References
- Ackermann, H.-W., and D. Prangishvili. 2012. Prokaryote viruses studied by electron microscopy. Archives of Virology 157 (10):1843–9. doi: https://doi.org/10.1007/s00705-012-1383-y.
- Alarcón-Schumacher, T., S. Guajardo-Leiva, J. Antón, and B. Díez. 2019. Elucidating viral communities during a phytoplankton bloom on the West Antarctic Peninsula. Frontiers in Microbiology 10:1014doi: https://doi.org/10.3389/fmicb.2019.01014.
- Armour, C. R., S. Nayfach, K. S. Pollard, and T. J. Sharpton. 2019. A metagenomic meta-analysis reveals functional signatures of health and disease in the human gut microbiome. MSystems 4 (4):e00332. doi: https://doi.org/10.1128/mSystems.00332-18.
- Bag, S., B. Saha, O. Mehta, D. Anbumani, N. Kumar, M. Dayal, A. Pant, P. Kumar, S. Saxena, K. H. Allin, et al. 2016. An improved method for high quality metagenomics DNA extraction from human and environmental samples. Scientific Reports 6 (1):26775–9. doi: https://doi.org/10.1038/srep26775.
- Beuve, M., J.-M. Hily, A. Alliaume, C. Reinbold, J. Le Maguet, T. Candresse, E. Herrbach, and O. Lemaire. 2018. A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms. Archives of Virology 163 (11):2937–46. doi: https://doi.org/10.1007/s00705-018-3949-9.
- Bikel, S., A. Valdez-Lara, F. Cornejo-Granados, K. Rico, S. Canizales-Quinteros, X. Soberón, L. Del Pozo-Yauner, and A. Ochoa-Leyva. 2015. Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: Towards a systems-level understanding of human microbiome. Computational and Structural Biotechnology Journal 13:390–401. doi: https://doi.org/10.1016/j.csbj.2015.06.001.
- Breitbart, M., and F. Rohwer. 2005. Here a virus, there a virus, everywhere the same virus? Trends in Microbiology 13 (6):278–84. doi: https://doi.org/10.1016/j.tim.2005.04.003.
- Bruijns, B.,. R. Tiggelaar, and H. Gardeniers. 2018. Massively parallel sequencing techniques for forensics: A review. Electrophoresis 39 (21):2642–54. doi: https://doi.org/10.1002/elps.201800082.
- Catel-Ferreira, M., H. Tnani, C. Hellio, P. Cosette, and L. Lebrun. 2015. Antiviral effects of polyphenols: Development of bio-based cleaning wipes and filters. Journal of Virological Methods 212:1–7. doi: https://doi.org/10.1016/j.jviromet.2014.10.008.
- Chaïb, A., C. Philippe, F. Jaomanjaka, O. Claisse, M. Jourdes, P. Lucas, S. Cluzet, and C. L. Marrec. 2019. Lysogeny in the lactic acid bacterium oenococcus oeni is responsible for modified colony morphology on red grape juice agar. Applied and Environmental Microbiology 85 (19):e00997. doi: https://doi.org/10.1128/AEM.00997-19.
- Clooney, A. G., F. Fouhy, R. D. Sleator, A. O. Driscoll, C. Stanton, P. D. Cotter, and M. J. Claesson. 2016. Comparing apples and oranges? Next generation sequencing and its impact on microbiome analysis. PLoS ONE 11 (2):e0148028doi: https://doi.org/10.1371/journal.pone.0148028.
- Conceição-Neto, N., M. Zeller, H. Lefrère, P. De Bruyn, L. Beller, W. Deboutte, C. K. Yinda, R. Lavigne, P. Maes, M. V. Ranst, et al. 2015. Modular approach to customise sample preparation procedures for viral metagenomics: A reproducible protocol for virome analysis. Scientific Reports 5 (1):16532–14. doi: https://doi.org/10.1038/srep16532.
- Costantini, A., F. Doria, J.-C. Saiz, and E. Garcia-Moruno. 2017. Phage-host interactions analysis of newly characterized Oenococcus oeni bacteriophages: Implications for malolactic fermentation in wine. International Journal of Food Microbiology 246:12–9. doi: https://doi.org/10.1016/j.ijfoodmicro.2017.01.020.
