E.Dgat-Bony.位ad Food Microbiology 85 (2020)103278 二 0. m世肝 roc.Natl.Aca wale D mmprocedures to generate viral metagenomes. Nat. Protoc. 4, 470–483. https://doi.org/ 10.1038/nprot.2009.10. Ulve, V. m., Monnet, C., Valence, F., Fauquant, J., Falentin, H., Lortal, S., 2008. RNA extraction from cheese for analysis of in situ gene expression of Lactococcus lactis. J. Appl. Microbiol. 105, 1327–1333. https://doi.org/10.1111/j.1365-2672.2008. 03869.x. Varsani, A., Krupovic, M., 2018. Smacoviridae: a new family of animal-associated single￾stranded DNA viruses. Arch. Virol. 163 2005–2015. https://doi.org/10.1007/ s00705-018-3820-z. Weynberg, K.D., Wood-Charlson, E.M., Suttle, C.A., Oppen, V., H, M.J., 2014. Generating viral metagenomes from the coral holobiont. Front. Microbiol. 5. https://doi.org/10. 3389/fmicb.2014.00206. Willner, D., Furlan, M., Schmieder, R., Grasis, J.A., Pride, D.T., Relman, D.A., Angly, F.E., McDole, T., Mariella, R.P., Rohwer, F., Haynes, M., 2011. Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc. Natl. Acad. Sci. 108, 4547–4553. https://doi.org/10.1073/pnas.1000089107. Wolfe, B.E., Button, J.E., Santarelli, M., Dutton, R.J., 2014. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158, 422–433. https://doi.org/10.1016/j.cell.2014.05.041. Yaron, S., Kolling, G.L., Simon, L., Matthews, K.R., 2000. Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria. Appl. Environ. Microbiol. 66, 4414–4420. https://doi.org/10.1128/AEM.66.10.4414- 4420.2000. Zablocki, O., Zyl, L. van, Adriaenssens, E.M., Rubagotti, E., Tuffin, M., Cary, S.C., Cowan, D., 2014. High-level diversity of tailed phages, eukaryote-associated viruses, and virophage-like elements in the metaviromes of antarctic soils. Appl. Environ. Microbiol. 80, 6888–6897. https://doi.org/10.1128/AEM.01525-14. Zhang, Y., Kastman, E.K., Guasto, J.S., Wolfe, B.E., 2018. Fungal networks shape dy￾namics of bacterial dispersal and community assembly in cheese rind microbiomes. Nat. Commun. 9, 336. https://doi.org/10.1038/s41467-017-02522-z. Zimmermann, L., Stephens, A., Nam, S.-Z., Rau, D., Kübler, J., Lozajic, M., Gabler, F., Söding, J., Lupas, A.N., Alva, V., 2018. A completely reimplemented MPI bioinfor￾matics toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237–2243. https://doi.org/10.1016/j.jmb.2017.12.007. E. Dugat-Bony, et al. Food Microbiology 85 (2020) 103278 11