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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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.
Karst, S. M. The influence of commensal bacteria on infection with enteric viruses. Nat. Rev. Microbiol. 14, 197–204 (2016).
Pfeiffer, J. K. & Virgin, H. W. Transkingdom control of viral infection and immunity in the mammalian intestine. Science 351, aad5872 (2016).
Kuss, S. K. et al. Intestinal microbiota promote enteric virus replication and systemic pathogenesis. Science 334, 249–252 (2011).
Kane, M. et al. Successful transmission of a retrovirus depends on the commensal microbiota. Science 334, 245–249 (2011).
Kernbauer, E., Ding, Y. & Cadwell, K. An enteric virus can replace the beneficial function of commensal bacteria. Nature 516, 94–98 (2014).
Jones, M. K. et al. Enteric bacteria promote human and murine norovirus infection of B cells. Science 346, 755–759 (2014).
Baldridge, M. T. et al. Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection. Science 347, 266–269 (2015).
Uchiyama, R., Chassaing, B., Zhang, B. & Gewirtz, A. T. Antibiotic treatment suppresses rotavirus infection and enhances specific humoral immunity. J. Infect. Dis. 210, 171–182 (2014).
Robinson, C. M., Jesudhasan, P. R. & Pfeiffer, J. K. Bacterial lipopolysaccharide binding enhances virion stability and promotes environmental fitness of an enteric virus. Cell Host Microbe 15, 36–46 (2014).
Wilks, J. et al. Mammalian lipopolysaccharide receptors incorporated into the retroviral envelope augment virus transmission. Cell Host Microbe 18, 456–462 (2015).
Sansone, C. L. et al. Microbiota-dependent priming of antiviral intestinal immunity in Drosophila. Cell Host Microbe 18, 571–581 (2015).
Ramirez, J. L. et al. Reciprocal tripartite interactions between the Aedes aegypti midgut microbiota, innate immune system and dengue virus influences vector competence. PLoS Negl. Trop. Dis. 6, e1561 (2012).
Wu, P. et al. A gut commensal bacterium promotes mosquito permissiveness to arboviruses. Cell Host Microbe 25, 101–112 (2019).
Ichinohe, T. et al. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc. Natl Acad. Sci. USA 108, 5354–5359 (2011).
Abt, M. C. et al. Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Immunity 37, 158–170 (2012).
McFarlane, A. J. et al. Enteric helminth-induced type I interferon signaling protects against pulmonary virus infection through interaction with the microbiota. J. Allergy Clin. Immunol. 140, 1068–1078 (2017).
Thackray, L. B. et al. Oral antibiotic treatment of mice exacerbates the disease severity of multiple flavivirus infections. Cell Rep. 22, 3440–3453 (2018).
Steed, A. L. et al. The microbial metabolite desaminotyrosine protects from influenza through type I interferon. Science 357, 498–502 (2017).
Zhu, S. et al. Regulation of norovirus virulence by the VP1 protruding domain correlates with B cell infection efficiency. J. Virol. 90, 2858–2867 (2015).
Zhu, S. et al. Identification of immune and viral correlates of norovirus protective immunity through comparative study of intra-cluster norovirus strains. PLoS Pathog. 9, e1003592 (2013).
Thackray, L. B. et al. Murine noroviruses comprising a single genogroup exhibit biological diversity despite limited sequence divergence. J. Virol. 81, 10460–10473 (2007).
Hsu, C. C., Riley, L. K., Wills, H. M. & Livingston, R. S. Persistent infection with and serologic crossreactivity of three novel murine noroviruses. Comp. Med. 56, 247–251 (2006).
Arias, A., Bailey, D., Chaudhry, Y. & Goodfellow, I. G. Development of a reverse genetics system for murine norovirus 3; long-term persistence occurs in the caecum and colon. J. Gen. Virol. 93, 1432–1441 (2012).
Grau, K. R. et al. The major targets of acute norovirus infection are immune cells in the gut-associated lymphoid tissue. Nat. Microbiol. 2, 1586–1591 (2017).
Sommereyns, C., Paul, S., Staeheli, P. & Michiels, T. IFN-lambda (IFN-λ) is expressed in a tissue-dependent fashion and primarily acts on epithelial cells in vivo. PLoS Pathog. 4, e1000017 (2008).
Wilen, C. B. et al. Tropism for tuft cells determines immune promotion of norovirus pathogenesis. Science 360, 204–208 (2018).
Lazear, H. M., Nice, T. J. & Diamond, M. S. Interferon-λ: immune functions at barrier surfaces and beyond. Immunity 43, 15–28 (2015).
