REFERENCES
1. Samson JE, Moineau S. Bacteriophages in food fermentations: new frontiers in a continuous arms race. Annu Rev Food Sci Technol 2013;4:347-68.
2. Komora N, Bruschi C, Ferreira V, et al. The protective effect of food matrices on Listeria lytic bacteriophage P100 application towards high pressure processing. Food Microbiol 2018;76:416-25.
3. Shebs-Maurine EL, Giotto FM, Laidler ST, de Mello AS. Effects of bacteriophages and peroxyacetic acid applications on beef contaminated with Salmonella during different grinding stages. Meat Sci 2021;173:108407.
4. Merabishvili M, Pirnay JP, Verbeken G, et al. Quality-controlled small-scale production of a well-defined bacteriophage cocktail for use in human clinical trials. PLoS One 2009;4:e4944.
5. Loessner MJ. Bacteriophage endolysins - current state of research and applications. Curr Opin Microbiol 2005;8:480-7.
6. Lunde M, Aastveit AH, Blatny JM, Nes IF. Effects of diverse environmental conditions on ϕ LC3 prophage stability in Lactococcus lactis. Appl Environ Microbiol 2005;71:721-7.
7. Feyereisen M, Mahony J, Neve H, et al. Biodiversity and classification of phages infecting Lactobacillus brevis. Front Microbiol 2019;10:2396.
8. Oh JH, Lin XB, Zhang S, et al. Prophages in Lactobacillus reuteri are associated with fitness trade-offs but can increase competitiveness in the gut ecosystem. Appl Environ Microbiol 2019;86:e01922-19.
9. Wendling CC, Refardt D, Hall AR. Fitness benefits to bacteria of carrying prophages and prophage-encoded antibiotic-resistance genes peak in different environments. Evolution 2021;75:515-28.
10. Brown EM, Arellano-Santoyo H, Temple ER, et al. Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors. Cell Host Microbe 2021;29:1351-65.e11.
11. Liu Y, Tempelaars MH, Boeren S, Alexeeva S, Smid EJ, Abee T. Extracellular vesicle formation in Lactococcus lactis is stimulated by prophage-encoded holin-lysin system. Microb Biotechnol 2022;15:1281-95.
12. Briggiler Marcó M, Garneau JE, Tremblay D, Quiberoni A, Moineau S. Characterization of two virulent phages of Lactobacillus plantarum. Appl Environ Microbiol 2012;78:8719-34.
13. Ehrmann MA, Angelov A, Picozzi C, Foschino R, Vogel RF. The genome of the Lactobacillus sanfranciscensis temperate phage EV3. BMC Res Notes 2013;6:514.
14. Pei Z, Sadiq FA, Han X, et al. Comprehensive scanning of prophages in Lactobacillus: distribution, diversity, antibiotic resistance genes, and linkages with CRISPR-Cas systems. mSystems 2021;6:e0121120.
15. Leroy F, Verluyten J, De Vuyst L. Functional meat starter cultures for improved sausage fermentation. Int J Food Microbiol 2006;106:270-85.
16. Bassi D, Milani G, Belloso Daza MV, et al. Taxonomical identification and safety characterization of lactobacillaceae from mediterranean natural fermented sausages. Foods 2022;11:2776.
17. Jo SG, Noh EJ, Lee JY, et al. Lactobacillus curvatus WiKim38 isolated from kimchi induces IL-10 production in dendritic cells and alleviates DSS-induced colitis in mice. J Microbiol 2016;54:503-9.
18. Baek HW, Bae JH, Lee YG, et al. Dynamic interactions of lactic acid bacteria in Korean sourdough during back-slopping process. J Appl Microbiol 2021;131:2325-35.
19. Sánchez I, Seseña S, Poveda JM, Cabezas L, Palop L. Phenotypic and genotypic characterization of lactobacilli isolated from Spanish goat cheeses. Int J Food Microbiol 2005;102:355-62.
20. Bulgasem BY, Lani MN, Hassan Z, Wan Yusoff WM, Fnaish SG. Antifungal activity of lactic acid bacteria strains isolated from natural honey against pathogenic candida species. Mycobiology 2016;44:302-9.
21. Ambros CL, Ehrmann MA. Distribution, inducibility, and characterisation of prophages in Latilactobacillus sakei. BMC Microbiol 2022;22:267.
22. Mo SJ, Lee K, Hong HJ, et al. Effects of Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 on overweight and the gut microbiota in humans: randomized, double-blinded, placebo-controlled clinical trial. Nutrients 2022;14:2484.
23. Zhang Y, Liang S, Zhao MD, Yang X, Choi SH, Li GY. Screening and identification of Latilactobacillus curvatus Z12 from rumen fluid of an adult female sika deer as a potential probiotic for feed additives. Front Vet Sci 2021;8:753527.
24. Koch C, Hertwig S, Lurz R, Appel B, Beutin L. Isolation of a lysogenic bacteriophage carrying the stx1OX3 gene, which is closely associated with Shiga toxin-producing Escherichia coli strains from sheep and humans. J Clin Microbiol 2001;39:3992-8.
