{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T13:03:24Z","timestamp":1790427804686,"version":"4.1.0"},"reference-count":33,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2019,12,6]],"date-time":"2019-12-06T00:00:00Z","timestamp":1575590400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2019.02820","type":"journal-article","created":{"date-parts":[[2019,12,6]],"date-time":"2019-12-06T08:25:08Z","timestamp":1575620708000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":9,"title":["Whole-Genome Sequencing and Bioinformatics as Pertinent Tools to Support Helicobacteracae Taxonomy, Based on Three Strains Suspected to Belong to Novel Helicobacter Species"],"prefix":"10.3389","volume":"10","author":[{"given":"Elvire","family":"Berthenet","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucie","family":"B\u00e9n\u00e9jat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Armelle","family":"M\u00e9nard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Varon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabrina","family":"Lacomme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Etienne","family":"Gontier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josette","family":"Raymond","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ouahiba","family":"Boussaba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Toulza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Astrid","family":"Ducournau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice","family":"Buissonni\u00e8re","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alban","family":"Giese","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francis","family":"Megraud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilie","family":"Bess\u00e8de","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quentin","family":"Jehanne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Lehours","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2019,12,6]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"Spades: a new genome assembly algorithm and its applications to single-cell sequencing.","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"2174","DOI":"10.1016\/j.ajpath.2014.04.008","article-title":"Neonatal thymectomy favors Helicobacter pylori-promoted gastric mucosa-associated lymphoid tissue lymphoma lesions in BALB\/c mice.","volume":"184","author":"Chrisment","year":"2014","journal-title":"Am. J. Pathol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1913","DOI":"10.1099\/ijs.0.057141-0","article-title":"Description of Helicobacter valdiviensis sp. nov., an Epsilonproteobacteria isolated from wild bird faecal samples.","volume":"64","author":"Collado","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1111\/hel.12343","article-title":"Other Helicobacters and gastric microbiota.","volume":"21","author":"De Witte","year":"2016","journal-title":"Helicobacter."},{"key":"B5","doi-asserted-by":"publisher","first-page":"2231","DOI":"10.1099\/00207713-50-6-2231","article-title":"Recommended minimal standards for describing new species of the genus Helicobacter.","volume":"50","author":"Dewhirst","year":"2000","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1099\/00207713-44-3-553","article-title":"Phylogeny of Helicobacter isolates from bird and swine feces and description of Helicobacter pametensis sp. nov.","volume":"44","author":"Dewhirst","year":"1994","journal-title":"Int. J. Syst. Bacteriol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"6106","DOI":"10.1128\/jb.187.17.6106-6118.2005","article-title":"Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics.","volume":"187","author":"Dewhirst","year":"2005","journal-title":"J. Bacteriol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1473","DOI":"10.1016\/j.ajpath.2017.03.004","article-title":"A new animal model of gastric Lymphomagenesis: april transgenic mice infected by Helicobacter species.","volume":"187","author":"Floch","year":"2017","journal-title":"Am. J. Pathol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1099\/00207713-42-1-166","article-title":"How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity.","volume":"42","author":"Fox","year":"1992","journal-title":"Int. J. Syst. Bacteriol."},{"key":"B10","doi-asserted-by":"crossref","first-page":"2546","DOI":"10.1128\/JCM.38.7.2546-2549.2000","article-title":"Helicobacter canadensis sp. nov. isolated from humans with diarrhea as an example of an emerging pathogen.","volume":"38","author":"Fox","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"3920","DOI":"10.1128\/jcm.39.11.3920-3926.2001","article-title":"Helicobacter typhlonius sp. nov., a novel murine urease-negative Helicobacter species.","volume":"39","author":"Franklin","year":"2001","journal-title":"J. Clin. Microbiol."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"B13","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1099\/00207713-47-4-975","article-title":"Helicobacter salomonis sp. nov., a canine gastric Helicobacter sp. related to Helicobacter felis and Helicobacter bizzozeronii.","volume":"47","author":"Jalava","year":"1997","journal-title":"Int. J. Syst. Bacteriol."