- Coton, M., A. Pawtowski, B. Taminiau, G. Burgaud, F. Deniel, L. Coulloumme-Labarthe, A. Fall, G. Daube, and E. Coton. 2017. Unraveling microbial ecology of industrial-scale Kombucha fermentations by metabarcoding and culture-based methods. FEMS Microbiology Ecology 93 (5):fix048. doi: https://doi.org/10.1093/femsec/fix048.
- Cousin, F. J., R. Le Guellec, M. Schlusselhuber, M. Dalmasso, J.-M. Laplace, and M. Cretenet. 2017. Microorganisms in fermented apple beverages: Current knowledge and future directions. Microorganisms 5 (3):39.
- Dalmasso, M., C. Hill, and R. P. Ross. 2014. Exploiting gut bacteriophages for human health. Trends in Microbiology 22 (7):399–405. doi: https://doi.org/10.1016/j.tim.2014.02.010.
- Deasy, T., J. Mahony, H. Neve, K. J. Heller, and D. Van Sinderen. 2011. Isolation of a virulent Lactobacillus brevis phage and its application in the control of beer spoilage. Journal of Food Protection 74 (12):2157–61. doi: https://doi.org/10.4315/0362-028X.JFP-11-262.
- Deng, L., R. Silins, J. L. Castro-Mejía, W. Kot, L. Jessen, J. Thorsen, S. Shah, J. Stokholm, H. Bisgaard, S. Moineau, et al. 2019. A protocol for extraction of infective viromes suitable for metagenomics sequencing from low volume fecal samples. Viruses 11 (7):667. doi: https://doi.org/10.3390/v11070667.
- Dinan, T. G., and J. F. Cryan. 2017. Brain-gut-microbiota axis and mental health. Psychosomatic Medicine 79 (8):920–6. doi: https://doi.org/10.1097/PSY.0000000000000519.
- Draper, L. A., F. J. Ryan, M. Dalmasso, P. G. Casey, A. McCann, V. Velayudhan, R. P. Ross, and C. Hill. 2019. Autochthonous faecal virome transplantation (FVT) reshapes the murine microbiome after antibiotic perturbation. Biorxiv 591099.
- Duenas, M., A. Irastorza, K. Fernandez, and A. Bilbao. 1995. Heterofermentative Lactobacilli causing ropiness in Basque country ciders. Journal of Food Protection 58 (1):76–80. doi: https://doi.org/10.4315/0362-028X-58.1.76.
- Dugat-Bony, E., J. Lossouarn, M. De Paepe, A.-S. Sarthou, Y. Fedala, M.-A. Petit, and S. Chaillou. 2020. Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles. Food Microbiology 85:103278doi: https://doi.org/10.1016/j.fm.2019.103278.
- Dugat-Bony, E., L. Garnier, J. Denonfoux, S. Ferreira, A. S. Sarthou, P. Bonnarme, and F. Irlinger. 2016. Highlighting the microbial diversity of 12 French cheese varieties. International Journal of Food Microbiology 238:265–73. doi: https://doi.org/10.1016/j.ijfoodmicro.2016.09.026.
- Dugat-Bony, E., C. Straub, A. Teissandier, D. Onésime, V. Loux, C. Monnet, F. Irlinger, S. Landaud, M.-N. Leclercq-Perlat, P. Bento, et al. 2015. Overview of a surface-ripened cheese community functioning by meta-omics analyses. Plos ONE 10 (4):e0124360doi: https://doi.org/10.1371/journal.pone.0124360.
- Feyereisen, M., J. Mahony, G. A. Lugli, M. Ventura, H. Neve, C. M. Franz, J.-P. Noben, T. O’Sullivan, and D. Sinderen. 2019. Isolation and characterization of Lactobacillus brevis phages. Viruses 11 (5):393. doi: https://doi.org/10.3390/v11050393.
- García, P., B. Martínez, J. M. Obeso, and A. Rodríguez. 2008. Bacteriophages and their application in food safety. Letters in Applied Microbiology 47 (6):479–85. doi: https://doi.org/10.1111/j.1472-765X.2008.02458.x.
