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Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection

Abstract

Lack of reproducibility is a prominent problem in biomedical research. An important source of variation in animal experiments is the microbiome, but little is known about specific changes in the microbiota composition that cause phenotypic differences. Here, we show that genetically similar laboratory mice obtained from four different commercial vendors exhibited marked phenotypic variation in their susceptibility to Salmonella infection. Faecal microbiota transplant into germ-free mice replicated donor susceptibility, revealing that variability was due to changes in the gut microbiota composition. Co-housing of mice only partially transferred protection against Salmonella infection, suggesting that minority species within the gut microbiota might confer this trait. Consistent with this idea, we identified endogenous Enterobacteriaceae, a low-abundance taxon, as a keystone species responsible for variation in the susceptibility to Salmonella infection. Protection conferred by endogenous Enterobacteriaceae could be modelled by inoculating mice with probiotic Escherichia coli, which conferred resistance by using its aerobic metabolism to compete with Salmonella for resources. We conclude that a mechanistic understanding of phenotypic variation can accelerate development of strategies for enhancing the reproducibility of animal experiments.

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Fig. 1: Phenotypic variation in the susceptibility to Salmonella infection is observed in C57BL/6 mice from different vendors.
Fig. 2: The gut microbiota is a driver of phenotypic variation.
Fig. 3: Enterobacteriaceae are biomarkers of phenotypic variation.
Fig. 4: E. coli requires an aerobic metabolism to confer colonization resistance.

Data availability

Illumina sequences obtained in the present study were deposited in the Sequence Read Archives (SRA) NCBI database under accession number SRP148888. Sanger sequences were deposited in GenBank under accession numbers MH759762 to MH759768.

References

  1. Baker, M. 1,500 scientists lift the lid on reproducibility. Nature 533, 452–454 (2016).

    Article  CAS  Google Scholar 

  2. Stappenbeck, T. S. & Virgin, H. W. Accounting for reciprocal host–microbiome interactions in experimental science. Nature 534, 191–199 (2016).

    Article  CAS  Google Scholar 

  3. Franklin, C. L. & Ericsson, A. C. Microbiota and reproducibility of rodent models. Lab Anim. 46, 114–122 (2017).

    Article  Google Scholar 

  4. Hanage, W. P. Microbiology: microbiome science needs a healthy dose of scepticism. Nature 512, 247–248 (2014).

    Article  CAS  Google Scholar 

  5. Ivanov, I. I. et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485–498 (2009).

    Article  CAS  Google Scholar 

  6. Tsolis, R. M., Xavier, M. N., Santos, R. L. & Bäumler, A. J. How to become a top model: impact of animal experimentation on human Salmonella disease research. Infect. Immun. 79, 1806–1814 (2011).

    Article  CAS  Google Scholar 

  7. Thiemann, S. et al. Enhancement of IFNγ production by distinct commensals ameliorates Salmonella-induced disease. Cell Host Microbe 21, 682–694 (2017).

    Article  CAS  Google Scholar 

  8. Fallon, M. T., Benjamin, W. H. Jr., Schoeb, T. R. & Briles, D. E. Mouse hepatitis virus strain UAB infection enhances resistance to Salmonella typhimurium in mice by inducing suppression of bacterial growth. Infect. Immun. 59, 852–856 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Bohnhoff, M., Drake, B. L. & Miller, C. P. Effect of streptomycin on susceptibility of intestinal tract to experimental Salmonella infection. Proc. Soc. Exp. Biol. Med. 86, 132–137 (1954).

    Article  CAS  Google Scholar 

  10. Mekada, K. et al. Genetic differences among C57BL/6 substrains. Exp. Anim. 58, 141–149 (2009).

    Article  CAS  Google Scholar 

  11. Zurita, E. et al. Genetic polymorphisms among C57BL/6 mouse inbred strains. Transgenic Res. 20, 481–489 (2011).

    Article  CAS  Google Scholar 

  12. Simon, M. M. et al. A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains. Genome Biol. 14, R82 (2013).

    Article  Google Scholar 

  13. Rivera-Chavez, F. et al. Depletion of butyrate-producing Clostridia from the gut microbiota drives an aerobic luminal expansion of Salmonella. Cell Host Microbe 19, 443–454 (2016).

    Article  CAS  Google Scholar 

  14. Kim, Y. G. et al. Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens. Science 356, 315–319 (2017).

    Article  CAS  Google Scholar 

  15. Splichalova, A. et al. Interference of Bifidobacterium choerinum or Escherichia coli Nissle 1917 with Salmonella Typhimurium in gnotobiotic piglets correlates with cytokine patterns in blood and intestine. Clin. Exp. Immunol. 163, 242–249 (2011).