},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: scalable analysis of bacterial genome variation at the population level.","volume":"11","author":"Jolley","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"B15","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1099\/ijs.0.64483-0","article-title":"DNA\u2013DNA hybridization values and their relationship to whole-genome sequence similarities.","volume":"57","author":"Klappenbach","year":"2007","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"1315","DOI":"10.1016\/0016-5085(90)91156-z","article-title":"A small animal model of human Helicobacter pylori active chronic gastritis.","volume":"99","author":"Lee","year":"1990","journal-title":"Gastroenterology"},{"key":"B17","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1136\/gutjnl-2016-312288","article-title":"Management of Helicobacter pylori infection-the Maastricht v\/florence consensus report.","volume":"66","author":"Malfertheiner","year":"2017","journal-title":"Gut"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1016\/s0140-6736(84)91816-6","article-title":"Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration.","volume":"323","author":"Marshall","year":"1984","journal-title":"Lancet"},{"key":"B19","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.syapm.2015.09.008","article-title":"The GyrA encoded gene: a pertinent marker for the phylogenetic revision of Helicobacter genus.","volume":"39","author":"M\u00e9nard","year":"2016","journal-title":"Syst. Appl. Microbiol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1099\/ijs.0.64279-0","article-title":"Helicobacter equorum sp. nov., a urease-negative Helicobacter species isolated from horse faeces.","volume":"57","author":"Moyaert","year":"2007","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B21","author":"On","year":"2015","journal-title":"Helicobacter: Bergey\u2019s Manual of Systematics of Archaea and Bacteria."},{"key":"B22","doi-asserted-by":"crossref","first-page":"3722","DOI":"10.1128\/JCM.38.10.3722-3728.2000","article-title":"Helicobacter aurati sp. nov., a urease-positive Helicobacter species cultured from gastrointestinal tissues of Syrian hamsters.","volume":"38","author":"Patterson","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"1881","DOI":"10.1099\/00207713-51-5-1881","article-title":"Helicobacter ganmani sp. nov., a urease-negative anaerobe isolated from the intestines of laboratory mice.","volume":"51","author":"Robertson","year":"2001","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/j.mimet.2015.10.018","article-title":"EUCAST recommendations for antimicrobial susceptibility testing applied to the three main Campylobacter species isolated in humans.","volume":"119","author":"Sifr\u00e9","year":"2015","journal-title":"J. Microbiol. Methods"},{"key":"B25","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1128\/JCM.38.5.1811-1817.2000","article-title":"Helicobacter mesocricetorum sp. nov., a novel Helicobacter isolated from the feces of Syrian hamsters.","volume":"38","author":"Simmons","year":"2000","journal-title":"J. Clin. Microbiol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"2518","DOI":"10.1038\/s41396-018-0199-5","article-title":"Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence.","volume":"12","author":"Smet","year":"2018","journal-title":"ISME J."},{"key":"B27","author":"Solnick","year":"2001","journal-title":"Taxonomy of the Helicobacter Genus. Helicobacter Pylori: Physiology and Genetics."},{"key":"B28","doi-asserted-by":"publisher","first-page":"2725","DOI":"10.1093\/molbev\/mst197","article-title":"MEGA6: molecular evolutionary genetics analysis version 6.0.","volume":"30","author":"Tamura","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1099\/ijs.0.63860-0","article-title":"Helicobacter cynogastricus sp. nov., isolated from the canine gastric mucosa.","volume":"56","author":"Van den Bulck","year":"2006","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02533","article-title":"a potential new human pathogen belonging to Helicobacter genus, identified in a bloodstream infection.","volume":"8","author":"van der Mee-Marquet","year":"2017","journal-title":"Front. Microbiol."},{"key":"B31","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1128\/MR.60.2.407-438.1996","article-title":"Polyphasic taxonomy, a consensus approach to bacterial systematics.","volume":"60","author":"Vandamme","year":"1996","journal-title":"Microbiol. Rev."},{"key":"B32","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1053\/j.gastro.2011.10.036","article-title":"Helicobacter pylori infection recruits bone marrow-derived cells that participate in gastric preneoplasia in mice.","volume":"142","author":"Varon","year":"2012","journal-title":"Gastroenterology"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.15931.2","article-title":"Fastq screen: a tool for multi-genome mapping and quality control.","volume":"7","author":"Wingett","year":"2018","journal-title":"F1000Res"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2019.02820\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,2,10]],"date-time":"2021-02-10T18:44:32Z","timestamp":1612982672000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2019.02820\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12,6]]},"references-count":33,"alternative-id":["10.3389\/fmicb.2019.02820"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2019.02820","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,12,6]]},"article-number":"2820"}}