Suttle CA. Marine viruses — major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12.
Article
CAS
PubMed
Google Scholar
Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nat Rev Microbiol. 2010;8:317–27.
Article
CAS
PubMed
Google Scholar
Hyman P, Abedon ST. Bacteriophage host range and bacterial resistance. In: Advances in applied microbiology; 2010. p. 217–48.
Chapter
Google Scholar
Hendrix RW. Bacteriophage evolution and the role of phages in host evolution. In: Phages. Washington: American Society of Microbiology; 2005. p. 55–65.
Drexler K, Riede I, Montag D, Eschbach ML, Henning U. Receptor specificity of the Escherichia coli T-even type phage Ox2. Mutational alterations in host range mutants. J Mol Biol. 1989;207:797–803.
Article
CAS
PubMed
Google Scholar
Buckling A, Rainey PB. Antagonistic coevolution between a bacterium and a bacteriophage. Proc Biol Sci. 2002;269:931–6.
Article
PubMed
PubMed Central
Google Scholar
Bayliss CD. Determinants of phase variation rate and the fitness implications of differing rates for bacterial pathogens and commensals. FEMS Microbiol Rev. 2009;33:504–20.
Article
CAS
PubMed
Google Scholar
Kwan LY, Isaacson RE. Identification and characterization of a phase-variable nonfimbrial Salmonella typhimurium gene that alters O-antigen production. Infect Immun. 1998;66:5725–30.
CAS
PubMed Central
PubMed
Google Scholar
Broadbent SE, Davies MR, van der Woude MW. Phase variation controls expression of Salmonella lipopolysaccharide modification genes by a DNA methylation-dependent mechanism. Mol Microbiol. 2010;77:337–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kamp D, Kahmann R, Zipser D, Broker TR, Chow LT. Inversion of the G DNA segment of phage mu controls phage infectivity. Nature. 1978;271:577–80.
Article
CAS
PubMed
Google Scholar
Sandmeier H, Iida S, Arber W. DNA inversion regions min of plasmid p15B and Cin of bacteriophage P1: evolution of bacteriophage tail fiber genes. J Bacteriol. 1992;174:3936–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dybvig K. DNA rearrangements and phenotypic switching in prokaryotes. Mol Microbiol. 1993;10:465–71.
Article
CAS
PubMed
Google Scholar
Bertani G. Studies on lysogenesis. III. Superinfection of lysogenic Shigella dysenteriae with temperate mutants of the carried phage. J Bacteriol. 1954;67:696–707.
CAS
PubMed Central
PubMed
Google Scholar
McCloy EW. Lysogenicity and immunity to Bacillus phage W. J Gen Microbiol. 1958;18:198–220.
Article
CAS
PubMed
Google Scholar
Hofer B, Ruge M, Dreiseikelmann B. The superinfection exclusion gene (sieA) of bacteriophage P22: identification and overexpression of the gene and localization of the gene product. J Bacteriol. 1995;177:3080–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ferdy J, Godelle B. Diversification of transmission modes and the evolution of mutualism. Am Nat. 2005;166:613–27.
Article
PubMed
Google Scholar
Wagner PL, Neely MN, Zhang X, Acheson DW, Waldor MK, Friedman DI. Role for a phage promoter in Shiga toxin 2 expression from a pathogenic Escherichia coli strain. J Bacteriol. 2001;183:2081–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wagner PL, Waldor MK. Bacteriophage control of bacterial virulence. Infect Immun. 2002;70:3985–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stern A, Sorek R. The phage-host arms race: shaping the evolution of microbes. BioEssays. 2011;33:43–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meyer JR, Dobias DT, Weitz JS, Barrick JE, Quick RT, Lenski RE. Repeatability and contingency in the evolution of a key innovation in phage lambda. Science. 2012;335:428–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Römling U, Bian Z, Hammar M, Sierralta WD, Normark S. Curli fibers are highly conserved between Salmonella typhimurium and Escherichia coli with respect to operon structure and regulation. J Bacteriol. 1998;180:722–31.
PubMed Central
PubMed
Google Scholar
Kim M, Kim S, Park B, Ryu S. Core lipopolysaccharide-specific phage SSU5 as an auxiliary component of a phage cocktail for Salmonella biocontrol. Appl Environ Microbiol. 2014;80:1026–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wilkinson RG, Gemski P, Stocker BA. Non-smooth mutants of Salmonella typhimurium: differentiation by phage sensitivity and genetic mapping. J Gen Microbiol. 1972;70:527–54.
Article
CAS
PubMed
Google Scholar
Jarrell KF, Kropinski AM. Isolation and characterization of a bacteriophage specific for the lipopolysaccharide of rough derivatives of Pseudomonas aeruginosa strain PAO. J Virol. 1981;38:529–38.
CAS
PubMed Central
PubMed
Google Scholar
Scott AE, Timms AR, Connerton PL, Loc Carrillo C, Adzfa Radzum K, Connerton IF. Genome dynamics of campylobacter jejuni in response to bacteriophage predation. PLoS Pathog. 2007;3:e119.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seed KD, Faruque SM, Mekalanos JJ, Calderwood SB, Qadri F, Camilli A. Phase variable O antigen biosynthetic genes control expression of the major protective antigen and bacteriophage receptor in Vibrio cholerae O1. PLoS Pathog. 2012;8:e1002917.
