{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:35:33Z","timestamp":1761863733744,"version":"3.41.2"},"reference-count":32,"publisher":"Frontiers Media SA","content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"DOI":"10.3389\/fcimb.2017.00385","type":"journal-article","created":{"date-parts":[[2017,8,31]],"date-time":"2017-08-31T03:50:03Z","timestamp":1504151403000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":11,"title":["Developmental Cycle and Genome Analysis of Protochlamydia massiliensis sp. nov. a New Species in the Parachlamydiacae Family"],"prefix":"10.3389","volume":"7","author":[{"given":"Samia","family":"Benamar","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jacques Y.","family":"Bou Khalil","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caroline","family":"Blanc-Tailleur","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melhem","family":"Bilen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lina","family":"Barrassi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernard","family":"La Scola","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2017,8,31]]},"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":"1709","DOI":"10.1126\/science.1138140","article-title":"CRISPR provides acquired resistance against viruses in prokaryotes","volume":"315","author":"Barrangou","year":"2007","journal-title":"Science"},{"key":"B3","doi-asserted-by":"publisher","first-page":"2376","DOI":"10.1093\/gbe\/evw138","article-title":"CRISPR system acquisition and evolution of an obligate intracellular chlamydia-related bacterium","volume":"8","author":"Bertelli","year":"2016","journal-title":"Genome Biol. Evol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"31","DOI":"10.3389\/fcimb.2016.00031","article-title":"Developmental cycle and genome analysis of \u201cRubidus massiliensis,\u201d a new Vermamoeba vermiformis pathogen","volume":"6","author":"Bou Khalil","year":"2016","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/j.micinf.2017.02.003","article-title":"Protochlamydia phocaeensis sp. nov., a new Chlamydiales species with host dependent replication cycle","volume":"19","author":"Bou Khalil","year":"2017","journal-title":"Microbes Infect."},{"key":"B6","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"Camacho","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"1390","DOI":"10.1128\/JB.01412-07","article-title":"Phage response to CRISPR-encoded resistance in Streptococcus thermophilus","volume":"190","author":"Deveau","year":"2008","journal-title":"J. Bacteriol."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","author":"Eddy","year":"2011","journal-title":"PLoS Comp. Biol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"B10","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1099\/00207713-49-2-415","article-title":"Emended description of the orderChlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., eachcontaining onemonotypic genus, revised taxonomy of the family Chlamydiaceae, includinga new genusand five new species, and standards for the identification of organisms","volume":"49","author":"Everett","year":"1999","journal-title":"Int. J.Syst. Bacteriol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1186\/1471-2164-12-542","article-title":"Insightintocross-talk between intra-amoebal pathogens","volume":"12","author":"Gimenez","year":"2011","journal-title":"BMC Genomics"},{"key":"B12","doi-asserted-by":"publisher","first-page":"5530","DOI":"10.1128\/AEM.69.9.5530-5535.2003","article-title":"History of the ADP\/ATP-translocase-encoding gene, a parasitismgene transferred from a Chlamydiales ancestor to plants 1 billion years ago","volume":"69","author":"Greub","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"2647","DOI":"10.1099\/mic.0.28057-0","article-title":"Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification","author":"Griffiths","year":"2005","journal-title":"Microbiology"},{"key":"B14","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1093\/nar\/gkg006","article-title":"Rfam: an RNA family database","volume":"31","author":"Griffiths-Jones","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"B15","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1186\/1471-2105-8-172","article-title":"The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats","volume":"8","author":"Grissa","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"B16","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1146\/annurev.micro.62.081307.162818","article-title":"Chlamydiae as symbionts in eukaryotes","volume":"62","author":"Horn","year":"2008","journal-title":"Annu. Rev. Microbiol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"728","DOI":"10.1126\/science.1096330","article-title":"Illuminating the evolutionary history of chlamydiae","volume":"304","author":"Horn","year":"2004","journal-title":"Science"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1099\/00221287-146-5-1231","article-title":"Neochlamydia hartmannellae gen. nov., sp. nov. (Parachlamydiaceae), an endoparasite of the amoeba Hartmannella vermiformis","volume":"146","author":"Horn","year":"2000","journal-title":"Microbiology"},{"key":"B19","doi-asserted-by":"publisher","first-page":"1401","DOI":"10.1128\/JB.01415-07","article-title":"Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus","volume":"190","author":"Horvath","year":"2008","journal-title":"J. Bacteriol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"B21","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1111\/j.1574-6968.1993.tb06189.x","article-title":"Description and partial characterization of a new Chlamydia-like microorganism","volume":"109","author":"Kahane","year":"1993","journal-title":"FEMS Microbiol. Lett."},{"key":"B22","doi-asserted-by":"publisher","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"Lagesen","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"B23","first-page":"129","article-title":"Isolation of new fastidious alpha Proteobacteria and Afipia felis from hospital water supplies by direct plating and amoebal co-cultureprocedures","volume":"34","author":"La Scola","year":"2000","journal-title":"FEMS Microbiol. Ecol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1093\/nar\/gkh152","article-title":"ARAGORN, a program to detect tRNA genes and tmRNAgenes innucleotide sequences","volume":"32","author":"Laslett","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40793-015-0019-8","article-title":"High-quality genome sequence and description of Bacillus dielmoensis strain FF4T sp. nov","volume":"10","author":"Lo","year":"2015","journal-title":"Stand. Genomic Sci."},{"key":"B26","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1053\/jcpa.2002.0629","article-title":"Animal chlamydioses and zoonotic implications","volume":"128","author":"Longbottom","year":"2003","journal-title":"J. Comp. Pathol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"1335","DOI":"10.1093\/bioinformatics\/btp157","article-title":"Infernal 1.0: inference of RNA alignments","volume":"25","author":"Nawrocki","year":"2009","journal-title":"J. Gerontol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.micpath.2015.02.006","article-title":"Isolation of Vermamoeba vermiformis and associated bacteria in hospital water","volume":"80","author":"Pagnier","year":"2015","journal-title":"Microb. Pathog."},{"key":"B29","doi-asserted-by":"publisher","first-page":"1381","DOI":"10.1099\/ijs.0.000090","article-title":"Taxogenomics of the order Chlamydiales","volume":"65","author":"Pillonel","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1099\/ijs.0.000161","article-title":"Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterialspecies","volume":"65","author":"Rossi-Tamisier","year":"2015","journal-title":"Int. J.Syst. Evol. Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1080\/10635150701472164","article-title":"Improvement of phylogenies after removing divergent andambiguously aligned blocks from protein sequence alignments","volume":"56","author":"Talavera","year":"2007","journal-title":"Syst. Biol."},{"key":"B32","doi-asserted-by":"publisher","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":"Tamura","year":"2011","journal-title":"Mol. Biol. Evol."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fcimb.2017.00385\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,8,31]],"date-time":"2017-08-31T03:50:06Z","timestamp":1504151406000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fcimb.2017.00385\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,31]]},"references-count":32,"alternative-id":["10.3389\/fcimb.2017.00385"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2017.00385","relation":{},"ISSN":["2235-2988"],"issn-type":[{"type":"electronic","value":"2235-2988"}],"subject":[],"published":{"date-parts":[[2017,8,31]]},"article-number":"385"}}