{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T06:09:10Z","timestamp":1791266950012,"version":"4.1.0"},"reference-count":36,"publisher":"Frontiers Media SA","content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2016.00757","type":"journal-article","created":{"date-parts":[[2016,5,18]],"date-time":"2016-05-18T23:55:02Z","timestamp":1463615702000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":26,"title":["New Insights into the Genetic Diversity of Clostridium botulinum Group III through Extensive Genome Exploration"],"prefix":"10.3389","volume":"7","author":[{"given":"C\u00e9dric","family":"Woudstra","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Le Mar\u00e9chal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rozenn","family":"Souillard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie-H\u00e9l\u00e8ne","family":"Bayon-Auboyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Mermoud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denise","family":"Desoutter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Fach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2016,5,19]]},"reference":[{"issue":"e39107","key":"B1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0039107","article-title":"Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups.","volume":"7","author":"Agren","year":"2012","journal-title":"PLoS ONE"},{"issue":"402","key":"B2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-12-402","article-title":"BLAST ring image generator (BRIG): simple prokaryote genome comparisons.","volume":"12","author":"Alikhan","year":"2011","journal-title":"BMC Genomics"},{"key":"B3","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.anaerobe.2014.01.002","article-title":"The same clade of Clostridium botulinum strains is causing avian botulism in southern and northern Europe.","volume":"26","author":"Anza","year":"2014","journal-title":"Anaerobe"},{"issue":"209","key":"B4","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-8-209","article-title":"CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.","volume":"8","author":"Bland","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"B5","doi-asserted-by":"publisher","first-page":"3485","DOI":"10.1128\/JCM.01656-12","article-title":"Specific detection of enteroaggregative hemorrhagic Escherichia coli O104:H4 strains by use of the CRISPR locus as a target for a diagnostic real-time PCR.","volume":"50","author":"Delannoy","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1111\/eva.12178","article-title":"A field guide to whole-genome sequencing, assembly and annotation.","volume":"7","author":"Ekblom","year":"2014","journal-title":"Evol. Appl."},{"key":"B7","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.meegid.2015.08.042","article-title":"Genomic characterization of Italian Clostridium botulinum group I strains.","volume":"36","author":"Giordani","year":"2015","journal-title":"Infect. Genet. Evol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/hdy.2014.85","article-title":"Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads.","volume":"114","author":"Gouin","year":"2015","journal-title":"Heredity (Edinb)"},{"issue":"199","key":"B9","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-015-1421-8","article-title":"The dnd operon for DNA phosphorothioation modification system in Escherichia coli is located in diverse genomic islands.","volume":"16","author":"Ho","year":"2015","journal-title":"BMC Genomics"},{"key":"B10","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/j.gene.2010.04.010","article-title":"Genome analysis of the Clostridium difficile phage PhiCD6356, a temperate phage of the Siphoviridae family.","volume":"462","author":"Horgan","year":"2010","journal-title":"Gene"},{"key":"B11","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1093\/molbev\/msj030","article-title":"Application of phylogenetic networks in evolutionary studies.","volume":"23","author":"Huson","year":"2006","journal-title":"Mol. Biol. Evol."},{"issue":"e104984","key":"B12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0104984","article-title":"Solving the problem of comparing whole bacterial genomes across different sequencing platforms.","volume":"9","author":"Kaas","year":"2014","journal-title":"PLoS ONE"},{"key":"B13","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1016\/j.vetmic.2010.04.030","article-title":"Real-time PCR for Clostridium botulinum type C neurotoxin (BoNTC) gene, also covering a chimeric C\/D sequence\u2013application on outbreaks of botulism in poultry.","volume":"146","author":"Lindberg","year":"2010","journal-title":"Vet. Microbiol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1038\/nrmicro2577","article-title":"Evolution and classification of the CRISPR-Cas systems.","volume":"9","author":"Makarova","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"issue":"e48837","key":"B15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0048837","article-title":"The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.","volume":"7","author":"Mavromatis","year":"2012","journal-title":"PLoS ONE"},{"key":"B16","doi-asserted-by":"publisher","first-page":"1031","DOI":"10.1101\/gr.5238106","article-title":"Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens.","volume":"16","author":"Myers","year":"2006","journal-title":"Genome Res."