Dataset 1

    Metabolite feature metadata

  4. Supplementary Dataset 2

    Per-subject metabolite relative abundance profiles

  5. Supplementary Dataset 3

    IBD-metabolite associations

  6. Supplementary Dataset 4

    Per-subject microbial species relative abundance profiles

  7. Supplementary Dataset 5

    IBD-microbial species associations

  8. Supplementary Dataset 6

    Per-subject microbial enzyme relative abundance profiles

  9. Supplementary Dataset 7

    IBD-microbial enzyme associations

  10. Supplementary Dataset 8

    Genedata Expressionist configuration

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