Article
CAS
PubMed
PubMed Central
Google Scholar
Orsi RH, Bowen BM, Wiedmann M. Homopolymeric tracts represent a general regulatory mechanism in prokaryotes. BMC Genomics. 2010;11:102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Johnson LP, Schlievert PM. Group a streptococcal phage T12 carries the structural gene for pyrogenic exotoxin type a. Mol Gen Genet. 1984;194:52–6.
Article
CAS
PubMed
Google Scholar
Rabinovich L, Sigal N, Borovok I, Nir-Paz R, Herskovits AA. Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence. Cell. 2012;150:792–802.
Article
CAS
PubMed
Google Scholar
Kirby JE, Trempy JE, Gottesman S. Excision of a P4-like cryptic prophage leads to alp protease expression in Escherichia coli. J Bacteriol. 1994;176:2068–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scott J, Thompson-Mayberry P, Lahmamsi S, King CJ, McShan WM. Phage-associated Mutator phenotype in group a streptococcus. J Bacteriol. 2008;190:6290–301.
Article
CAS
PubMed
PubMed Central
Google Scholar
Perry EB, Barrick JE, Bohannan BJM. The molecular and genetic basis of repeatable coevolution between Escherichia coli and bacteriophage T3 in a laboratory microcosm. PLoS One. 2015;10:e0130639.
Article
CAS
PubMed
PubMed Central
Google Scholar
Denes T, den Bakker HC, Tokman JI, Guldimann C, Wiedmann M. Selection and characterization of phage-resistant mutant strains of Listeria monocytogenes reveal host genes linked to phage adsorption. Appl Environ Microbiol. 2015;81:4295–305.
Article
CAS
PubMed
PubMed Central
Google Scholar
Blount ZD, Borland CZ, Lenski RE. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A. 2008;105:7899–906.
Article
CAS
PubMed
PubMed Central
Google Scholar
Scholz CFP, Brüggemann H, Lomholt HB, Tettelin H, Kilian M. Genome stability of Propionibacterium acnes: a comprehensive study of indels and homopolymeric tracts. Sci Rep. 2016;6:20662.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zaleski P, Wojciechowski M, Piekarowicz A. The role of dam methylation in phase variation of Haemophilus influenzae genes involved in defence against phage infection. Microbiology. 2005;151(Pt 10):3361–9.
Article
CAS
Google Scholar
Brooks JL, Jefferson KK. Phase variation of poly-N-Acetylglucosamine expression in Staphylococcus aureus. PLoS Pathog. 2014;10:e1004292.
Article
CAS
PubMed
PubMed Central
Google Scholar
Capparelli R, Parlato M, Borriello G, Salvatore P, Iannelli D. Experimental phage therapy against Staphylococcus aureus in mice. Antimicrob Agents Chemother. 2007;51:2765–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual. New York: Cold Spring Harbor Laboratory Press; 1989.
Barak JD, Gorski L, Naraghi-Arani P, Charkowski AO. Salmonella enterica virulence genes are required for bacterial attachment to plant tissue. Appl Environ Microbiol. 2005;71:5685–91. https://doi.org/10.1128/AEM.71.10.5685-5691.2005.
Article
CAS
PubMed Central
PubMed
Google Scholar
Casillo A, Papa R, Ricciardelli A, Sannino F, Ziaco M, Tilotta M, et al. Anti-biofilm activity of a long-chain fatty aldehyde from Antarctic Pseudoalteromonas haloplanktis TAC125 against Staphylococcus epidermidis biofilm. Front Cell Infect Microbiol. 2017;7:46. https://doi.org/10.3389/fcimb.2017.00046.
Article
CAS
PubMed Central
PubMed
Google Scholar
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12. https://doi.org/10.1186/gb-2004-5-2-r12.
Article
PubMed Central
PubMed
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
Article
CAS
PubMed
PubMed Central
Google Scholar
Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970;227:680–5. https://doi.org/10.1038/227680a0.
Article
CAS
PubMed Central
Google Scholar
Carillo S, Casillo A, Pieretti G, Parrilli E, Sannino F, Bayer-Giraldi M, et al. A unique capsular polysaccharide structure from the psychrophilic marine bacterium Colwellia psychrerythraea 34H that mimics antifreeze (Glyco)proteins. J Am Chem Soc. 2015;137:179–89. https://doi.org/10.1021/ja5075954.
Article
CAS
PubMed
Google Scholar
Casillo A, Parrilli E, Filomena S, Lindner B, Lanzetta R, Parrilli M, et al. Structural investigation of the oligosaccharide portion isolated from the Lipooligosaccharide of the permafrost Psychrophile Psychrobacter arcticus 273-4. Mar Drugs. 2015;13:4539–55. https://doi.org/10.3390/md13074539.
Article
CAS
PubMed Central
PubMed
Google Scholar
Rao X, Huang X, Zhou Z, Lin X. An improvement of the 2ˆ(−delta delta CT) method for quantitative real-time polymerase chain reaction data analysis. Biostat Bioinforma Biomath. 2013;3:71–85 http://www.ncbi.nlm.nih.gov/pubmed/25558171. Accessed 22 Nov 2018.
PubMed Central
PubMed
Google Scholar
Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.
Article
CAS
Google Scholar
Djordjevic D, Wiedmann M, McLandsborough LA. Microtiter plate assay for assessment of Listeria monocytogenes biofilm formation. Appl Environ Microbiol. 2002;68:2950–8.
Article
CAS
PubMed
PubMed Central
Google Scholar