Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection


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.


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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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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 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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