{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T14:40:32Z","timestamp":1791297632998,"version":"4.1.0"},"reference-count":42,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2014,3,1]],"date-time":"2014-03-01T00:00:00Z","timestamp":1393632000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2014,3,1]],"date-time":"2014-03-01T00:00:00Z","timestamp":1393632000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Systematic and Applied Microbiology"],"published-print":{"date-parts":[[2014,3]]},"DOI":"10.1016\/j.syapm.2013.12.004","type":"journal-article","created":{"date-parts":[[2014,1,21]],"date-time":"2014-01-21T23:30:29Z","timestamp":1390347029000},"page":"79-88","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":173,"title":["Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov."],"prefix":"10.1016","volume":"37","author":[{"given":"Konrad","family":"Sachse","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine","family":"Laroucau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Konstantin","family":"Riege","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie","family":"Wehner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meik","family":"Dilcher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather Huot","family":"Creasy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manfred","family":"Weidmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garry","family":"Myers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabien","family":"Vorimore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadia","family":"Vicari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone","family":"Magnino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Liebler-Tenorio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anke","family":"Ruettger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrik M.","family":"Bavoil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank T.","family":"Hufert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramon","family":"Rossell\u00f3-M\u00f3ra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manja","family":"Marz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.syapm.2013.12.004_bib0005","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1111\/2049-632X.12026","article-title":"In Chlamydia veritas","volume":"67","author":"Bavoil","year":"2013","journal-title":"Pathog. Dis."},{"key":"10.1016\/j.syapm.2013.12.004_bib0010","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0015","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0378-1135(00)00213-3","article-title":"Chlamydia and Chlamydiales: more than meets the eye","volume":"75","author":"Everett","year":"2000","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0020","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1099\/00207713-49-2-415","volume":"49","author":"Everett","year":"1999","journal-title":"Int. J. Syst. Bacteriol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0025","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1099\/00207713-42-2-306","article-title":"Proposal of Chlamydia pecorum sp. nov. for Chlamydia strains derived from ruminants","volume":"42","author":"Fukushi","year":"1992","journal-title":"Int. J. Syst. Bacteriol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0030","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1111\/j.1863-2378.2008.01108.x","article-title":"Chlamydophila psittaci infections in humans during an outbreak of psittacosis from poultry in Germany","volume":"55","author":"Gaede","year":"2008","journal-title":"Zoonoses Public Health"},{"key":"10.1016\/j.syapm.2013.12.004_bib0035","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkq1129","article-title":"Rfam: wikipedia, clans and the decimal release","volume":"39","author":"Gardner","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.syapm.2013.12.004_bib0040","doi-asserted-by":"crossref","first-page":"3186","DOI":"10.1111\/j.1462-2920.2011.02575.x","article-title":"Impact of urban environment and host phenotype on the epidemiology of Chlamydiaceae in feral pigeons (Columba livia)","volume":"13","author":"Gasparini","year":"2011","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0045","doi-asserted-by":"crossref","first-page":"4801","DOI":"10.1128\/IAI.01487-05","article-title":"Transcriptional response patterns of Chlamydophila psittaci in different in vitro models of persistent infection","volume":"74","author":"Goellner","year":"2006","journal-title":"Infect. Immun."},{"key":"10.1016\/j.syapm.2013.12.004_bib0050","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1378\/chest.95.3.664","article-title":"Chlamydia pneumoniae, strain TWAR","volume":"95","author":"Grayston","year":"1989","journal-title":"Chest"},{"key":"10.1016\/j.syapm.2013.12.004_bib0055","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1111\/j.1469-0691.2008.02633.x","article-title":"Parachlamydia acanthamoebae, an emerging agent of pneumonia","volume":"15","author":"Greub","year":"2009","journal-title":"Clin. Microbiol. Infect."