25. Townsend EM, Kelly L, Muscatt G, et al. The human gut phageome: origins and roles in the human gut microbiome. Front Cell Infect Microbiol 2021;11:643214.
26. DSMZ. MRS medium.doc. 2007. Available from: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium11.pdf. [Last accessed on 5 Sep 2023].
27. Cold Spring Harbor Protocols. SM buffer with gelatin. Available from: https://cshprotocols.cshlp.org/content/2006/1/pdb.rec466.full?text-only=true. [Last accessed on 5 Sep 2023].
28. Kaletta J, Pickl C, Griebler C, Klingl A, Kurmayer R, Deng L. A rigorous assessment and comparison of enumeration methods for environmental viruses. Sci Rep 2020;10:18625.
29. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017;13:e1005595.
30. Li W, O’Neill KR, Haft DH, et al. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 2021;49:D1020-8.
31. Haft DH, DiCuccio M, Badretdin A, et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018;46:D851-60.
32. Tatusova T, DiCuccio M, Badretdin A, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016;44:6614-24.
34. Protocol for phage DNA extraction with Phenol:chloroform. Available from: https://cpt.tamu.edu/wordpress/wp-content/uploads/2018/09/Phage-DNA-Extraction-by-PhenolChloroform-Protocol.pdf. [Last accessed on 5 Sep 2023].
35. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32:929-31.
36. Arndt D, Grant JR, Marcu A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016;44:W16-21.
37. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011;39:W347-52.
38. Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016;44:W54-7.
39. Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 2021;49:9077-96.
40. Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE: a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 2023;51:D629-30.
41. ICTV. Taxon names are written differently from virus names. Available from: https://talk.ictvonline.org/information/w/faq/386/how-to-write-virus-species-and-other-taxa-names. [Last accessed on 5 Sep 2023].
42. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011;27:1009-10.
43. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018;35:1547-9.
44. Lee J, Jang J, Kim B, Kim J, Jeong G, Han H. Identification of Lactobacillus sakei and Lactobacillus curvatus by multiplex PCR-based restriction enzyme analysis. J Microbiol Methods 2004;59:1-6.
45. Williams KP. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res 2002;30:866-75.
46. Qin Y, Polacek N, Vesper O, et al. The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell 2006;127:721-33.
47. Bobay LM, Rocha EP, Touchon M. The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol 2013;30:737-51.
48. Hotopp JCD, Grifantini R, Kumar N, et al. Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes. Microbiology 2006;152:3733-49.
49. Bobay LM, Touchon M, Rocha EP. Pervasive domestication of defective prophages by bacteria. Proc Natl Acad Sci U S A 2014;111:12127-32.
50. Yang JY, Fang W, Miranda-Sanchez F, et al. Degradation of host translational machinery drives tRNA acquisition in viruses. Cell Syst 2021;12:771-9.e5.
51. Bailly-Bechet M, Vergassola M, Rocha E. Causes for the intriguing presence of tRNAs in phages. Genome Res 2007;17:1486-95.
52. Yoshikawa G, Askora A, Blanc-Mathieu R, et al. Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes. Sci Rep 2018;8:4486.
53. Tomikawa C, Auxilien S, Guérineau V, et al. Characterization of redundant tRNAIles with CAU and UAU anticodons in Lactobacillus plantarum. J Biochem 2018;163:233-41.
54. McDonald MJ, Chou CH, Swamy KB, Huang HD, Leu JY. The evolutionary dynamics of tRNA-gene copy number and codon-use in E. coli. BMC Evol Biol 2015;15:163.
55. Murphy J, Mahony J, Ainsworth S, Nauta A, van Sinderen D. Bacteriophage orphan DNA methyltransferases: insights from their bacterial origin, function, and occurrence. Appl Environ Microbiol 2013;79:7547-55.
56. Pingoud A, Fuxreiter M, Pingoud V, Wende W. Type II restriction endonucleases: structure and mechanism. Cell Mol Life Sci 2005;62:685-707.
58. Sternberg N, Coulby J. Cleavage of the bacteriophage P1 packaging site (pac) is regulated by adenine methylation. Proc Natl Acad Sci U S A 1990;87:8070-4.
59. Jensen TØ, Tellgren-Roth C, Redl S, et al. Genome-wide systematic identification of methyltransferase recognition and modification patterns. Nat Commun 2019;10:3311.
60. Marinus MG, Morris NR. Biological function for 6-methyladenine residues in the DNA of Escherichia coli K12. J Mol Biol 1974;85:309-22.
61. Lahue RS, Au KG, Modrich P. DNA mismatch correction in a defined system. Science 1989;245:160-4.
62. Smith MJ, Jeddeloh JA. DNA methylation in lysogens of pathogenic Burkholderia spp. Requires prophage induction and is restricted to excised phage DNA. J Bacteriol 2005;187:1196-200.