- Hatcher, E. L., S. A. Zhdanov, Y. Bao, O. Blinkova, E. P. Nawrocki, Y. Ostapchuck, A. A. Schäffer, and J. R. Brister. 2017. Virus variation resource - Improved response to emergent viral outbreaks. Nucleic Acids Research 45 (D1):D482–D490. doi: https://doi.org/10.1093/nar/gkw1065.
- Hayes, S., J. Mahony, A. Nauta, and D. Van Sinderen. 2017. Metagenomic approaches to assess bacteriophages in various environmental niches. Viruses 9 (6):127. doi: https://doi.org/10.3390/v9060127.
- d’Humières, C., M. Touchon, S. Dion, J. Cury, A. Ghozlane, M. Garcia-Garcera, C. Bouchier, L. Ma, E. Denamur, and E. P.C.Rocha. 2019. A simple, reproducible and cost-effective procedure to analyse gut phageome: From phage isolation to bioinformatic approach. Scientific Reports 9 (1):1–13. doi: https://doi.org/10.1038/s41598-019-47656-w.
- Hurwitz, B. L., J. M. U'Ren, and K. Youens-Clark. 2016. Computational prospecting the great viral unknown. FEMS Microbiology Letters 363 (10):fnw077. doi: https://doi.org/10.1093/femsle/fnw077.
- Janež, N., and C. Loc-Carrillo. 2013. Use of phages to control Campylobacter spp. Journal of Microbiological Methods 95 (1):68–75. doi: https://doi.org/10.1016/j.mimet.2013.06.024.
- Jaomanjaka, F., P. Ballestra, M. Dols-Lafargue, and C. Le Marrec. 2013. Expanding the diversity of oenococcal bacteriophages: Insights into a novel group based on the integrase sequence. International Journal of Food Microbiology 166 (2):331–40. doi: https://doi.org/10.1016/j.ijfoodmicro.2013.06.032.
- Jaomanjaka, F., O. Claisse, M. Blanche-Barbat, M. Petrel, P. Ballestra, and C. Le Marrec. 2016. Characterization of a new virulent phage infecting the lactic acid bacterium Oenococcus oeni. Food Microbiology 54:167–77. doi: https://doi.org/10.1016/j.fm.2015.09.016.
- Jaomanjaka, F., O. Claisse, C. Philippe, and C. Le Marrec. 2018. Complete genome sequence of lytic Oenococcus oeni bacteriophage OE33PA. Microbiology Resource Announcements 7 (6):e00818. doi: https://doi.org/10.1128/MRA.00818-18.
- Jovel, J.,. J. Patterson, W. Wang, N. Hotte, S. O'Keefe, T. Mitchel, T. Perry, D. Kao, A. L. Mason, K. L. Madsen, et al. 2016. Characterization of the gut microbiome using 16S or shotgun metagenomics. Frontiers in Microbiology 7: 459. doi: https://doi.org/10.3389/fmicb.2016.00459.
- Jung, J. Y., S. H. Lee, H. M. Jin, Y. Hahn, E. L. Madsen, and C. O. Jeon. 2013. Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation. International Journal of Food Microbiology 163 (2-3):171–9. doi: https://doi.org/10.1016/j.ijfoodmicro.2013.02.022.
- Jung, M.-J., M.-S. Kim, J.-H. Yun, J.-Y. Lee, P. S. Kim, H.-W. Lee, J.-H. Ha, S. W. Roh, and J.-W. Bae. 2018. Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community. Food Microbiology 76:319–27. doi: https://doi.org/10.1016/j.fm.2018.06.010.
- Kim, M.-S., and J.-W. Bae. 2018. Lysogeny is prevalent and widely distributed in the murine gut microbiota. The ISME Journal 12 (4):1127–41. doi: https://doi.org/10.1038/s41396-018-0061-9.
- King, A. M. Q., M. J. Adams, E. B. Carstens, and E. J. Lefkowitz. eds., 2012. Order - Caudovirales. In Virus taxonomy, 39–45. San Diego: Elsevier.
- Kleiner, M., L. V. Hooper, and B. A. Duerkop. 2015. Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics 16 (1):7doi: https://doi.org/10.1186/s12864-014-1207-4.