},{"key":"10.1016\/j.syapm.2013.12.004_bib0060","doi-asserted-by":"crossref","first-page":"2691","DOI":"10.1099\/ijs.0.028225-0","article-title":"Subcommittee on the taxonomy of the Chlamydiae: minutes of the inaugural closed meeting, 21 March 2009, Little Rock, AR, USA","volume":"60","author":"Greub","year":"2010","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0065","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1093\/bioinformatics\/btn364","article-title":"EPoS: a modular software framework for phylogenetic analysis","volume":"24","author":"Griebel","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/j.syapm.2013.12.004_bib0070","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1038\/nature07578","article-title":"Chlamydia causes fragmentation of the Golgi compartment to ensure reproduction","volume":"457","author":"Heuer","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.syapm.2013.12.004_bib0075","first-page":"843","article-title":"Phylum XXIV. Chlamydiae Garrity and Holt 2001","volume":"vol. 4","author":"Horn","year":"2011"},{"key":"10.1016\/j.syapm.2013.12.004_bib0080","first-page":"22","article-title":"Improvement in the accuracy of multiple sequence alignment program MAFFT","volume":"16","author":"Katoh","year":"2005","journal-title":"Genome Inform."},{"key":"10.1016\/j.syapm.2013.12.004_bib0085","first-page":"392","article-title":"Efficacy of doxycyclin for chlamydioses in pigeon flocks","volume":"41","author":"Krautwald-Junghanns","year":"2013","journal-title":"Tierarztl. Prax. Ausg. K Kleintiere Heimtiere"},{"key":"10.1016\/j.syapm.2013.12.004_bib0090","first-page":"846","article-title":"Genus Chlamydia Jones, Rake and Stearns 1945, 55","volume":"vol. 4","author":"Kuo","year":"2011"},{"key":"10.1016\/j.syapm.2013.12.004_bib0095","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.syapm.2013.12.004_bib0100","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and clustal X version 2.0","volume":"23","author":"Larkin","year":"2007","journal-title":"Bioinformatics"},{"key":"10.1016\/j.syapm.2013.12.004_bib0105","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.vetmic.2008.09.048","article-title":"Chlamydial infections in duck farms associated with human cases of psittacosis in France","volume":"135","author":"Laroucau","year":"2009","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0110","doi-asserted-by":"crossref","first-page":"1240","DOI":"10.1016\/j.meegid.2009.08.005","article-title":"Isolation of a new chlamydial agent from infected domestic poultry coincided with cases of atypical pneumonia among slaughterhouse workers in France","volume":"9","author":"Laroucau","year":"2009","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0115","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.syapm.2013.12.004_bib0120","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1093\/nar\/gkh293","article-title":"ARB: a software environment for sequence data","volume":"32","author":"Ludwig","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.syapm.2013.12.004_bib0125","first-page":"356","article-title":"Morphological studies of the association of mitochondria with chlamydial inclusions and the fusion of chlamydial inclusions","volume":"40","author":"Matsumoto","year":"1991","journal-title":"J. Electron. Microsc. (Tokyo)"},{"key":"10.1016\/j.syapm.2013.12.004_bib0130","doi-asserted-by":"crossref","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":"Bioinformatics"},{"key":"10.1016\/j.syapm.2013.12.004_bib0135","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1099\/00207713-16-2-223","article-title":"Revision of the family Chlamydiaceae Rake (Rickettsiales): unification of the psittacosis-lymphogranuloma venereum-trachoma group of organisms in the genus Chlamydia Jones, Rahe and Stearns 1945","volume":"16","author":"Page","year":"1966","journal-title":"Int. J. Syst. Bacteriol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0140","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1099\/00207713-18-1-51","article-title":"Proposal for the recognition of two species in the genus Chlamydia Jones, Rake and Stearns 1945","volume":"18","author":"Page","year":"1968","journal-title":"Int. J. Syst. Bacteriol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0145","doi-asserted-by":"crossref","first-page":"e14179","DOI":"10.1371\/journal.pone.0014179","article-title":"Multi locus sequence typing of Chlamydia reveals an association between Chlamydia psittaci genotypes and host species","volume":"5","author":"Pannekoek","year":"2010","journal-title":"PLoS