{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T01:36:40Z","timestamp":1763429800880,"version":"build-2065373602"},"reference-count":70,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2022,2,26]],"date-time":"2022-02-26T00:00:00Z","timestamp":1645833600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","doi-asserted-by":"publisher","award":["PTDC\/BTM-SAL\/28978\/2017","CEECIND\/03023\/2017","UIDB\/04138\/2020","UIDP\/04138\/2020","POCI-01-0145-FEDER-022184","UID\/BIM\/00009\/2019"],"award-info":[{"award-number":["PTDC\/BTM-SAL\/28978\/2017","CEECIND\/03023\/2017","UIDB\/04138\/2020","UIDP\/04138\/2020","POCI-01-0145-FEDER-022184","UID\/BIM\/00009\/2019"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Campylobacter coli and C. jejuni, the causing agents of campylobacteriosis, are described to be undergoing introgression events, i.e., the transference of genetic material between different species, with some isolates sharing almost a quarter of its genome. The participation of phages in introgression events and consequent impact on host ecology and evolution remain elusive. Three distinct prophages, named C. jejuni integrated elements 1, 2, and 4 (CJIE1, CJIE2, and CJIE4), are described in C. jejuni. Here, we identified two unreported prophages, Campylobacter coli integrated elements 1 and 2 (CCIE1 and CCIE2 prophages), which are C. coli homologues of CJIE1 and CJIE2, respectively. No induction was achieved for both prophages. Conversely, induction assays on CJIE1 and CJIE2 point towards the inducibility of these prophages. CCIE2-, CJIE1-, and CJIE4-like prophages were identified in a Campylobacter spp. population of 840 genomes, and phylogenetic analysis revealed clustering in three major groups: CJIE1-CCIE1, CJIE2-CCIE2, and CJIE4, clearly segregating prophages from C. jejuni and C. coli, but not from human- and nonhuman-derived isolates, corroborating the flowing between animals and humans in the agricultural context. Punctual bacteriophage host-jumps were observed in the context of C. jejuni and C. coli, and although random chance cannot be fully discarded, these observations seem to implicate prophages in evolutionary introgression events that are modulating the hybridization of C. jejuni and C. coli species.<\/jats:p>","DOI":"10.3390\/microorganisms10030516","type":"journal-article","created":{"date-parts":[[2022,2,27]],"date-time":"2022-02-27T20:47:17Z","timestamp":1645994837000},"page":"516","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Cryptic Prophages Contribution for Campylobacter jejuni and Campylobacter coli Introgression"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3879-3398","authenticated-orcid":false,"given":"Lu\u00eds","family":"Tanoeiro","sequence":"first","affiliation":[{"name":"Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6360-2576","authenticated-orcid":false,"given":"M\u00f3nica","family":"Oleastro","sequence":"additional","affiliation":[{"name":"National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisboa, Portugal"}]},{"given":"Alexandra","family":"Nunes","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7302-1193","authenticated-orcid":false,"given":"Andreia T.","family":"Marques","sequence":"additional","affiliation":[{"name":"Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal"}]},{"given":"S\u00edlvia Vaz","family":"Duarte","sequence":"additional","affiliation":[{"name":"Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2697-2399","authenticated-orcid":false,"given":"Jo\u00e3o Paulo","family":"Gomes","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisboa, Portugal"}]},{"given":"Ant\u00f3nio Pedro Alves","family":"Matos","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o Interdisciplinar Egas Moniz (CiiEM), Cooperativa de Ensino Superior Egas Moniz, Quinta da Granja, 2829-511 Caparica, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6486-3444","authenticated-orcid":false,"given":"Jorge M. B.","family":"V\u00edtor","sequence":"additional","affiliation":[{"name":"Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4635-0105","authenticated-orcid":false,"given":"Filipa F.","family":"Vale","sequence":"additional","affiliation":[{"name":"Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2022,2,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"European Food Safety Authority, and European Centre for Disease Prevention and Control (2019). The European Union One Health 2018 Zoonoses Report. EFSA J., 17, 5926.","DOI":"10.2903\/j.efsa.2019.5926"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/j.cll.2015.03.001","article-title":"Campylobacter.","volume":"35","author":"Fitzgerald","year":"2015","journal-title":"Clin. Lab. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1128\/CMR.00006-15","article-title":"Global Epidemiology of Campylobacter Infection","volume":"28","author":"Kaakoush","year":"2015","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"a018119","DOI":"10.1101\/cshperspect.a018119","article-title":"The Evolution of Campylobacter jejuni and Campylobacter coli","volume":"7","author":"Sheppard","year":"2015","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"280","DOI":"10.3201\/eid1202.050936","article-title":"Fresh Chicken as Main Risk Factor for Campylobacteriosis, Denmark","volume":"12","author":"Wingstrand","year":"2006","journal-title":"Emerg. Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"407","DOI":"10.2105\/AJPH.76.4.407","article-title":"The Role of Poultry and Meats in the Etiology of Campylobacter jejuni\/coli Enteritis","volume":"76","author":"Harris","year":"1986","journal-title":"Am. J. Public Health"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1093\/molbev\/msn264","article-title":"Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni","volume":"26","author":"Wilson","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"E8053","DOI":"10.1073\/pnas.1703331114","article-title":"Methylation-dependent DNA discrimination in natural transformation of Campylobacter jejuni","volume":"114","author":"Beauchamp","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1111\/mec.12162","article-title":"Progressive genome-wide introgression in agricultural Campylobacter coli","volume":"22","author":"Sheppard","year":"2013","journal-title":"Mol. Ecol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1126\/science.1155532","article-title":"Convergence of Campylobacter species: Implications for bacterial evolution","volume":"320","author":"Sheppard","year":"2008","journal-title":"Science"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Bobay, L.M. (2020). The prokaryotic species concept and challenges. Pangenome Divers. Dyn. Evol. Genomes, 21\u201349.","DOI":"10.1007\/978-3-030-38281-0_2"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Fouts, D.E., Mongodin, E.F., Mandrell, R.E., Miller, W.G., Rasko, D.A., Ravel, J., Brinkac, L.M., Deboy, R.T., Parker, C.T., and Daugherty, S.C. (2005). Major Structural Differences and Novel Potential Virulence Mechanisms from the Genomes of Multiple Campylobacter Species. PLoS Biol., 3.","DOI":"10.1371\/journal.pbio.0030015"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"17300","DOI":"10.1038\/srep17300","article-title":"Comparative genomics and genome biology of invasive Campylobacter jejuni","volume":"5","author":"Skarp","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Clark, C.G., Chong, P.M., Mccorrister, S.J., Mabon, P., Walker, M., and Westmacott, G.R. (2014). DNA Sequence Heterogeneity of Campylobacter jejuni CJIE4 Prophages and Expression of Prophage Genes. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0095349"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"15455","DOI":"10.1038\/s41598-017-15379-5","article-title":"The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species","volume":"7","author":"Negretti","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Clark, C.G., Chong, P.M., McCorrister, S.J., Simon, P., Walker, M., Lee, D.M., Nguy, K., Cheng, K., Gilmour, M.W., and Westmacott, G.R. (2014). The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts. BMC Microbiol., 14.","DOI":"10.1186\/1471-2180-14-70"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Clark, C.G., Grant, C.C.R., Pollari, F., Marshall, B., Moses, J., Tracz, D.M., and Gilmour, M.W. (2012). Effects of the Campylobacter jejuni CJIE1 prophage homologs on adherence and invasion in culture, patient symptoms, and source of infection. BMC Microbiol., 12.","DOI":"10.1186\/1471-2180-12-269"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2296","DOI":"10.1128\/JB.01430-08","article-title":"A DNase Encoded by Integrated Element CJIE1 Inhibits Natural Transformation of Campylobacter jejuni","volume":"191","author":"Gaasbeek","year":"2009","journal-title":"J. Bacteriol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1128\/JB.00867-09","article-title":"Nucleases Encoded by the Integrated Elements CJIE2 and CJIE4 Inhibit Natural Transformation of Campylobacter jejuni","volume":"192","author":"Gaasbeek","year":"2010","journal-title":"J. Bacteriol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Lemos, M.L., Nunes, A., Ancora, M., Camm\u00e0, C., Martins da Costa, P., and Oleastro, M. (2021). Campylobacter jejuni in Different Canine Populations: Characteristics and Zoonotic Potential. Microorganisms, 9.","DOI":"10.3390\/microorganisms9112231"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1093\/nar\/gkz380","article-title":"Prophage Hunter: An integrative hunting tool for active prophages","volume":"47","author":"Song","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e01056-13","DOI":"10.1128\/genomeA.01056-13","article-title":"Complete Genome Sequence of The Campylobacter coli Clinical Isolate 15-537360","volume":"1","author":"Pearson","year":"2013","journal-title":"Genome Announc."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: A modular and extensible implementation of the RAST algorithm for annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/nar\/gkt282","article-title":"BLAST: A more efficient report with usability improvements","volume":"41","author":"Boratyn","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1017\/S1431927608089721","article-title":"Helicobacter pylori phage screening","volume":"14","author":"Vale","year":"2008","journal-title":"Microsc. Microanal."