- Knowles, B., C. B. Silveira, B. A. Bailey, K. Barott, V. A. Cantu, A. G. Cobián-Güemes, F. H. Coutinho, E. A. Dinsdale, B. Felts, K. A. Furby, et al. 2016. Lytic to temperate switching of viral communities. Nature 531 (7595):466–70. doi: https://doi.org/10.1038/nature17193.
- Kot, W., H. Neve, K. J. Heller, and F. K. Vogensen. 2014. Bacteriophages of Leuconostoc, Oenococcus, and Weissella. Frontiers in Microbiology 5:186. doi: https://doi.org/10.3389/fmicb.2014.00186.
- Kurokawa, K.,. T. Itoh, T. Kuwahara, K. Oshima, H. Toh, A. Toyoda, H. Takami, H. Morita, V. K. Sharma, T. P. Srivastava, et al. 2007. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14 (4):169–81. doi: https://doi.org/10.1093/dnares/dsm018.
- Lavelle, K., I. Martinez, H. Neve, G. A. Lugli, C. M. A. P. Franz, M. Ventura, F. D. Bello, D. V. Sinderen, and J. Mahony. 2018. Biodiversity of Streptococcus thermophilus phages in global dairy fermentations. Viruses 10 (10):577. doi: https://doi.org/10.3390/v10100577.
- Lavelle, K., J. Murphy, B. Fitzgerald, G. A. Lugli, A. Zomer, H. Neve, M. Ventura, C. M. Franz, C. Cambillau, D. Sinderen, et al. 2018. A decade of Streptococcus thermophilus phage evolution in an Irish dairy plant. Applied and Environmental Microbiology 84 (10):e02855-17. doi: https://doi.org/10.1128/AEM.02855-17.
- Lee, M., J. H. Song, M. Y. Jung, S. H. Lee, and J. Y. Chang. 2017. Large-scale targeted metagenomics analysis of bacterial ecological changes in 88 kimchi samples during fermentation. Food Microbiology 66:173–83. doi: https://doi.org/10.1016/j.fm.2017.05.002.
- Lee, M., J. H. Song, J. M. Park, and J. Y. Chang. 2019. Bacterial diversity in Korean temple kimchi fermentation. Food Research International (Ottawa, Ont.) 126:108592doi: https://doi.org/10.1016/j.foodres.2019.108592.
- Lefkowitz, E. J., D. M. Dempsey, R. C. Hendrickson, R. J. Orton, S. G. Siddell, and D. B. Smith. 2018. Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV)). Nucleic Acids Res 46 (D1):D708–D717. doi: https://doi.org/10.1093/nar/gkx932.
- LeLièvre, V., A. Besnard, M. Schlusselhuber, N. Desmasures, and M. Dalmasso. 2019. Phages for biocontrol in foods: What opportunities for Salmonella sp. control along the dairy food chain? Food Microbiology 78:89–98. doi: https://doi.org/10.1016/j.fm.2018.10.009.
- Li, L., J. G. Victoria, C. Wang, M. Jones, G. M. Fellers, T. H. Kunz, and E. Delwart. 2010. Bat guano virome: Predominance of dietary viruses from insects and plants plus novel mammalian viruses. Journal of Virology 84 (14):6955–65. doi: https://doi.org/10.1128/JVI.00501-10.
- Lim, E. S., Y. Zhou, G. Zhao, I. K. Bauer, L. Droit, I. M. Ndao, B. B. Warner, P. I. Tarr, D. Wang, and L. R. Holtz. 2015. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nature Medicine 21 (10):1228–34. doi: https://doi.org/10.1038/nm.3950.
- Liu, W.-T., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Applied and Environmental Microbiology 63 (11):4516–22. doi: https://doi.org/10.1128/AEM.63.11.4516-4522.1997.
- López-Bueno, A., J. Tamames, D. Velázquez, A. Moya, A. Quesada, and A. Alcamí. 2009. High diversity of the viral community from an Antarctic Lake. Science (New York, N.Y.) 326 (5954):858–61. doi: https://doi.org/10.1126/science.1179287.
- Luque, A., and C. Silveira. 2020. Quantification of lysogeny caused by phage coinfections in microbial communities from biophysical principles. bioRxiv 2020.
