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The intestinal regionalization of acute norovirus infection is regulated by the microbiota via bile acid-mediated priming of type III interferon

Nature Microbiology volume 5, pages 84–92 (2020)Cite this article

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Abstract

Evidence has accumulated to demonstrate that the intestinal microbiota enhances mammalian enteric virus infections1. For example, we and others previously reported that commensal bacteria stimulate acute and persistent murine norovirus infections2,3,4. However, in apparent contradiction of these results, the virulence of murine norovirus infection was unaffected by antibiotic treatment. This prompted us to perform a detailed investigation of murine norovirus infection in microbially deplete mice, revealing a more complex picture in which commensal bacteria inhibit viral infection of the proximal small intestine while simultaneously stimulating the infection of distal regions of the gut. Thus, commensal bacteria can regulate viral regionalization along the intestinal tract. We further show that the mechanism underlying bacteria-dependent inhibition of norovirus infection in the proximal gut involves bile acid priming of type III interferon. Finally, the regional effects of the microbiota on norovirus infection may result from distinct regional expression profiles of key bile acid receptors that regulate the type III interferon response. Overall, these findings reveal that the biotransformation of host metabolites by the intestinal microbiota directly and regionally impacts infection by a pathogenic enteric virus.

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Fig. 1: The intestinal microbiota plays opposing roles in the regulation of proximal gut versus distal gut MNV infection.
Fig. 2: Bacteria-dependent type III IFN signalling in the proximal gut protects intestinal immune cells from MNV-1 infection.
Fig. 3: Bile acids biotransformed by the intestinal microbiota prime type III IFN induction to suppress MNV infection of the proximal gut.
Fig. 4: Bile acids prime IFN-λ induction in vitro.

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Data availability

All of the data that support the findings of this study are available from the corresponding authors on request. The source data for bile acid analyses performed in this study are included in Supplementary Table 2.

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Acknowledgements

We acknowledge the Washington University Genome Engineering and iPSC Center, M. White and D. Kreamalmeyer. S.M.K. was funded by grant nos. NIH R01AI116892, NIH R01AI081921 and NIH R01AI141478. M.T.B. was supported by grant nos. NIH R01AI141478, NIH K22 AI127846-01, DDRCC P30 DK052574 and the Global Probiotics Council’s Young Investigator Grant for Probiotics Research. C.E.W. was funded in part by NIH R21 AI103961 and the University of Michigan Host–Microbiome Initiative. E.W.H. and M.P. were supported by grant no. T90DE021990. H.T. was supported by grant no. T32DK094775. C.B.W. was supported by grant no. NIH K08 AI28043 and the Burroughs Wellcome Fund.

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Authors and Affiliations

  1. Department of Molecular Genetics & Microbiology, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA

    Katrina R. Grau, Shu Zhu, Emily W. Helm, Drake Philip, Matthew Phillips, Abel Hernandez & Stephanie M. Karst

  2. Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA

    Stefan T. Peterson, Philip Frasse & Megan T. Baldridge

  3. Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA

    Holly Turula & Christiane E. Wobus

  4. Departments of Laboratory Medicine and Immunobiology, Yale University School of Medicine, New Haven, CT, USA

    Vincent R. Graziano & Craig B. Wilen

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Contributions

K.R.G., S.Z., S.T.P., E.W.H., D.P., M.P., A.H., H.T., P.F., V.R.G. and M.T.B. performed the experiments. K.R.G., S.Z., E.W.H., D.P., M.P., H.T., C.B.W., C.E.W., M.T.B. and S.M.K. analysed the results. M.T.B. and S.M.K. designed the project. K.R.G., M.T.B. and S.M.K. wrote the manuscript. All of the authors read and edited the manuscript.

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Correspondence to Megan T. Baldridge or Stephanie M. Karst.

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Extended data

Extended Data Fig. 1 Cumulative intestinal titers.

Intestinal titers from SI-1, SI-2, SI-3 cecum and colon were combined for each mouse, and data for all mice per group averaged. Data for individual intestinal regions for Ifnar-/- mice are shown in Fig. 1c, for B6 mice are shown in Fig. 1d, and for germ-free mice are shown in Fig. 1e.

Extended Data Fig. 2 Tuft cells are not required for MNV-1 infection.

Tuft cell-deficient Pou2f3-/- or wild-type littermates (n = 9 mice per group) were challenged with 106 plaque-forming units (PFU) MNV-1 and viral genomes were quantified at 7 dpi. Pou2f3-/- (KO) and WT mice had statistically similar viral genomes in ileum, colon. MLNs, and spleen. Data is pooled from three independent experiments. Error bars indicate the mean of all data points. LOD, limit of detection.

Extended Data Fig. 3 Measurements of individual bile acids.

Lumenal contents were collected from SI-1 (a) and SI-3 (b) of groups of B6 mice (n = 5) treated with PBS, Abx, clindamycin, or nalidixic acid. The indicated bile acids were measured at the University of Pennsylvania Microbial Culture and Metabolomics Core using a Waters Acquity vPLC System. Source data are provided in Supplementary Table 2.

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Grau, K.R., Zhu, S., Peterson, S.T. et al. The intestinal regionalization of acute norovirus infection is regulated by the microbiota via bile acid-mediated priming of type III interferon. Nat Microbiol 5, 84–92 (2020). https://doi.org/10.1038/s41564-019-0602-7

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