Abstract

Resource limitation is a fundamental factor governing the composition and function of ecological communities. However, the role of resource supply in structuring the intestinal microbiome has not been established and represents a challenge for mammals that rely on microbial symbionts for digestion: too little supply might starve the microbiome while too much might starve the host. We present evidence that microbiota occupy a habitat that is limited in total nitrogen supply within the large intestines of 30 mammal species. Lowering dietary protein levels in mice reduced their faecal concentrations of bacteria. A gradient of stoichiometry along the length of the gut was consistent with the hypothesis that intestinal nitrogen limitation results from host absorption of dietary nutrients. Nitrogen availability is also likely to be shaped by host–microbe interactions: levels of host-secreted nitrogen were altered in germ-free mice and when bacterial loads were reduced via experimental antibiotic treatment. Single-cell spectrometry revealed that members of the phylum Bacteroidetes consumed nitrogen in the large intestine more readily than other commensal taxa did. Our findings support a model where nitrogen limitation arises from preferential host use of dietary nutrients. We speculate that this resource limitation could enable hosts to regulate microbial communities in the large intestine. Commensal microbiota may have adapted to nitrogen-limited settings, suggesting one reason why excess dietary protein has been associated with degraded gut-microbial ecosystems.

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Data availability

The 16S rRNA gene nucleotide sequences generated in this study can be downloaded from the European Nucleotide Archive under study accession numbers PRJEB26478 (protein manipulation and NanoSIMS experiments) and PRJEB26446 (antibiotics experiment). NanoSIMS and bulk isotopic data for the dietary and injected 15N study is included in Supplementary Table 4. Other data that support these findings are available from the corresponding author upon request.

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Acknowledgements

W. Cook carried out C/N ratio measurements in the Duke Environmental Isotope Laboratory. Samples were provided by S. Mills and D. Lafferty (snowshoe hare); E. Ehmke (lemurs); L. McGraw, A. Vogel and C. Clement (prairie vole); D. Koeberl, V. Sakach and L. Morgan (dog); C. Drea (meerkat). Statistical advice was provided by K. Choudhury and S. Mukherjee. The manuscript was improved thanks to comments from J. Heffernan, J. Rawls and P. Turnbaugh. This work was funded by an NSF Doctoral Dissertation Improvement grant to A.T.R., J.P.W. and L.A.D. (grant no. DEB-1501495) and grants from the Hartwell Foundation, Alfred P. Sloan Foundation and Searle Scholars Programme to L.A.D. A.T.R. was supported by the NSF Graduate Research Fellowship Programme under grant no. DGE 1106401. F.C.P. was supported by a European Research Council Marie Curie Individual Fellowship (grant no. 658718). D.B. was supported in part by Austrian Science Fund (grant nos. P26127-B20 and P27831-B28) and European Research Council (Starting Grant: FunKeyGut 741623). M.W. was supported by the European Research Council via the Advanced Grant project ‘NITRICARE 294343’. The contents of this paper are the responsibility of the authors and do not necessarily represent the views of the funding institutions.

Author information

Affiliations

  1. Department of Biology, Duke University, Durham, NC, USA

    • Aspen T. Reese
    • , Susan C. Alberts
    •  & Justin P. Wright
  2. Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA

    • Aspen T. Reese
    • , Anchi Wu
    • , Sharon Jiang
    • , Heather K. Durand
    • , Anna Mae Diehl
    •  & Lawrence A. David
  3. Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria

    • Fátima C. Pereira
    • , Arno Schintlmeister
    • , David Berry
    •  & Michael Wagner
  4. Large-Instrument Facility for Advanced Isotope Research, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria

    • Arno Schintlmeister
    •  & Michael Wagner
  5. Department of Pathology, Duke University Medical Center, Durham, NC, USA

    • Laura P. Hale
  6. Department of Medicine, Duke University Medical Center, Durham, NC, USA

    • Xiyou Zhou
    • , Richard T. Premont
    •  & Anna Mae Diehl
  7. Department of Otolaryngology – Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, USA

    • Thomas M. O’Connell
  8. Department of Evolutionary Anthropology, Duke University, Durham, NC, USA

    • Susan C. Alberts
  9. Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya

    • Susan C. Alberts
  10. Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA

    • Tyler R. Kartzinel
  11. Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA

    • Robert M. Pringle
  12. Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA

    • Robert R. Dunn
  13. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA

    • Lawrence A. David

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Contributions

A.T.R., F.P., A.S., D.B. and M.W. carried out FISH / NanoSIMS work. A.T.R., X.Z. and R.P. performed diet manipulation experiments. L.P.H., S.J. and H.K.D. processed samples. T.M.O., S.C.A., T.R.K. and R.M.P. contributed data. A.T.R. performed all other experiments. A.M.D., R.R.D. and J.P.W. were involved in study design. A.T.R. and L.A.D. designed the study, analysed data and wrote the paper. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Lawrence A. David.

Supplementary

  1. Supplementary Information

    Supplementary Figures 1–7, Supplementary Tables 1–3, Supplementary Tables 5–9.

  2. Reporting Summary

  3. Supplementary Table 4

    Isotope data for single-cell and whole-gut contents for data presented in Fig. 3, Supplementary Fig. 7.

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https://doi.org/10.1038/s41564-018-0267-7