{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T06:10:41Z","timestamp":1791180641498,"version":"4.1.0"},"reference-count":66,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2014,1,24]],"date-time":"2014-01-24T00:00:00Z","timestamp":1390521600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0085131","type":"journal-article","created":{"date-parts":[[2014,1,24]],"date-time":"2014-01-24T21:29:54Z","timestamp":1390598994000},"page":"e85131","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":119,"title":["What Does the Talking?: Quorum Sensing Signalling Genes Discovered in a Bacteriophage Genome"],"prefix":"10.1371","volume":"9","author":[{"given":"Katherine R.","family":"Hargreaves","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew M.","family":"Kropinski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martha R. J.","family":"Clokie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2014,1,24]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"2192","DOI":"10.1073\/pnas.96.5.2192","article-title":"Evolutionary relationships among diverse bacteriophages and prophages: All the world&apos;s a phage","volume":"96","author":"RW Hendrix","year":"1999","journal-title":"Proc Natl Acad Sci US A"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1128\/MMBR.67.1.86-156.2003","article-title":"Bacteriophage T4 genome","volume":"67","author":"ES Miller","year":"2003","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1016\/j.coviro.2011.06.009","article-title":"Bacteriophages and their genomes","volume":"1","author":"GF Hatfull","year":"2011","journal-title":"Curr Opin Virol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/S0092-8674(01)00637-7","article-title":"Phage genomics: Small is beautiful","volume":"108","author":"H Brussow","year":"2002","journal-title":"Cell"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1038\/424741a","article-title":"Marine ecosystems: Bacterial photosynthesis genes in a virus","volume":"424","author":"NH Mann","year":"2003","journal-title":"Nature"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1016\/j.cell.2012.04.034","article-title":"A Phage Tubulin Assembles Dynamic Filaments by an Atypical Mechanism to Center Viral DNA within the Host Cell","volume":"149","author":"JA Kraemer","year":"2012","journal-title":"Cell"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1910","DOI":"10.1126\/science.272.5270.1910","article-title":"Lysogenic conversion by a filamentous phage encoding cholera toxin","volume":"272","author":"MK Waldor","year":"1996","journal-title":"Science"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1126\/science.6387911","article-title":"Shiga-like toxin-converting phages from <italic>Escherichia coli<\/italic> strains that cause hemorrhagic colitis or infantile diarrhea","volume":"226","author":"AD Obrien","year":"1984","journal-title":"Science"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1111\/1469-0691.12064","article-title":"Consequences of <italic>Clostridium difficile<\/italic> infection: understanding the healthcare burden","volume":"18","author":"E Bouza","year":"2012","journal-title":"Clin Microbiol Infec"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1093\/cid\/cis614","article-title":"Changing Epidemiology of <italic>Clostridium difficile<\/italic> Infection Following the Introduction of a National Ribotyping-Based Surveillance Scheme in England","volume":"55","author":"MH Wilcox","year":"2012","journal-title":"Clin Infect Dis"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1001\/archpedi.1935.01970020105010","article-title":"Intestinal flora in new-born infants: with a description of a new pathogenic anaerobe, <italic>Bacillus difficilis<\/italic>","volume":"49","author":"IC Hall","year":"1935","journal-title":"Am J Dis Child"},{"key":"ref12","article-title":"Enteric bacterial pathogen detection in southern sea otters (<italic>Enhydra lutris nereis<\/italic>) is associated with coastal urbanization and freshwater runoff","volume":"41","author":"MA Miller","year":"2010","journal-title":"Vat Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/j.anaerobe.2009.09.006","article-title":"Varied prevalence of <italic>Clostridium difficile<\/italic> in an integrated swine operation","volume":"15","author":"KN Norman","year":"2009","journal-title":"Anaerobe"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1099\/00222615-45-2-133","article-title":"The distribution of <italic>Clostridium difficile<\/italic> in the environment of South Wales","volume":"45","author":"N AlSaif","year":"1996","journal-title":"J Med Microbiol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"6236","DOI":"10.1128\/AEM.01849-13","article-title":"Genetically diverse <italic>Clostridium difficile<\/italic> strains harbouring abundant prophages in an estuarine environment","volume":"79","author":"KR Hargreaves","year":"2013","journal-title":"Appl Environ Microbiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1038\/nrmicro2164","article-title":"<italic>Clostridium difficile<\/italic> infection: new developments in epidemiology and pathogenesis","volume":"7","author":"M Rupnik","year":"2009","journal-title":"Nat Rev Microbiol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1038\/ng1830","article-title":"The multidrug-resistant human pathogen <italic>Clostridium difficile<\/italic> has a highly mobile, mosaic genome","volume":"38","author":"M Sebaihia","year":"2006","journal-title":"Nat Genet"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2704","DOI":"10.1128\/IAI.00147-12","article-title":"The <italic>Clostridium difficile<\/italic> spo0A Gene Is a Persistence and Transmission Factor","volume":"80","author":"LJ Deakin","year":"2012","journal-title":"Infect Immun"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1146\/annurev.micro.55.1.165","article-title":"Quorum sensing in bacteria","volume":"55","author":"MB Miller","year":"2001","journal-title":"Annu Rev Microbiol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1099\/jmm.0.45817-0","article-title":"Quorum sensing in <italic>Clostridium difficile<\/italic>: analysis of a luxS-type signalling system","volume":"54","author":"GP Carter","year":"2005","journal-title":"J Med Microbiol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1016\/j.bbrc.2005.07.131","article-title":"LuxS\/autoinducer-2 quorum sensing molecule regulates transcriptional virulence gene expression in <italic>Clostridium difficile<\/italic>","volume":"335","author":"ASY Lee","year":"2005","journal-title":"Biochem Biophys Res Commun"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1128\/JB.01980-12","article-title":"Multiple factors modulate biofilm formation by the anaerobic pathogen <italic>Clostridium difficile<\/italic>","volume":"195","author":"T Dapa","year":"2013","journal-title":"J Bacteriol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"3672","DOI":"10.1128\/JB.00473-13","article-title":"The <italic>agr<\/italic> Locus Regulates Virulence and Colonization Genes in <italic>Clostridium difficile<\/italic> 027","volume":"195","author":"MJ Martin","year":"2013","journal-title":"J Bacteriol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1111\/j.1699-0463.1991.tb05156.x","article-title":"Electron Microscope investigation of lysogeny of <italic>Clostridium difficile<\/italic> strains isolates from antibiotic-associated diarrhea cases and from healthy carriers","volume":"99","author":"E Nagy","year":"1991","journal-title":"APMIS"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"6027","DOI":"10.1128\/AEM.01311-12","article-title":"Prophage Carriage and Diversity within Clinically Relevant Strains of <italic>Clostridium difficile<\/italic>","volume":"78","author":"J Shan","year":"2012","journal-title":"Appl Environ Microbiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1099\/mic.0.2006\/002436-0","article-title":"The complete genome sequence of <italic>Clostridium difficile<\/italic> phage phi C2 and comparisons to phi CD119 and inducible prophages of CD630","volume":"153","author":"S Goh","year":"2007","journal-title":"Microbiology-SGM"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2568","DOI":"10.1128\/JB.188.7.2568-2577.2006","article-title":"Genomic organization and molecular characterization of <italic>Clostridium difficile<\/italic> bacteriophage PhiCD119","volume":"188","author":"R Govind","year":"2006","journal-title":"J Bacteriol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"6734","DOI":"10.1128\/JB.00686-08","article-title":"Molecular characterization of a <italic>Clostridium difficile<\/italic> bacteriophage and its cloned biologically active endolysin","volume":"190","author":"M Mayer","year":"2008","journal-title":"J Bacteriol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.gene.2010.04.010","article-title":"Genome analysis of the <italic>Clostridium difficile<\/italic> phage PhiCD6356, a temperate phage of the Siphoviridae family","volume":"462","author":"M Horgan","year":"2010","journal-title":"Gene"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"2726","DOI":"10.1128\/JB.00787-10","article-title":"Prophage-Stimulated Toxin Production in <italic>Clostridium difficile<\/italic> NAP1\/027 Lysogens","volume":"193","author":"O Sekulovic","year":"2011","journal-title":"J Bacteriol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"7662","DOI":"10.1128\/AEM.02275-12","article-title":"Evidence of <italic>In Vivo<\/italic> Prophage Induction