    Article  CAS  Google Scholar 

  16. Lima-Filho, J. V., Vieira, L. Q., Arantes, R. M. & Nicoli, J. R. Effect of the Escherichia coli EMO strain on experimental infection by Salmonella enterica serovar Typhimurium in gnotobiotic mice. Braz. J .Med. Biol. Res. 37, 1005–1013 (2004).

    Article  CAS  Google Scholar 

  17. Rivera-Chavez, F. & Lopez, C. A. & Bäumler, A. J. Oxygen as a driver of gut dysbiosis. Free Radic. Biol. Med. 105, 93–101 (2016).

    Article  Google Scholar 

  18. Hughes, E. R. et al. Microbial respiration and formate oxidation as metabolic signatures of inflammation-associated dysbiosis. Cell Host Microbe 21, 208–219 (2017).

    Article  CAS  Google Scholar 

  19. Byndloss, M. X. et al. Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion. Science 357, 570–575 (2017).

    Article  CAS  Google Scholar 

  20. Faber, F. et al. Respiration of microbiota-derived 1,2-propanediol drives Salmonella expansion during colitis. PLoS Pathog. 13, e1006129 (2017).

    Article  Google Scholar 

  21. Spiga, L. et al. An oxidative central metabolism enables Salmonella to utilize microbiota-derived succinate. Cell Host Microbe 22, 291–301 (2017).

    Article  CAS  Google Scholar 

  22. Meynell, G. G. Antibacterial mechanisms of the mouse gut. II. The role of Eh and volatile fatty acids in the normal gut. Br. J. Exp. Pathol. 44, 209–219 (1963).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Gillis, C. C. et al. Dysbiosis-associated change in host metabolism generates lactate to support Salmonella growth. Cell Host Microbe 23, 54–64 (2018).

    Article  CAS  Google Scholar 

  24. Bohnhoff, M., Miller, C. P. & Martin, W. R. Resistance of the mouse’s intestinal tract to experimental Salmonella infection. II. Factors responsible for its loss following streptomycin treatment. J. Exp. Med. 120, 817–828 (1964).

    Article  CAS  Google Scholar 

  25. Brugiroux, S. et al. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat. Microbiol. 2, 16215 (2016).

    Article  CAS  Google Scholar 

  26. Nedialkova, L. P. et al. Inflammation fuels colicin Ib-dependent competition of Salmonella serovar Typhimurium and E. coli in enterobacterial blooms. PLoS Pathog. 10, e1003844 (2014).

    Article  Google Scholar 

  27. Deriu, E. et al. Probiotic bacteria reduce Salmonella Typhimurium intestinal colonization by competing for iron. Cell Host Microbe 14, 26–37 (2013).

    Article  CAS  Google Scholar 

  28. Faith, J. J., Ahern, P. P., Ridaura, V. K., Cheng, J. & Gordon, J. I. Identifying gut microbe–host phenotype relationships using combinatorial communities in gnotobiotic mice. Sci. Transl. Med. 6, 220ra211 (2014).

    Article  Google Scholar 

  29. Kumar, S., Stecher, G. & Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).

    Article  CAS  Google Scholar 

  30. Tamura, K. & Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512–526 (1993).

    CAS  PubMed  Google Scholar 

  31. Wang, R. F. & Kushner, S. R. Construction of versatile low-copy-number vectors for cloning, sequencing and gene expression in Escherichia coli. Gene 100, 195–199 (1991).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by PHS grants AI044170, AI112445, AI096528 and AI112949 to A.J.B. E.M.V. was supported by AI060555, OD010931 and OD010956. Y.L. was supported by Vaadia-BARD Postdoctoral Fellowship FI-505–2014. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NIH.

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Contributions

E.M.V., H.N., K.T.H., L.M.G., A.W.L.R., B.M.M. M.J.L. and C.H.S performed and analysed the experiments. E.M.V., H.N., K.T.H., Y.L., C.A.L., F.F., D.N.B., C.R.T., M.X.B. and A.J. Byndloss performed experiments involving germ-free mice. E.M.V. and M.R.R. analysed 16S profiling data. E.M.V. and A.J.Bäumler designed the experiments, interpreted the data and wrote the manuscript with contributions from all authors.

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Correspondence to Andreas J. Bäumler.

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Supplementary information

Supplementary Information

Supplementary Table 2, Supplementary References and Supplementary Figures 1–9.

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Supplementary Table 1

Statistical analysis and group sizes (for Supplementary Figures).

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Velazquez, E.M., Nguyen, H., Heasley, K.T. et al. Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection. Nat Microbiol 4, 1057–1064 (2019). https://doi.org/10.1038/s41564-019-0407-8

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