Jeanthon C. Molecular ecology of hydrothermal vent microbial communities. Antonie Van Leeuwenhoek. 2000;77:117–33.
Google Scholar
Nercessian O, Reysenbach A-L, Prieur D, Jeanthon C. Archaeal diversity associated with in situ samplers deployed on hydrothermal vents on the East Pacific Rise (13oN). Environ Microbiol. 2003;5:492–502.
Google Scholar
Nakagawa S, Takai K, Inagaki F, Hirayama H, Nunoura T, Horikoshi K, et al. Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol. 2005;7:1619–32.
Google Scholar
Brazelton WJ, Schrenk MO, Kelley DS, Baross JA. Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Appl Environ Microbiol. 2006;72:6257–70.
Google Scholar
Takai K, Nakagawa S, Reysenbach A-L, Hoek J. Microbial ecology of mid-ocean ridges and back-arc basins. In: Christie DM, Fisher CR, Lee S-M, Givens S, editors. Geophysical Monograph Series. 2006. Washington, D. C.: American Geophysical Union; 2006. pp. 185–213.
Nakagawa S, Takai K. Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance. FEMS Microbiol Ecol. 2008;65:1–14.
Google Scholar
Jørgensen BB, Boetius A. Feast and famine—microbial life in the deep-sea bed. Nat Rev Microbiol. 2007;5:770–81.
Google Scholar
Campbell BJ, Engel AS, Porter ML, Takai K. The versatile ε-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol. 2006;4:458–68.
Google Scholar
Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol. 2021;71:005056.
Google Scholar
Nakagawa S, Takaki Y. Nonpathogenic Epsilonproteobacteria. Encyclopedia of Life Sciences (eLS). Chichester, UK: John Wiley & Sons, Ltd; 2009.
Nakagawa S, Takaki Y, Shimamura S, Reysenbach A-L, Takai K, Horikoshi K. Deep-sea vent ε-proteobacterial genomes provide insights into emergence of pathogens. Proc Natl Acad Sci USA. 2007;104:12146–50.
Google Scholar
Porcelli I, Reuter M, Pearson BM, Wilhelm T, van Vliet AH. Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria. BMC Genom. 2013;14:616.
Google Scholar
Zhang Y, Sievert SM. Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria. Front Microbiol. 2014;5:110.
Google Scholar
Vorwerk H, Huber C, Mohr J, Bunk B, Bhuju S, Wensel O, et al. A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose. Mol Microbiol. 2015;98:809–30.
Google Scholar
Jiang SC, Kellogg CA, Paul JH. Characterization of marine temperate phage-host systems isolated from Mamala Bay, Oahu, Hawaii. Appl Environ Microbiol. 1998;64:535–42.
Google Scholar
Paul JH. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J. 2008;2:579–89.
Google Scholar
Harrison E, Brockhurst MA. Ecological and evolutionary benefits of temperate phage: what does or doesn’t kill you makes you stronger. BioEssays. 2017;39:1700112.
Google Scholar
Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, et al. Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter species. PLoS Biol. 2005;3:e15.
Google Scholar
Zhang M, He L, Li Q, Sun H, Gu Y, You Y, et al. Genomic characterization of the Guillain-Barre syndrome-associated Campylobacter jejuni ICDCCJ07001 isolate. PLoS ONE. 2010;5:e15060.
Google Scholar
Miller WG, Yee E, Chapman MH, Smith TPL, Bono JL, Huynh S, et al. Comparative genomics of the Campylobacter lari group. Genome Biol Evol. 2014;6:3252–66.
Google Scholar
Parker CT, Quiñones B, Miller WG, Horn ST, Mandrell RE. Comparative genomic analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221. J Clin Microbiol. 2006;44:4125–35.
Google Scholar
Clark CG, Ng L-K. Sequence variability of Campylobacter temperate bacteriophages. BMC Microbiol. 2008;8:49.