during <italic>Clostridium difficile<\/italic> Infection","volume":"78","author":"M Meessen-Pinard","year":"2012","journal-title":"Appl Environ Microbiol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"12037","DOI":"10.1128\/JVI.01256-09","article-title":"Bacteriophage-Mediated Toxin Gene Regulation in <italic>Clostridium difficile<\/italic>","volume":"83","author":"R Govind","year":"2009","journal-title":"J Virol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1101\/gr.8.3.175","article-title":"Base-calling of automated sequencer traces using phred. I. Accuracy assessment","volume":"8","author":"B Ewing","year":"1998","journal-title":"Genome Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","article-title":"Base-calling of automated sequencer traces using phred. II. Error probabilities","volume":"8","author":"B Ewing","year":"1998","journal-title":"Genome Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1093\/bioinformatics\/16.10.944","article-title":"Artemis: sequence visualization and annotation","volume":"16","author":"K Rutherford","year":"2000","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"3911","DOI":"10.1093\/nar\/27.19.3911","article-title":"Heuristic approach to deriving models for gene finding","volume":"27","author":"J Besemer","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"ref37","first-page":"365","article-title":"Primer3 on the WWW for general users and for biologist programmers","volume":"132","author":"S Rozen","year":"2000","journal-title":"Methods in molecular biology (Clifton, N.J.)"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"D225","DOI":"10.1093\/nar\/gkq1189","article-title":"CDD: a Conserved Domain Database for the functional annotation of proteins","volume":"39","author":"A Marchler-Bauer","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"W686","DOI":"10.1093\/nar\/gki366","article-title":"The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs","volume":"33","author":"P Schattner","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"11","author":"F Sievers","year":"2011","journal-title":"Mol Syst Biol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/bioinformatics\/btn578","article-title":"DNAPlotter: circular and linear interactive genome visualization","volume":"25","author":"T Carver","year":"2009","journal-title":"Bioinformatics"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"3422","DOI":"10.1093\/bioinformatics\/bti553","article-title":"ACT: the Artemis comparison tool","volume":"21","author":"TJ Carver","year":"2005","journal-title":"Bioinformatics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btr039","article-title":"Easyfig: a genome comparison visualizer","volume":"27","author":"MJ Sullivan","year":"2011","journal-title":"Bioinformatics"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods","volume":"28","author":"K Tamura","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref45","first-page":"275","article-title":"The rapid generation of mutation data matrices from protein sequences","volume":"8","author":"DT Jones","year":"1992","journal-title":"Comput Appl Biosci"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"783","DOI":"10.2307\/2408678","article-title":"Confidence limits on phylogenies: an approach using the bootstrap","volume":"39","author":"J Felsenstein","year":"1985","journal-title":"Evolution"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1111\/j.1365-2672.2004.02409.x","article-title":"Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR","volume":"97","author":"T Rinttila","year":"2004","journal-title":"J Appl Microbiol"},{"key":"ref48","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2180-9-224","article-title":"Classification of <italic>Myoviridae<\/italic> bacteriophages using protein sequence similarity","volume":"9","author":"R Lavigne","year":"2009","journal-title":"BMC Microbiol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1146\/annurev.genet.42.110807.091640","article-title":"Quorum Sensing in <italic>Staphylococci<\/italic>","volume":"42","author":"RP Novick","year":"2008","journal-title":"Annu Rev Genet"},{"key":"ref50","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2009-10-9-r102","article-title":"Comparative genome and phenotypic analysis of <italic>Clostridium difficile<\/italic> 027 strains provides insight into the evolution of a hypervirulent bacterium","volume":"10","author":"R Stabler","year":"2009","journal-title":"Genome Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/S0092-8674(03)00233-2","article-title":"Origins of highly mosaic mycobacteriophage genomes","volume":"113","author":"ML