- Ma, Y., A. Marais, M. Lefebvre, S. Theil, L. Svanella-Dumas, C. Faure, and T. Candresse. 2019. Phytovirome analysis of wild plant populations: Comparison of double-stranded RNA and virion-associated nucleic acid metagenomic approaches. Journal of Virology 94 (1):e0146219. doi: https://doi.org/10.1128/JVI.01462-19.
- Ma, Y., X. You, G. Mai, T. Tokuyasu, and C. Liu. 2018. A human gut phage catalog correlates the gut phageome with type 2 diabetes. Microbiome 6 (1):24. doi: https://doi.org/10.1186/s40168-018-0410-y.
- Mahony, J., A. Moscarelli, P. Kelleher, G. A. Lugli, M. Ventura, L. Settanni, and D. Van Sinderen. 2017. Phage biodiversity in artisanal cheese wheys reflects the complexity of the fermentation process. Viruses 9 (3):45. doi: https://doi.org/10.3390/v9030045.
- Mahony, J., S. R. Stockdale, B. Collins, S. Spinelli, F. P. Douillard, C. Cambillau, and D. Van Sinderen. 2016. Lactococcus lactis phage TP901-1 as a model for Siphoviridae virion assembly. Bacteriophage 6 (1):e1123795doi: https://doi.org/10.1080/21597081.2015.1123795.
- Mahony, J., and D. Van Sinderen. 2014. Current taxonomy of phages infecting lactic acid bacteria. Frontiers in Microbiology 5:7. doi: https://doi.org/10.3389/fmicb.2014.00007.
- Manrique, P., B. Bolduc, S. T. Walk, J. van der Oost, W. M. de Vos, and M. J. Young. 2016. Healthy human gut phageome. Proceedings of the National Academy of Sciences of the United States of America 113 (37):10400–5. doi: https://doi.org/10.1073/pnas.1601060113.
- Marco, M. L., D. Heeney, S. Binda, C. J. Cifelli, P. D. Cotter, B. Foligné, M. Gänzle, R. Kort, G. Pasin, A. Pihlanto, et al. 2017. Health benefits of fermented foods: Microbiota and beyond. Current Opinion in Biotechnology 44:94–102. doi: https://doi.org/10.1016/j.copbio.2016.11.010.
- Marsh, A. J., C. Hill, R. P. Ross, and P. D. Cotter. 2014. Fermented beverages with health-promoting potential: Past and future perspectives. Trends in Food Science & Technology 38 (2):113–24. doi: https://doi.org/10.1016/j.tifs.2014.05.002.
- Mavrich, T. N., E. Casey, J. Oliveira, F. Bottacini, K. James, C. M. A. P. Franz, G. A. Lugli, H. Neve, M. Ventura, G. F. Hatfull, et al. 2018. Characterization and induction of prophages in human gut-associated Bifidobacterium hosts. Scientific Reports 8 (1):12772. doi: https://doi.org/10.1038/s41598-018-31181-3.
- May, A., S. Narayanan, J. Alcock, A. Varsani, C. Maley, and A. Aktipis. 2019. Kombucha: A novel model system for cooperation and conflict in a complex multi-species microbial ecosystem. PeerJ 7:e7565. doi: https://doi.org/10.7717/peerj.7565.
- Milani, C., E. Casey, G. A. Lugli, R. Moore, J. Kaczorowska, C. Feehily, M. Mangifesta, L. Mancabelli, S. Duranti, F. Turroni, et al. 2018. Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. Microbiome 6 (1):145. doi: https://doi.org/10.1186/s40168-018-0527-z.
- Mills, S., F. Shanahan, C. Stanton, C. Hill, A. Coffey, and R. P. Ross. 2013. Movers and shakers: Influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes 4 (1):4–16. doi: https://doi.org/10.4161/gmic.22371.
- Minot, S., A. Bryson, C. Chehoud, G. D. Wu, J. D. Lewis, and F. D. Bushman. 2013. Rapid evolution of the human gut virome. Proceedings of the National Academy of Sciences of the United States of America 110 (30):12450–5. doi: https://doi.org/10.1073/pnas.1300833110.