Google Scholar
Quiñones B, Guilhabert MR, Miller WG, Mandrell RE, Lastovica AJ, Parker CT. Comparative genomic analysis of clinical strains of Campylobacter jejuni from South Africa. PLoS ONE. 2008;3:e2015.
Google Scholar
Clark CG, Chen C, Berry C, Walker M, McCorrister SJ, Chong PM, et al. Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds. PLoS ONE. 2018;13:e0190836.
Google Scholar
Clark CG, Grant CC, Pollari F, Marshall B, Moses J, Tracz DM, et al. Effects of the Campylobacter jejuni CJIE1 prophage homologs on adherence and invasion in culture, patient symptoms, and source of infection. BMC Microbiol. 2012;12:269.
Google Scholar
Gaasbeek EJ, Wagenaar JA, Guilhabert MR, Wösten MMSM, van Putten JPM, van der Graaf-van Bloois L, et al. A DNase encoded by integrated element CJIE1 inhibits natural transformation of Campylobacter jejuni. J Bacteriol. 2009;191:2296–306.
Google Scholar
Gaasbeek EJ, Wagenaar JA, Guilhabert MR, van Putten JPM, Parker CT, van der Wal FJ. Nucleases encoded by the integrated elements CJIE2 and CJIE4 inhibit natural transformation of Campylobacter jejuni. J Bacteriol. 2010;192:936–41.
Google Scholar
Yoshida-Takashima Y, Takaki Y, Shimamura S, Nunoura T, Takai K. Genome sequence of a novel deep-sea vent epsilonproteobacterial phage provides new insight into the co-evolution of Epsilonproteobacteria and their phages. Extremophiles. 2013;17:405–19.
Google Scholar
Glasby GP, Notsu K. Submarine hydrothermal mineralization in the Okinawa Trough, SW of Japan: an overview. Ore Geol Rev. 2003;23:299–339.
Google Scholar
Yoshida-Takashima Y, Nunoura T, Kazama H, Noguchi T, Inoue K, Akashi H, et al. Spatial distribution of viruses associated with planktonic and attached microbial communities in hydrothermal environments. Appl Environ Microbiol. 2012;78:1311–20.
Google Scholar
Takai K, Inagaki F, Nakagawa S, Hirayama H, Nunoura T, Sako Y, et al. Isolation and phylogenetic diversity of members of previously uncultivated ε-Proteobacteria in deep-sea hydrothermal fields. FEMS Microbiol Lett. 2003;217:167–74.
Sako Y, Takai K, Ishida Y, Uchida A, Katayama Y. Rhodothemus obamensis sp. nov., a modern lineage of extremely thermophilic marine bacteria. Int J Syst Bacteriol. 1996;46:1099–104.
Google Scholar
Yoshida M, Yoshida-Takashima Y, Nunoura T, Takai K. Genomic characterization of a temperate phage of the psychrotolerant deep-sea bacterium Aurantimonas sp. Extremophiles. 2015;19:49–58.
Google Scholar
Yoshida T, Takashima Y, Tomaru Y, Shirai Y, Takao Y, Hiroishi S, et al. Isolation and characterization of a cyanophage infecting the toxic cyanobacterium Microcystis aeruginosa. Appl Environ Microbiol. 2006;72:1239–47.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Google Scholar
Leggett RM, Clavijo BJ, Clissold L, Clark MD, Caccamo M. NextClip: an analysis and read preparation tool for Nextera long mate pair libraries. Bioinformatics. 2014;30:566–8.
Google Scholar
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011;27:578–9.
Google Scholar
Corkill JE, Graham R, Hart CA, Stubbs S. Pulsed-field gel electrophoresis of degradation-sensitive DNAs from Clostridium difficile PCR ribotype 1 strains. J Clin Microbiol. 2000;38:2791–2.
Google Scholar
Besemer J. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001;29:2607–18.
Google Scholar
Delcher A. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999;27:4636–41.
Google Scholar
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, et al. The Pfam protein families database. Nucleic Acids Res. 2012;40:D290–301.