},{"key":"B17","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1099\/00221287-92-1-67","article-title":"The stability of toxigenicity in Clostridium botulinum types C and D.","volume":"92","author":"Oguma","year":"1976","journal-title":"J. Gen. Microbiol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B19","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/nrg3642","article-title":"Sequencing depth and coverage: key considerations in genomic analyses.","volume":"15","author":"Sims","year":"2014","journal-title":"Nat. Rev. Genet."},{"issue":"185","key":"B20","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-12-185","article-title":"Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.","volume":"12","author":"Skarin","year":"2011","journal-title":"BMC Genomics"},{"key":"B21","doi-asserted-by":"publisher","first-page":"213","DOI":"10.4161\/mge.1.3.17617","article-title":"Horizontal gene transfer of toxin genes in Clostridium botulinum: involvement of mobile elements and plasmids.","volume":"1","author":"Skarin","year":"2011","journal-title":"Mob. Genet. Elements"},{"issue":"e107777","key":"B22","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0107777","article-title":"Plasmidome interchange between Clostridium botulinum, Clostridium novyi and Clostridium haemolyticum converts strains of independent lineages into distinctly different pathogens.","volume":"9","author":"Skarin","year":"2014","journal-title":"PLoS ONE"},{"key":"B23","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1086\/444507","article-title":"Botulism.","volume":"41","author":"Sobel","year":"2005","journal-title":"Clin. Infect. Dis."},{"key":"B24","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1080\/03079457.2014.957644","article-title":"Investigation of Clostridium botulinum in commercial poultry farms in France between 2011 and 2013.","volume":"43","author":"Souillard","year":"2014","journal-title":"Avian. Pathol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1637\/7347-022305R1.1","article-title":"Characterization of the neurotoxin produced by isolates associated with avian botulism.","volume":"49","author":"Takeda","year":"2005","journal-title":"Avian. Dis."},{"key":"B26","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1038\/nchembio.2007.39","article-title":"Phosphorothioation of DNA in bacteria by dnd genes.","volume":"3","author":"Wang","year":"2007","journal-title":"Nat. Chem. Biol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"5938","DOI":"10.1128\/AEM.01155-15","article-title":"Clostridium botulinum group ii isolate phylogenomic profiling using whole-genome sequence data.","volume":"81","author":"Weedmark","year":"2015a","journal-title":"Appl. Environ. Microbiol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1128\/AEM.01155-15","article-title":"Phylogenomic profiling of Clostridium botulinum group II isolates using whole genome sequence data.","volume":"8","author":"Weedmark","year":"2015b","journal-title":"Appl. Environ. Microbiol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"2495","DOI":"10.1128\/AEM.03915-14","article-title":"Molecular gene profiling of Clostridium botulinum group III and its detection in naturally contaminated samples originating from various European countries.","volume":"81","author":"Woudstra","year":"2015a","journal-title":"Appl. Environ. Microbiol."},{"issue":"e01105","key":"B30","doi-asserted-by":"publisher","DOI":"10.1128\/genomeA.01105-15","article-title":"Draft Genome Sequences of 17 French Clostridium botulinum Group III Strains.","volume":"3","author":"Woudstra","year":"2015b","journal-title":"Genome Announc."},{"key":"B31","doi-asserted-by":"publisher","first-page":"3120","DOI":"10.1128\/AEM.07568-11","article-title":"Neurotoxin gene profiling of clostridium botulinum types C and D native to different countries within Europe.","volume":"78","author":"Woudstra","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"9115","DOI":"10.1093\/nar\/gks650","article-title":"Phosphorothioate DNA as an antioxidant in bacteria.","volume":"40","author":"Xie","year":"2012","journal-title":"Nucleic Acids Res."},{"issue":"41","key":"B33","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-9-41","article-title":"DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus.","volume":"9","author":"Xu","year":"2009","journal-title":"BMC Microbiol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1428","DOI":"10.1111\/j.1365-2958.2005.04764.x","article-title":"A novel DNA modification by sulphur.","volume":"57","author":"Zhou","year":"2005","journal-title":"Mol. Microbiol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"W347","DOI":"10.1093\/nar\/gkr485","article-title":"PHAST: a fast phage search tool.","volume":"39","author":"Zhou","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"B36","doi-asserted-by":"publisher","first-page":"4359","DOI":"10.1128\/JB.184.16.4359-4368.2002","article-title":"Genomic analysis of Clostridium perfringens bacteriophage phi3626, which integrates into guaA and possibly affects sporulation.","volume":"184","author":"Zimmer","year":"2002","journal-title":"J. Bacteriol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"deposited":{"date-parts":[[2016,6,21]],"date-time":"2016-06-21T12:59:17Z","timestamp":1466513957000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/Article\/10.3389\/fmicb.2016.00757\/abstract"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,5,19]]},"references-count":36,"URL":"https:\/\/doi.org\/10.3389\/fmicb.2016.00757","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,5,19]]}}}