- Minot, S., R. Sinha, J. Chen, H. Li, S. A. Keilbaugh, G. D. Wu, J. D. Lewis, and F. D. Bushman. 2011. The human gut virome: Inter-individual variation and dynamic response to diet. Genome Res 21 (10):1616–25. doi: https://doi.org/10.1101/gr.122705.111.
- Mitchell, A. E., Y.-J. Hong, J. C. May, C. A. Wright, and C. W. Bamforth. 2005. A comparison of polyvinylpolypyrrolidone (PVPP), silica xerogel and a polyvinylpyrrolidone (PVP)–silica co-product for their ability to remove polyphenols from beer. Journal of the Institute of Brewing 111 (1):20–5. doi: https://doi.org/10.1002/j.2050-0416.2005.tb00644.x.
- Moreno, P. S., J. Wagner, C. S. Mansfield, M. Stevens, J. R. Gilkerson, and C. D. Kirkwood. 2017. Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics. PLoS ONE 12 (6):e0178433. doi: https://doi.org/10.1371/journal.pone.0178433.
- Nalbantoglu, U., A. Cakar, H. Dogan, N. Abaci, D. Ustek, K. Sayood, and H. Can. 2014. Metagenomic analysis of the microbial community in kefir grains. Food microbiology 41:42–51. doi: https://doi.org/10.1016/j.fm.2014.01.014.
- Nieminen, T. T., K. Koskinen, P. Laine, J. Hultman, E. Säde, L. Paulin, A. Paloranta, P. Johansson, J. Björkroth, and P. Auvinen. 2012. Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics. International Journal of Food Microbiology 157 (2):142–9. doi: https://doi.org/10.1016/j.ijfoodmicro.2012.04.016.
- Nishida, A., R. Inoue, O. Inatomi, S. Bamba, Y. Naito, and A. Andoh. 2018. Gut microbiota in the pathogenesis of inflammatory bowel disease. Clinical Journal of Gastroenterology 11 (1):1–10. doi: https://doi.org/10.1007/s12328-017-0813-5.
- Norman, J. M., S. A. Handley, M. T. Baldridge, L. Droit, C. Y. Liu, B. C. Keller, A. Kambal, C. L. Monaco, G. Zhao, P. Fleshner, et al. 2015. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160 (3):447–60. doi: https://doi.org/10.1016/j.cell.2015.01.002.
- Oliveira, J., J. Mahony, L. Hanemaaijer, T. R. H. M. Kouwen, and D. van Sinderen. 2018. Biodiversity of bacteriophages infecting Lactococcus lactis starter cultures. Journal of Dairy Science 101 (1):96–105. doi: https://doi.org/10.3168/jds.2017-13403.
- O'Toole, P. W., and I. B. Jeffery. 2015. Gut microbiota and aging. Science (New York, N.Y.) 350 (6265):1214–5. doi: https://doi.org/10.1126/science.aac8469.
- Parikka, K. J., S. Jacquet, J. Colombet, D. Guillaume, and M. Le Romancer. 2018. Abundance and observations of thermophilic microbial and viral communities in submarine and terrestrial hot fluid systems of the French Southern and Antarctic Lands. Polar Biology 41 (7):1335–52. doi: https://doi.org/10.1007/s00300-018-2288-3.
- Park, E.-J., K.-H. Kim, G. C. Abell, M.-S. Kim, S. W. Roh, and J.-W. Bae. 2011. Metagenomic analysis of the viral communities in fermented foods. Applied and Environmental Microbiology 77 (4):1284–91. doi: https://doi.org/10.1128/AEM.01859-10.
- Patterson, E., P. M. Ryan, J. F. Cryan, T. G. Dinan, R. P. Ross, G. F. Fitzgerald, and C. Stanton. 2016. Gut microbiota, obesity and diabetes. Postgraduate Medical Journal 92 (1087):286–300. doi: https://doi.org/10.1136/postgradmedj-2015-133285.
- Philippe, C., F. Jaomanjaka, O. Claisse, R. Laforgue, J. Maupeu, M. Petrel, and C. Le Marrec. 2017. A survey of oenophages during wine making reveals a novel group with unusual genomic characteristics. International Journal of Food Microbiology 257:138–47. doi: https://doi.org/10.1016/j.ijfoodmicro.2017.06.014.