Thomas, C., Pellicciari, R., Pruzanski, M., Auwerx, J. & Schoonjans, K. Targeting bile-acid signalling for metabolic diseases. Nat. Rev. Drug Discov. 7, 678–693 (2008).
Joyce, S. A. & Gahan, C. G. M. The gut microbiota and the metabolic health of the host. Curr. Opin. Gastroenterol. 30, 120–127 (2014).
Fiorucci, S. & Distrutti, E. Bile acid-activated receptors, intestinal microbiota, and the treatment of metabolic disorders. Trends Mol. Med. 21, 702–714 (2015).
Vavassori, P., Mencarelli, A., Renga, B., Distrutti, E. & Fiorucci, S. The bile acid receptor FXR is a modulator of intestinal innate immunity. J. Immunol. 183, 6251–6261 (2009).
Schupp, A.-K. et al. Bile acids act as soluble host restriction factors limiting cytomegalovirus replication in hepatocytes. J. Virol. 90, 6686–6698 (2016).
Kim, Y. & Chang, K.-O. Inhibitory effects of bile acids and synthetic farnesoid X receptor agonists on rotavirus replication. J. Virol. 85, 12570–12577 (2011).
Chang, K.-O. et al. Bile acids are essential for porcine enteric calicivirus replication in association with down-regulation of signal transducer and activator of transcription 1. Proc. Natl Acad. Sci. USA 101, 8733–8738 (2004).
Ettayebi, K. et al. Replication of human noroviruses in stem cell–derived human enteroids. Science 353, 1387–1393 (2016).
Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015).
Sun, X. et al. Microbiota-derived metabolic factors reduce campylobacteriosis in mice. Gastroenterology 154, 1751–1763 (2018).
Wells, J. E. & Hylemon, P. B. Identification and characterization of a bile acid 7α-dehydroxylation operon in Clostridium sp. strain TO-931, a highly active 7α-dehydroxylating strain isolated from human feces. Appl. Environ. Microbiol. 66, 1107–1113 (2000).
Nelson, C. A. et al. Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor. Proc. Natl Acad. Sci. USA 115, E9201–E9210 (2018).
Lee, S. et al. Norovirus cell tropism is determined by combinatorial action of a viral non-structural protein and host cytokine. Cell Host Microbe 22, 449–459 (2017).
Zhang, Y., Kast-Woelbern, H. R. & Edwards, P. A. Natural structural variants of the nuclear receptor farnesoid X receptor affect transcriptional activation. J. Biol. Chem. 278, 104–110 (2003).
Bookout, A. L. et al. Anatomical profiling of nuclear receptor expression reveals a hierarchical transcriptional network. Cell 126, 789–799 (2006).
Higashiyama, H., Kinoshita, M. & Asano, S. Immunolocalization of farnesoid X receptor (FXR) in mouse tissues using tissue microarray. Acta Histochem. 110, 86–93 (2008).
Inagaki, T. et al. Regulation of antibacterial defense in the small intestine by the nuclear bile acid receptor. Proc. Natl Acad. Sci. USA 103, 3920–3925 (2006).
Chang, K.-O. & George, D. W. Bile acids promote the expression of hepatitis C virus in replicon-harboring cells. J. Virol. 81, 9633–9640 (2007).
Xiong, Q. et al. Metabolite-sensing G protein coupled receptor TGR5 protects host from viral infection through amplifying type I interferon responses. Front. Immunol. 9, 2289 (2018).
Mowat, A. M. & Agace, W. W. Regional specialization within the intestinal immune system. Nat. Rev. Immunol. 14, 667–685 (2014).
Padilla-Nash, H. M. et al. Spontaneous transformation of murine epithelial cells requires the early acquisition of specific chromosomal aneuploidies and genomic imbalances. Genes Chromosomes Cancer 51, 353–374 (2012).
González-Hernández, M. B., Perry, J. W. & Wobus, C. E. Neutral red assay for murine norovirus replication and detection in a mouse. Bio Protoc. 3, e415 (2013).
Kahan, S. M. et al. Comparative murine norovirus studies reveal a lack of correlation between intestinal virus titers and enteric pathology. Virology 421, 202–210 (2011).
Gonzalez-Hernandez, M. B. et al. Efficient norovirus and reovirus replication in the mouse intestine requires microfold (M) cells. J. Virol. 88, 6934–6943 (2014).
Bagyánszki, M. et al. Chronic alcohol consumption affects gastrointestinal motility and reduces the proportion of neuronal NOS‐immunoreactive myenteric neurons in the murine jejunum. Anat. Rec. 293, 1536–1542 (2010).
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.
The authors declare no competing interests.
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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.
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 (2019) doi:10.1038/s41564-019-0602-7