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e00239-11","DOI":"10.1128\/mBio.00239-11","article-title":"Genome sequencing reveals a phage in Helicobacter pylori","volume":"2","author":"Lehours","year":"2011","journal-title":"mBio"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"14333","DOI":"10.1038\/srep14333","article-title":"Dormant phages of Helicobacter pylori reveal distinct populations in Europe","volume":"5","author":"Vale","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: Improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Jukes, T.H., and Cantor, C. (1969). Evolution of Protein Molecules, Academic Press. Chapter 24.","DOI":"10.1016\/B978-1-4832-3211-9.50009-7"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Price, M.N., Dehal, P.S., and Arkin, A.P. (2010). FastTree 2\u2014Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009490"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1006\/jmbi.2002.5437","article-title":"Bacteriophage Mu genome sequence: Analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus","volume":"317","author":"Morgan","year":"2002","journal-title":"J. Mol. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"W256","DOI":"10.1093\/nar\/gkz239","article-title":"Interactive Tree Of Life (iTOL) v4: Recent updates and new developments","volume":"47","author":"Letunic","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1126\/science.1188021","article-title":"A draft sequence of the Neandertal genome","volume":"328","author":"Green","year":"2010","journal-title":"Science"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2239","DOI":"10.1093\/molbev\/msr048","article-title":"Testing for ancient admixture between closely related populations","volume":"28","author":"Durand","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1093\/molbev\/msu269","article-title":"Evaluating the use of ABBA-BABA statistics to locate introgressed loci","volume":"32","author":"Martin","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Martin, S.H., Davey, J.W., Salazar, C., and Jiggins, C.D. (2019). Recombination rate variation shapes barriers to introgression across butterfly genomes. PLoS Biol., 17.","DOI":"10.1371\/journal.pbio.2006288"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1534\/genetics.118.301831","article-title":"The Timing and Direction of Introgression Under the Multispecies Network Coalescent","volume":"211","author":"Hibbins","year":"2019","journal-title":"Genetics"},{"key":"ref_40","first-page":"e000056","article-title":"SNP-sites: Rapid efficient extraction of SNPs from multi-FASTA alignments","volume":"2","author":"Page","year":"2016","journal-title":"Microb. Genom."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1093\/molbev\/msu136","article-title":"PopGenome: An efficient Swiss army knife for population genomic analyses in R","volume":"31","author":"Pfeifer","year":"2014","journal-title":"Mol. Biol. Evol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4125","DOI":"10.1128\/JCM.01231-06","article-title":"Comparative genomic analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221","volume":"44","author":"Parker","year":"2006","journal-title":"J. Clin. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e02365-18","DOI":"10.1128\/AEM.02365-18","article-title":"Population Genetics and Characterization of Campylobacter jejuni isolates drom Western Jackdaws and Game Birds in Finland","volume":"85","author":"Kovanen","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Revez, J., Llarena, A., Schott, T., Kuusi, M., Hakkinen, M., Kivist\u00f6, R., H\u00e4nninen, M., and Rossi, M. (2014). Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak. BMC Genom., 15.","DOI":"10.1186\/1471-2164-15-768"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"2424","DOI":"10.1093\/gbe\/evu194","article-title":"Evolution and Comparative Genomics of Campylobacter jejuni","volume":"6","author":"Kovanen","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.micpath.2012.08.001","article-title":"Outcome of infection of C57BL\/6 IL-10\u2212\/\u2212 mice with Campylobacter jejuni strains is correlated with genome content of open reading frames up- and down-regulated in vivo","volume":"54","author":"Bell","year":"2014","journal-title":"Microb. Pathog."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1549","DOI":"10.1111\/j.1462-2920.2011.02461.x","article-title":"Genomic variations define divergence of water\/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes","volume":"13","author":"Hepworth","year":"2011","journal-title":"Environ. Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.mib.2017.04.010","article-title":"Embracing the enemy: The diversification of microbial gene repertoires by phage-mediated horizontal gene transfer","volume":"38","author":"Touchon","year":"2017","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1139\/w11-069","article-title":"Sequencing of CJIE1 prophages from Campylobacter jejuni isolates reveals the presence of inserted and (or) deleted genes","volume":"57","author":"Clark","year":"2011","journal-title":"Can. J. Microbiol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"3987","DOI":"10.2174\/0929867324666170413100136","article-title":"Phage Life Cycles Behind Bacterial Biodiversity","volume":"24","author":"Olszak","year":"2017","journal-title":"Curr. Med. Chem."