- Philippe, C., M. Krupovic, F. Jaomanjaka, O. Claisse, M. Petrel, and C. Le Marrec. 2018. Bacteriophage GC1, a novel tectivirus infecting Gluconobacter cerinus, an acetic acid bacterium associated with wine-making. Viruses 10 (1):39. doi: https://doi.org/10.3390/v10010039.
- Pietrysiak, E., S. Smith, and G. M. Ganjyal. 2019. Food safety interventions to control Listeria monocytogenes in the fresh apple packing industry: A review. Comprehensive Reviews in Food Science and Food Safety 18 (6):1705–26. doi: https://doi.org/10.1111/1541-4337.12496.
- Pinto, C., D. Pinho, R. Cardoso, V. Custódio, J. Fernandes, S. Sousa, M. Pinheiro, C. Egas, and A. C. Gomes. 2015. Wine fermentation microbiome: A landscape from different Portuguese wine appellations. Frontiers in Microbiology 6: 905. doi: https://doi.org/10.3389/fmicb.2015.00905.
- Połaska, M., and B. Sokołowska. 2019. Bacteriophages-a new hope or a huge problem in the food industry. AIMS Microbiology 5 (4):324–46. doi: https://doi.org/10.3934/microbiol.2019.4.324.
- Połka, J., A. Rebecchi, V. Pisacane, L. Morelli, and E. Puglisi. 2015. Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons. Food Microbiology 46:342–56. doi: https://doi.org/10.1016/j.fm.2014.08.023.
- Quigley, E. M. M. 2017. Microbiota-BRAIN-GUT AXIS AND NEURODEGENERATIVE DISEASES. Current Neurology and Neuroscience Reports 17 (12):94doi: https://doi.org/10.1007/s11910-017-0802-6.
- Reale, A., T. Di Renzo, F. Boscaino, F. Nazzaro, F. Fratianni, and M. Aponte. 2019. Lactic acid bacteria biota and aroma profile of Italian traditional sourdoughs from the Irpinian Area in Italy. Frontiers in Microbiology 10:1621. doi: https://doi.org/10.3389/fmicb.2019.01621.
- Roux, S., J. R. Brum, B. E. Dutilh, S. Sunagawa, M. B. Duhaime, A. Loy, B. T. Poulos, N. Solonenko, E. Lara, J. Poulain, et al. 2016. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537 (7622):689–93., doi: https://doi.org/10.1038/nature19366.
- Salih, A. G., J. F. Drilleau, F. F. Cavin, C. Divies, and C. M. Bourgeois. 1988. A survey of microbiological aspects of cider making. Journal of the Institute of Brewing 94 (1):5–8. doi: https://doi.org/10.1002/j.2050-0416.1988.tb04545.x.
- Sánchez, A., M. Coton, E. Coton, M. Herrero, L. A. García, and M. Díaz. 2012. Prevalent lactic acid bacteria in cider cellars and efficiency of Oenococcus oeni strains. Food Microbiol 32 (1):32–7. doi: https://doi.org/10.1016/j.fm.2012.02.008.
- Schueuermann, C., B. Khakimov, S. B. Engelsen, P. Bremer, and P. Silcock. 2016. GC-MS metabolite profiling of extreme southern pinot noir wines: Effects of vintage, barrel maturation, and fermentation dominate over vineyard site and clone selection. Journal of Agricultural and Food Chemistry 64 (11):2342–51. doi: https://doi.org/10.1021/acs.jafc.5b05861.
- Scott, A. J., J. L. Alexander, C. A. Merrifield, D. Cunningham, C. Jobin, R. Brown, J. Alverdy, S. J. O'Keefe, H. R. Gaskins, J. Teare, et al. 2019. International Cancer Microbiome Consortium consensus statement on the role of the human microbiome in carcinogenesis. Gut 68 (9):1624–32. doi: https://doi.org/10.1136/gutjnl-2019-318556.
- Selhub, E. M., A. C. Logan, and A. C. Bested. 2014. Fermented foods, microbiota, and mental health: Ancient practice meets nutritional psychiatry. Journal of Physiological Anthropology 33 (1):2. doi: https://doi.org/10.1186/1880-6805-33-2.
