13. Oh J. E., Kim B.-C., Chang D.-H., Kwon M., Lee S. Y., Kang D., Kim J. Y., Hwang I., Yu J.-W., Nakae S., Lee H. K. (2016). Dysbiosis-induced IL-33 contributes to impaired antiviral immunity in the genital mucosa. Proc. Natl. Acad. Sci. U.S.A. 113, E762–E771.
14. Monedero V., Buesa J., Rodríguez-Díaz J. (2018). The interactions between host glycobiology, bacterial microbiota, and viruses in the gut. Viruses 10, 1–14.
15. Wu S., Jiang Z.-Y., Sun Y.-F., Yu B., Chen J., Dai C.-Q., Wu X.-L., Tang X.-L., Chen X.-Y. (2013). Microbiota regulates the TLR7 signaling pathway against respiratory tract influenza A virus infection. Curr. Microbiol. 67, 414–422.
16. Ichinohe T., Pang I. K., Kumamoto Y., Peaper D. R., Ho J. H., Murray T. S., Iwasaki A. (2011). Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc. Natl. Acad. Sci. U.S.A. 108, 5354–5359.
17. Ichinohe T., Lee H. K., Ogura Y., Flavell R., Iwasaki A. (2009). Inflammasome recognition of influenza virus is essential for adaptive immune responses. J. Exp. Med. 206, 79–87.
18. Wilks J., Golovkina T. (2012). Influence of microbiota on viral infections. PLoS Pathog. 8: e1002681.
19. Steed A. L., Christophi G. P., Kaiko G. E., Sun L., Goodwin V. M., Jain U., Esaulova E., Artyomov M. N., Morales D. J., Holtzman M. J., Boon A. C. M., Lenschow D. J., Stappenbeck T. S. (2017). The microbial metabolite desaminotyrosine protects from influenza through type I interferon. Science 357, 498–502.
20. Park M.-K., Ngo V., Kwon Y.-M., Lee, Y.-T., Yoo S., Cho Y.-H., Hong S.-M., Hwang H.S., Ko E.-J., Jung Y.-J., Moon D.-W., Jeong E.-J., Kim M.-C., Lee Y.-N., Jang J.-H., Oh J.-S., Kim C. H. (2013). Lactobacillus plantarum DK119 as a probiotic confers protection against influenza virus by modulating innate immunity. PLoS ONE 8: e75368.
21. Belkacem N., Serafini N., Wheeler R., Derrien M., Boucinha L., Couesnon A., Cerf-Bensussan N., Boneca I.G., Di Santo J. P., Taha M. K., Bourdet-Sicard R. (2017). Lactobacillus paracasei feeding improves immune control of influenza infection in mice. PLoS ONE 12: e 0184976.
22. Kuss S. K., Best G. T., Etheredge C. A., Pruijssers A. J., Frierson J. M., Hooper L. V., Dermody T. S., Pfeiffer J. K. (2011). Intestinal microbiota promote enteric virus replication and systemic pathogenesis. Science 334, 249–252.
23. Jones M. K., Watanabe M., Zhu S., Graves C. L., Keyes L. R., Grau K. R., Gonzalez-Hernandez M. B., Iovine N. M., Wobus C. E., Vinjé J., Tibbetts S. A., Wallet S. M., Karst S. M. (2014). Enteric bacteria promote human and mouse norovirus infection of Bcells. Science 346, 755–759.
24. Almand E. A., Moore M. D., Outlaw J., Jaykus L.-A. (2017). Human norovirus binding to select bacteria representative of the human gut microbiota. PLoS ONE 12: e0173124.
25. Benedikz E. K., Bailey D., Cook C. N. L., Gonçalves-Carneiro D., Buckner M. M. C., Blair J. M. A., et al. (2019). Bacterial flagellin promotes viral entry via an NF-kB and toll like receptor 5 dependent pathway. Sci. Rep. 9: 7903.
26. Ginsburg A. S., Klugman K. P. (2020). COVID-19 pneumonia and the appropriate use of antibiotics. The Lancet, Vol. 8, Issue 12, E1453–1454.
27. Sieswerda E.et al. (2020). Recommendations for antibacterial therapy in adults with COVID-19 – an evidence based guideline. Clinical Microbiology and Infection, in press, journal pre-proof.
28. Beovic B. et al., (2020). Antibiotic use in patients with COVID-19: a ‘snapshot’ Infectious Diseases International Research Initiative (ID-IRI) survey. J Antimicrob Chemother, 75: 3386–3390.
29. Harris V. C., Haak B. W., Handley S. A., Jiang B., Velasquez D. E., Hykes B. L., Droit L., Berbers G. A. M., Kemper E. M., van Leeuwen E. M. M., van Hensbroek M. B., Wiersinga W. J. (2018). Effect of antibiotic-mediated microbiome modulation on rotavirus vaccine immunogenicity: a human, randomized-control proof-of-concept trial. Cell Host Microbe 24, 197–207.
30. Uchiyama R., Chassaing B., Zhang B., Gewirtz A. T. (2014). Antibiotic treatment suppresses rotavirus infection and enhances specific humoral immunity. J. Infect. Dis. 210, 171–182.
31. Kraemer S. A., Ramachandran A., Perron G. G. (2019). Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy. Microorganisms, 7, 18.
32. Frost I., Craig J., Joshi J., Faure K., Laxminarayan R. (2019). Access Barriers to Antibiotics. Washington, DC: Center for Disease Dynamics, Economics & Policy.
33. Higgins J. P. T, Soares-Weiser K., López-López J., Kakourou A., Chaplin K., Christensen H., Martin N. K., Sterne J. A. C., Reingold A. L. (2016). Association of BCG, DTP, and measles containing vaccines with childhood mortality: systematic review. BMJ; 355: i5170.
34. Hensel J., McAndrews K. M., McGrail D. J., Dowlatshahi D. P., LeBleu V. S., Kalluri R. (2020). Protection against SARS-CoV-2 by BCG vaccination is not supported by epidemiological analyses. Sci Rep 10, 18377.