ONE"},{"key":"10.1016\/j.syapm.2013.12.004_bib0150","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/1471-2180-8-42","article-title":"Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis","volume":"8","author":"Pannekoek","year":"2008","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0155","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1099\/00207713-47-2-425","article-title":"Phylogenetic analysis of the genus Chlamydia based on 16S rRNA gene sequences","volume":"47","author":"Pudjiatmoko Fukushi","year":"1997","journal-title":"Int. J. Syst. Bacteriol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0160","doi-asserted-by":"crossref","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.syapm.2013.12.004_bib0165","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/j.vetmic.2010.04.007","article-title":"Identification of chlamydial species in crocodiles and chickens by PCR-HRM curve analysis","volume":"145","author":"Robertson","year":"2010","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0170","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/j.vetmic.2012.01.002","article-title":"More than classical Chlamydia psittaci in urban pigeons","volume":"157","author":"Sachse","year":"2012","journal-title":"Vet. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0175","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1186\/1471-2180-8-63","article-title":"Genotyping of Chlamydophila psittaci using a new DNA microarray assay based on sequence analysis of ompA genes","volume":"8","author":"Sachse","year":"2008","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0180","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/0923-2508(96)80893-X","article-title":"Usefulness of omp1 restriction mapping for avian Chlamydia psittaci isolate differentiation","volume":"146","author":"Sayada","year":"1995","journal-title":"Res. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0185","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"Stamatakis","year":"2006","journal-title":"Bioinformatics"},{"key":"10.1016\/j.syapm.2013.12.004_bib0190","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1111\/j.1574-695X.2008.00516.x","article-title":"Divergence without difference: phylogenetics and taxonomy of Chlamydia resolved","volume":"55","author":"Stephens","year":"2009","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0215","doi-asserted-by":"crossref","first-page":"e74823","DOI":"10.1371\/journal.pone.0074823","article-title":"Isolation of a new Chlamydia species from the feral sacred ibis (Threskiornis aethiopicus): Chlamydia ibidis","author":"Vorimore","year":"2013","journal-title":"PLoS One 8"},{"key":"10.1016\/j.syapm.2013.12.004_bib0200","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.syapm.2012.12.006","article-title":"Sequencing orphan species initiative (SOS): filling the gaps in the 16S rRNA gene sequence database for all species with validly published names","volume":"36","author":"Yarza","year":"2013","journal-title":"Syst. Appl. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0205","doi-asserted-by":"crossref","first-page":"2212","DOI":"10.1111\/j.1462-2920.2012.02800.x","article-title":"Molecular characterization of atypical Chlamydia and evidence of their dissemination in different European and Asian chicken flocks by specific real-time PCR","volume":"14","author":"Zocevic","year":"2012","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.syapm.2013.12.004_bib0210","doi-asserted-by":"crossref","first-page":"e58741","DOI":"10.1371\/journal.pone.0058741","article-title":"A real-time PCR assay for the detection of atypical strains of Chlamydiaceae from pigeons","volume":"8","author":"Zocevic","year":"2013","journal-title":"PLoS ONE"}],"container-title":["Systematic and Applied Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0723202013001951?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0723202013001951?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T08:08:02Z","timestamp":1759997282000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0723202013001951"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,3]]},"references-count":42,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2014,3]]}},"alternative-id":["S0723202013001951"],"URL":"https:\/\/doi.org\/10.1016\/j.syapm.2013.12.004","relation":{},"ISSN":["0723-2020"],"issn-type":[{"value":"0723-2020","type":"print"}],"subject":[],"published":{"date-parts":[[2014,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov.","name":"articletitle","label":"Article Title"},{"value":"Systematic and Applied Microbiology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.syapm.2013.12.004","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2014 Elsevier GmbH. All rights reserved.","name":"copyright","label":"Copyright"}]}}