- Seth, R. K., R. Maqsood, A. Mondal, D. Bose, D. Kimono, L. A. Holland, P. Janulewicz Lloyd, N. Klimas, R. D. Horner, K. Sullivan, et al. 2019. Gut DNA virome diversity and its association with host bacteria regulate inflammatory phenotype and neuronal immunotoxicity in experimental gulf war illness. Viruses 11 (10):968. doi: https://doi.org/10.3390/v11100968.
- Shkoporov, A. N., and C. Hill. 2019. Bacteriophages of the human gut: The "Known Unknown" of the microbiome. Cell Host Microbe 25 (2):195–209. doi: https://doi.org/10.1016/j.chom.2019.01.017.
- Shkoporov, A. N., F. J. Ryan, L. A. Draper, A. Forde, S. R. Stockdale, K. M. Daly, S. A. McDonnell, J. A. Nolan, T. D. S. Sutton, M. Dalmasso, et al. 2018. Reproducible protocols for metagenomic analysis of human faecal phageomes. Microbiome 6 (1):68. doi: https://doi.org/10.1186/s40168-018-0446-z.
- Stuer-Lauridsen, B., T. Janzen, J. Schnabl, and E. Johansen. 2003. Identification of the host determinant of two prolate-headed phages infecting Lactococcus lactis. Virology 309 (1):10–7. doi: https://doi.org/10.1016/S0042-6822(03)00012-6.
- Tamang, J. P., P. D. Cotter, A. Endo, N. S. Han, R. Kort, S. Q. Liu, B. Mayo, N. Westerik, and R. Hutkins. 2020. Fermented foods in a global age: East meets West. Comprehensive Reviews in Food Science and Food Safety 19 (1):184–217. doi: https://doi.org/10.1111/1541-4337.12520.
- Thomas, T., J. Gilbert, and F. Meyer. 2012. Metagenomics – A guide from sampling to data analysis. Microbial Informatics and Experimentation 2 (1):3. doi: https://doi.org/10.1186/2042-5783-2-3.
- Trček, J., A. Mahnič, and M. Rupnik. 2016. Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing. International Journal of Food Microbiology 223:57–62. doi: https://doi.org/10.1016/j.ijfoodmicro.2016.02.007.
- Wei, H., R. H. Cheng, J. Berriman, W. J. Rice, D. L. Stokes, A. Katz, D. G. Morgan, and P. Gottlieb. 2009. Three-dimensional structure of the enveloped bacteriophage phi12: An incomplete T = 13 lattice is superposed on an enclosed T = 1 shell. PLoS ONE 4 (9):e6850. doi: https://doi.org/10.1371/journal.pone.0006850.
- Wolfe, B. E., J. E. Button, M. Santarelli, and R. J. Dutton. 2014. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158 (2):422–33. doi: https://doi.org/10.1016/j.cell.2014.05.041.
- Yolken, R. H., E. G. Severance, S. Sabunciyan, K. L. Gressitt, O. Chen, C. Stallings, A. Origoni, E. Katsafanas, L. A. B. Schweinfurth, C. L. G. Savage, et al. 2015. Metagenomic sequencing indicates that the oropharyngeal phageome of individuals with schizophrenia differs from that of controls. Schizophrenia Bulletin 41 (5):1153–61. doi: https://doi.org/10.1093/schbul/sbu197.
- Zabat, M. A., W. H. Sano, J. I. Wurster, D. J. Cabral, and P. Belenky. 2018. Microbial community analysis of sauerkraut fermentation reveals a stable and rapidly established community. Foods 7 (5):77. doi: https://doi.org/10.3390/foods7050077.
- Zamberi, N. R., N. E. Mohamad, S. K. Yeap, H. Ky, B. K. Beh, W. C. Liew, S. W. Tan, W. Y. Ho, S. Y. Boo, Y. H. Chua, et al. 2016. 16S Metagenomic microbial composition analysis of kefir grain using MEGAN and BaseSpace. Food Biotechnology 30 (3):219–30. doi: https://doi.org/10.1080/08905436.2016.1200987.