Bacterial metabolism plays a fundamental role in gut microbiota ecology and host–microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth characteristics of 96 phylogenetically diverse gut bacterial strains across 4 rich and 15 defined media. The vast majority of strains (76) grow in at least one defined medium, enabling accurate assessment of their biosynthetic capabilities. These do not necessarily match phylogenetic similarity, thus indicating a complex evolution of nutritional preferences. We identify mucin utilizers and species inhibited by amino acids and short-chain fatty acids. Our analysis also uncovers media for in vitro studies wherein growth capacity correlates well with in vivo abundance. Further value of the underlying resource is demonstrated by correcting pathway gaps in available genome-scale metabolic models of gut microorganisms. Together, the media resource and the extracted knowledge on growth abilities widen experimental and computational access to the gut microbiota.

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We thank H. KleinJan and L. Maier for experimental assistance, O. Ponomarova for advice on media design and D. Machado for advice on metabolic modelling. Sequencing was performed at Genecore, EMBL. We thank Dupont Health and Nutrition (formerly Danisco Sweeteners OY, Finland) for providing L. acidophilus NCFM, L. paracasei ATCC SDS275, B. animalis subsp. lactis Bl-04 and BI-07, D. Clarke for Shigella sonnei 53 G and the enteropathogenic Escherichia coli strains CFT073, E2348/69, H10407, HM605 and UTI89, E. Denamur for the Escherichia coli strains ED1a and IAI1, M. Blokesch for the Vibrio cholerae strains A1552 and N16961, H. Andrews-Polymenis for the Salmonella enterica typhimurium strains CDC 6516-60 and LT2 and C. Darby for Yersinia pseudotuberculosis YPIII. This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 686070. MT and MP were supported by the EMBL interdisciplinary postdoctoral program.

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Author notes

    • Mihaela Pruteanu

    Present address: Humboldt University Berlin, Berlin, Germany

    • Aleksej Zelezniak

    Present address: Chalmers University of Technology, Gothenburg, Sweden

  1. These authors contributed equally: Melanie Tramontano and Sergej Andrejev.


  1. European Molecular Biology Laboratory, Heidelberg, Germany

    • Melanie Tramontano
    • , Sergej Andrejev
    • , Mihaela Pruteanu
    • , Martina Klünemann
    • , Michael Kuhn
    • , Paula Jouhten
    • , Aleksej Zelezniak
    • , Georg Zeller
    • , Peer Bork
    • , Athanasios Typas
    •  & Kiran Raosaheb Patil
  2. EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, United Kingdom

    • Marco Galardini
  3. Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany

    • Peer Bork
  4. Molecular Medicine Partnership Unit, Heidelberg, Germany

    • Peer Bork
  5. Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany

    • Peer Bork


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M.T., P.B., A.T. and K.R.P. conceived the study. M.T., S.A., A.T. and K.R.P. designed the study. M.T., M.P., A.Z. and G.Z. selected gut bacterial strains. M.T. and M.Klünemann performed in vitro experiments. S.A. analysed data. S.A. and P.J. performed metabolic modelling. S.A. and G.Z. compiled figures. M.Kuhn contributed to in vivo abundance analysis. M.G. annotated sequenced genomes. P.B., A.T. and K.R.P. supervised the study. M.T., S.A. and K.R.P. wrote the manuscript. All authors read and commented on the manuscript.

Competing interests

A patent application has been filed based on this work.

Corresponding authors

Correspondence to Peer Bork or Athanasios Typas or Kiran Raosaheb Patil.

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