1 |
da Silva Duarte V, Giaretta S, Campanaro S, Treu L, Armani A, Tarrah A, et al. 2018. A Cryptic non-inducible prophage confers phage-immunity on the Streptococcus thermophilus M17PTZA496. Viruses 11: 7.
DOI
|
2 |
Muhammed MK, Olsen ML, Kot W, Neve H, Castro-Mejia JL, Janzen T, et al. 2018. Investigation of the bacteriophage community in induced lysates of undefined mesophilic mixed-strain DL-cultures using classical and metagenomic approaches. Int. J. Food Microbiol. 272: 61-72.
DOI
|
3 |
Mahony J, McGrath S, Fitzgerald GF, van Sinderen D. 2008. Identification and characterization of lactococcal-prophage-carried superinfection exclusion genes. Appl. Environ. Microbiol. 74: 6206-6215.
DOI
|
4 |
Jang SH, Hwang MH, Chang HI. 2010. Complete genome sequence of Phi MH1, a Leuconostoc temperate phage. Arch. Virol. 155: 1883-1885.
DOI
|
5 |
Park, DW, Kim SH, Park JH. 2022. Distribution and characterization of prophages in Lactobacillus plantarum derived from kimchi. Food Microbiol. 102: 103913.
DOI
|
6 |
Tisza MJ, Buck CB. 2021. A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. Proc. Natl. Acad. Sci. USA 118: e2023202118.
DOI
|
7 |
Kot W, Neve H, Heller KJ, Vogensen FK. 2014. Bacteriophages of Leuconostoc, Oenococcus, and Weissella. Front. Microbiol. 5: 186.
DOI
|
8 |
Murphy J, Mahony J, Ainsworth S, Nauta A, van Sinderen D. 2013. Bacteriophage orphan DNA methyltransferases: insights from their bacterial origin, function, and occurrence. Appl. Environ. Microbiol. 79: 7547-7555.
DOI
|
9 |
Oliveira J, Mahony J, Hanemaaijer L, Kouwen TRHM, Neve H, MacSharry J, et al. 2017. Detecting Lactococcus lactis prophages by mitomycin C-mediated induction coupled to flow cytometry analysis. Front. Microbiol. 8: 1343.
DOI
|
10 |
Kot W, Hansen LH, Neve H, Hammer K, Jacobsen S, Pedersen PD, et al. 2014. Sequence and comparative analysis of Leuconostoc dairy bacteriophages. Int. J. Food Microbiol. 176: 29-37.
DOI
|
11 |
Ackermann H-W. 2009. Basic Phage Electron Microscopy, pp. 113-126. In Clokie MRJ, Kropinski AM (eds.), Bacteriophages: Methods and Protocols, Volume 1: Isolation, Characterization, and Interactions. Humana Press, Totowa, NJ, USA.
|
12 |
Canchaya C, Proux C, Fournous G, Bruttin A, Brussow H. 2003. Prophage genomics. Microbiol. Mol. Biol. Rev. 67: 238-276.
DOI
|
13 |
Yoon BH, Jang SH, Chang HI. 2011. Sequence analysis of the Lactobacillus temperate phage Sha1. Arch. Virol. 156: 1681-1684.
DOI
|
14 |
Kleppen HP, Holo H, Jeon SR, Nes IF, Yoon SS. 2012. Novel Podoviridae family bacteriophage infecting Weissella cibaria isolated from Kimchi. Appl. Environ. Microbiol. 78: 7299-7308.
DOI
|
15 |
Lavelle K, Martinez I, Neve H, Lugli GA, Franz CMAP, Ventura M, et al. 2018. Biodiversity of Streptococcus thermophilus phages in global dairy fermentations. Viruses 10: 577.
DOI
|
16 |
Jung JY, Lee SH, Kim JM, Park MS, Bae JW, Hahn Y, et al. 2011. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl. Environ. Microbiol. 77: 2264-2274.
DOI
|
17 |
Lu Z, Perez-Diaz IM, Hayes JS, Breidt F. 2012. Bacteriophage ecology in a commercial cucumber fermentation. Appl. Environ. Microbiol. 78: 8571-8578.
DOI
|
18 |
Oliveira J, Mahony J, Hanemaaijer L, Kouwen TRHM, van Sinderen D. 2018. Biodiversity of bacteriophages infecting Lactococcus lactis starter cultures. J. Dairy Sci. 101: 96-105.
DOI
|
19 |
Park EJ, Kim KH, Abell GCJ, Kim MS, Roh SW, Bae JW. 2011. Metagenomic analysis of the viral communities in fermented foods. Appl. Environ. Microbiol. 77: 1284-1291.
DOI
|
20 |
Park WJ, Kong SJ, Park JH. 2021. Kimchi bacteriophages of lactic acid bacteria: population, characteristics, and their role in watery kimchi. Food Sci. Biotechnol. 30: 949-957.