Pedulla","year":"2003","journal-title":"Cell"},{"key":"ref52","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.0040234","article-title":"Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts","volume":"4","author":"MB Sullivan","year":"2006","journal-title":"PloS Biol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1128\/JB.01135-07","article-title":"Conservation and evolutionary dynamics of the <italic>agr<\/italic> cell-to-cell communication system across Firmicutes","volume":"190","author":"A Wuster","year":"2008","journal-title":"J Bacteriol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"7142","DOI":"10.1128\/AEM.00950-09","article-title":"Acyl-Homoserine Lactones Can Induce Virus Production in Lysogenic Bacteria: an Alternative Paradigm for Prophage Induction","volume":"75","author":"D Ghosh","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"2659","DOI":"10.1128\/AEM.02483-08","article-title":"Characterization of a New Plasmid-Like Prophage in a Pandemic <italic>Vibrio parahaemolyticus<\/italic> O3:K6 Strain","volume":"75","author":"S-F Lan","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1128\/AEM.02099-07","article-title":"Bacteriophage prevalence in the genus Azospirillum and analysis of the first genome sequence of an <italic>Azospirillum brasilense<\/italic> integrative phage","volume":"74","author":"M Boyer","year":"2008","journal-title":"Appl Environ Microbiol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1101\/gr.4106106","article-title":"Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of <italic>Sodalis glossinidius<\/italic> in the tsetse host","volume":"16","author":"H Toh","year":"2006","journal-title":"Genome Res"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"5415","DOI":"10.1128\/AEM.00989-10","article-title":"Genomic Sequence and Characterization of the Virulent Bacteriophage phi CTP1 from <italic>Clostridium tyrobutyricum<\/italic> and Heterologous Expression of Its Endolysin","volume":"76","author":"MJ Mayer","year":"2010","journal-title":"Appl Environ Microbiol"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1111\/j.1758-2229.2009.00055.x","article-title":"Isolation and genomic characterization of the first phage infecting Iodobacteria: phiPLPE, a myovirus having a novel set of features","volume":"1","author":"C Leblanc","year":"2009","journal-title":"Environ Microbiol Rep"},{"key":"ref60","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00362-12","article-title":"A quorum-sensing-induced bacteriophage defense mechanism","volume":"4","author":"NM Hoyland-Kroghsbo","year":"2013","journal-title":"mBio"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"6369","DOI":"10.1128\/JVI.00641-12","article-title":"Complete Genome Sequence of the Giant <italic>Pseudomonas<\/italic> Phage Lu11","volume":"86","author":"EM Adriaenssens","year":"2012","journal-title":"J Virol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"6066","DOI":"10.1128\/JB.182.21.6066-6074.2000","article-title":"Sequence of the genome of the temperate, serotype-converting, <italic>Pseudomonas aeruginosa<\/italic> bacteriophage D3","volume":"182","author":"AM Kropinski","year":"2000","journal-title":"J Bacteriol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1038\/ismej.2008.35","article-title":"Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?","volume":"2","author":"JH Paul","year":"2008","journal-title":"ISME J"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1177\/117693430500100001","article-title":"Why Bacteriophage Encode Exotoxins and other Virulence Factors","volume":"1","author":"ST Abedon","year":"2005","journal-title":"Evol Bioinform Online"},{"key":"ref65","doi-asserted-by":"crossref","unstructured":"Abedon ST (2011). Communication Among Phages, Bacteria and Soil Environments. In: Wittany G, editors. Biocommunication in Soil Microorganisms, Volume 23, Springer, pp. 37\u201365.","DOI":"10.1007\/978-3-642-14512-4_2"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"4448","DOI":"10.1128\/AEM.03038-09","article-title":"Regulation of Neurotoxin Production and Sporulation by a Putative <italic>agrBD<\/italic> Signaling System in Proteolytic <italic>Clostridium botulinum<\/italic>","volume":"76","author":"CM Cooksley","year":"2010","journal-title":"Appl Environ Microbiol"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0085131","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T01:04:58Z","timestamp":1565139898000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0085131"}},"subtitle":[],"editor":[{"given":"Gunnar F.","family":"Kaufmann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,1,24]]},"references-count":66,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2014,1,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0085131","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1,24]]}}}