Google Scholar
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, et al. InterProScan: protein domains identifier. Nucleic Acids Res. 2005;33:W116–20.
Google Scholar
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 2011;39:D225–9.
Google Scholar
Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol. 2001;305:567–80.
Google Scholar
Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol. 2019;37:420–3.
Google Scholar
Huang S, Wang K, Jiao N, Chen F. Genome sequences of siphoviruses infecting marine Synechococcus unveil a diverse cyanophage group and extensive phage-host genetic exchanges. Environ Microbiol. 2012;14:540–58.
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.
Google Scholar
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.
Google Scholar
Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44:W16–21.
Google Scholar
Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 2015;43:D298–9.
Google Scholar
Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018;46:W246–51.
Google Scholar
Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 2021;38:3022–7.
Google Scholar
Meier-Kolthoff JP, Göker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics. 2017;33:3396–404.
Google Scholar
Nakagawa S, Takai K, Inagaki F, Horikoshi K, Sako Y. Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the ε-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough. Int J Syst Evol Microbiol. 2005;55:925–33.
Google Scholar
Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA. 2009;106:19126–31.
Google Scholar
Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, et al. Origins of highly mosaic mycobacteriophage genomes. Cell. 2003;113:171–82.
Google Scholar
Mercier C, Lossouarn J, Nesbø CL, Haverkamp THA, Baudoux AC, Jebbar M, et al. Two viruses, MCV1 and MCV2, which infect Marinitoga bacteria isolated from deep-sea hydrothermal vents: functional and genomic analysis. Environ Microbiol. 2018;20:577–87.
Google Scholar
Samson JE, Magadán AH, Sabri M, Moineau S. Revenge of the phages: defeating bacterial defences. Nat Rev Microbiol. 2013;11:675–87.
Google Scholar
Meyer JL, Huber JA. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. ISME J. 2014;8:867–80.
Google Scholar
Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 2005;3:722–32.
Google Scholar
Ramisetty BCM, Sudhakari PA. Bacterial ‘grounded’ prophages: hotspots for genetic renovation and innovation. Front Genet. 2019;10:65.
Google Scholar
Labrie SJ, Samson JE, Moineau S. Bacteriophage resistance mechanisms. Nat Rev Microbiol. 2010;8:317–27.
Google Scholar
Piel D, Bruto M, Labreuche Y, Blanquart F, Goudenège D, Barcia-Cruz R, et al. Phage–host coevolution in natural populations. Nat Microbiol. 2022;7:1075–86.
Google Scholar
Lynch KH, Stothard P, Dennis JJ. Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex. BMC Genomics. 2010;11:599.
Google Scholar
Godde JS, Bickerton A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J Mol Evol. 2006;62:718–29.
Google Scholar
Nobrega FL, Walinga H, Dutilh BE, Brouns SJJ. Prophages are associated with extensive CRISPR–Cas auto-immunity. Nucleic Acids Res. 2020;48:12074–84.
Google Scholar
Yi H, Huang L, Yang B, Gomez J, Zhang H, Yin Y. AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses. Nucleic Acids Res. 2020;48:W358–65.
Google Scholar
Maier L-K, Lange SJ, Stoll B, Haas KA, Fischer SM, Fischer E, et al. Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B. RNA Biol. 2013;10:865–74.
Google Scholar
Boudry P, Semenova E, Monot M, Datsenko KA, Lopatina A, Sekulovic O, et al. Function of the CRISPR-Cas system of the human pathogen Clostridium difficile. mBio. 2015;6:e01112–5.
Google Scholar
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315:1709–12.
Google Scholar
Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, Boyaval P, et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol. 2008;190:1390–400.
Google Scholar
Nozawa T, Furukawa N, Aikawa C, Watanabe T, Haobam B, Kurokawa K, et al. CRISPR inhibition of prophage acquisition in Streptococcus pyogenes. PLoS ONE. 2011;6:e19543.
Google Scholar
Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 2020;18:67–83.
Google Scholar
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