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Clark, C.G., and Ng, L.K. (2008). Sequence variability of Campylobacter temperate bacteriophages. BMC Microbiol., 8.","DOI":"10.1186\/1471-2180-8-49"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1038\/nrmicro3527","article-title":"A new perspective on lysogeny: Prophages as active regulatory switches of bacteria","volume":"13","author":"Feiner","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1700112","DOI":"10.1002\/bies.201700112","article-title":"Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn\u2019t Kill You Makes You Stronger","volume":"39","author":"Harrison","year":"2017","journal-title":"BioEssays"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2226","DOI":"10.3201\/eid2512.190267","article-title":"Genomic analysis of fluoroquinolone- and tetracycline-resistant Campylobacter jejuni sequence type 6964 in humans and poultry, New Zealand, 2014\u20132016","volume":"25","author":"French","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Clark, C.G., Berry, C., Walker, M., Petkau, A., Barker, D.O.R., Guan, C., Reimer, A., and Taboada, E.N. (2016). Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population. BMC Genom., 17.","DOI":"10.1186\/s12864-016-3340-8"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications [version 1; referees: 2 approved]","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"835","DOI":"10.3389\/fmicb.2018.00835","article-title":"Evolutionary History of Bacteriophages in the Genus Paraburkholderia","volume":"9","author":"Pratama","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"e12394","DOI":"10.1111\/hel.12394","article-title":"Phylogeographic agreement between prophage and bacterial housekeeping genes in Helicobacter pylori strains from The Gambia","volume":"22","author":"Secka","year":"2017","journal-title":"Helicobacter"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Vale, F.F., and Lehours, P. (2018). Relating phage genomes to Helicobacter pylori population structure: General steps using whole-genome sequencing data. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19071831"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"42471","DOI":"10.1038\/srep42471","article-title":"Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins","volume":"7","author":"Vale","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"12127","DOI":"10.1073\/pnas.1405336111","article-title":"Pervasive domestication of defective prophages by bacteria","volume":"111","author":"Bobay","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"4852","DOI":"10.1038\/s41467-019-12825-y","article-title":"Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis","volume":"10","author":"Akter","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_63","unstructured":"Kasman, M. (2013). Bacteriophage. Brenner\u2019s Encyclopedia of Genetics, Academic Press. [2nd ed.]."},{"key":"ref_64","first-page":"4","article-title":"Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex","volume":"6","author":"Cavassim","year":"2020","journal-title":"Microb. Genom."},{"key":"ref_65","first-page":"795","article-title":"Hybridization, Introgression, and the Nature of Species Boundaries","volume":"105","author":"Harrison","year":"2014","journal-title":"J. Hered."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1128\/jb.172.2.949-955.1990","article-title":"Natural transformation in Campylobacter species","volume":"172","author":"Wang","year":"1990","journal-title":"J. Bacteriol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"354","DOI":"10.4161\/viru.24498","article-title":"Importance of prophages to evolution and virulence of bacterial pathogens","volume":"4","author":"Fortier","year":"2013","journal-title":"Virulence"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.virol.2012.10.028","article-title":"Pirates of the Caudovirales","volume":"434","author":"Christie","year":"2012","journal-title":"Virology"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Dokland, T. (2019). Molecular Piracy: Redirection of Bacteriophage Capsid Assembly by Mobile Genetic Elements. Viruses, 11.","DOI":"10.3390\/v11111003"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"D708","DOI":"10.1093\/nar\/gkx932","article-title":"Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV)","volume":"46","author":"Lefkowitz","year":"2018","journal-title":"Nucleic Acids Res."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/3\/516\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:28:30Z","timestamp":1760135310000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/3\/516"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,26]]},"references-count":70,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2022,3]]}},"alternative-id":["microorganisms10030516"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms10030516","relation":{},"ISSN":["2076-2607"],"issn-type":[{"type":"electronic","value":"2076-2607"}],"subject":[],"published":{"date-parts":[[2022,2,26]]}}}