DOI
|
21 |
Breitbart M, Rohwer F. 2005. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13: 278-284.
DOI
|
22 |
Casjens S. 2003. Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49: 277-300.
DOI
|
23 |
Hendrix RW. 2005. Bacteriophage HK97: Assembly of the capsid and evolutionary connections. Adv. Virus Res. 64: 1-14.
DOI
|
24 |
Barrangou R, Yoon SS, Breidt F, Fleming HP, Klaenhammer TR. 2002. Characterization of six Leuconostoc fallax bacteriophages isolated from an industrial sauerkraut fermentation. Appl. Environ. Microbiol. 68: 5452-5458.
DOI
|
25 |
Lee S, Park JH. 2021. Characteristics on host specificity, infection, and temperature stability of Weissella phages from watery kimchi. Food Sci. Biotechnol. 30: 843-851.
DOI
|
26 |
Oh JY, Park JH. 2021. Isolation and characterization of bacteriophage infecting Lactobacillus plantarum KCCM 12116. Korean J. Food Sci. Technol. 53: 348-355.
DOI
|
27 |
Raya RR, H'Bert E M. 2009. Isolation of phage via induction of lysogens. Methods Mol. Biol. 501: 23-32.
DOI
|
28 |
Modi SR, Lee HH, Spina CS, Collins JJ. 2013. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499: 219-222.
DOI
|
29 |
Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, et al. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 42: D581-D591.
DOI
|
30 |
Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, et al. 2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44: W16-W21.
DOI
|
31 |
Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33: 1870-1874.
DOI
|
32 |
Fortier LC, Sekulovic O. 2013. Importance of prophages to evolution and virulence of bacterial pathogens. Virulence 4: 354-365.
DOI
|
33 |
Song W, Sun HX, Zhang C, Cheng L, Peng Y, Deng Z, et al. 2019. Prophage Hunter: an integrative hunting tool for active prophages. Nucleic Acids Res. 47: W74-W80.
DOI
|
34 |
Thompson JD, Gibson TJ, Higgins DG. 2002. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinformatics Chapter 2: Unit 2.3.
|
35 |
Kelleher P, Mahony J, Schweinlin K, Neve H, Franz CM, van Sinderen D. 2018. Assessing the functionality and genetic diversity of lactococcal prophages. Int. J. Food Microbiol. 272: 29-40.
DOI
|
36 |
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. 2008. NCBI BLAST: a better web interface. Nucleic Acids Res. 36: W5-9.
DOI
|
37 |
Park SJ, Chang JH, Cha SK, Moon GS. 2008. Microbiological analysis of dongchimi, Korean watery radish kimchi, at the early and mid-phase fermentation. Food Sci. Biotechnol. 17: 892-894.
|
38 |
Rohwer F. 2003. Global phage diversity. Cell 113: 141-141.
DOI
|
39 |
Parsley LC, Consuegra EJ, Thomas SJ, Bhavsar J, Land AM, Bhuiyan NN, et al. 2010. Census of the viral metagenome within an activated sludge microbial assemblage. Appl. Environ. Microbiol. 76: 2673-2677.
DOI
|
40 |
Weinbauer MG. 2004. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28: 127-181.
DOI
|
41 |
Fernandez L, Rodriguez A, Garcia P. 2018. Phage or foe: an insight into the impact of viral predation on microbial communities. ISME J. 12: 1171-1179.
DOI
|
42 |
Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305: 567-580.
DOI
|
43 |
Rostol JT, Marraffini L. 2019. (Ph)ighting Phages: how bacteria resist their parasites. Cell Host Microbe 25: 184-194.
DOI
|
44 |
Kong SJ, Park JH. 2020. Acid tolerance and morphological characteristics of five Weissella cibaria bacteriophages isolated from kimchi. Food Sci. Biotechnol. 29: 873-878.
DOI
|
45 |
Sullivan MJ, Petty NK, Beatson SA. 2011. Easyfig: a genome comparison visualizer. Bioinformatics 27: 1009-1010.
DOI
|
46 |
Feyereisen M, Mahony J, Neve H, Franz C, Noben JP, O'Sullivan T, et al. 2019. Biodiversity and classification of phages infecting Lactobacillus brevis. Front. Microbiol. 10: 2396.
DOI
|
47 |
Tuohimaa A, Riipinen KA, Brandt K, Alatossava T. 2006. The genome of the virulent phage Lc-Nu of probiotic Lactobacillus rhamnosus, and comparative genomics with Lactobacillus casei phages. Arch. Virol. 151: 947-965.
DOI
|
48 |
Yoon BH, Jang SH, Chang HI. 2011. Sequence analysis of the Lactobacillus temperate phage Sha1. Arch. Virol. 156: 1681-1684.
DOI
|
49 |
Wang X, Wood TK. 2016. Cryptic prophages as targets for drug development. Drug Resist. Update 27: 30-38.
DOI
|