{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T14:33:23Z","timestamp":1772202803514,"version":"3.50.1"},"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2018,3,26]],"date-time":"2018-03-26T00:00:00Z","timestamp":1522022400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008190","name":"Holsworth Wildlife Research Endowment","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008190","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0194881","type":"journal-article","created":{"date-parts":[[2018,3,26]],"date-time":"2018-03-26T13:39:18Z","timestamp":1522071558000},"page":"e0194881","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without \u2018wet bottom\u2019"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2407-4496","authenticated-orcid":true,"given":"Alistair R.","family":"Legione","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jemima","family":"Amery-Gale","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Lynch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leesa","family":"Haynes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James R.","family":"Gilkerson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fiona M.","family":"Sansom","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanne M.","family":"Devlin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,3,26]]},"reference":[{"key":"ref1","unstructured":"Dickens RK, editor The koala in health and disease. Refresher Course for Veterinarians Proceedings No 29; 1976 22\u201323 June 1976; Taronga Zoo: The University of Sydney, New South Wales, Australia; 1976."},{"issue":"12","key":"ref2","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1111\/j.1751-0813.1984.tb07182.x","article-title":"Isolation of <italic>Chlamydia<\/italic> psittaci from koalas (<italic>Phascolarctos cinereus<\/italic>)","volume":"61","author":"AS Brown","year":"1984","journal-title":"Aust Vet J"},{"issue":"3\u20134","key":"ref3","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1016\/j.vetmic.2006.11.022","article-title":"Use of quantitative real-time PCR to monitor the shedding and treatment of <italic>Chlamydiae<\/italic> in the koala (<italic>Phascolarctos cinereus<\/italic>)","volume":"120","author":"B Markey","year":"2007","journal-title":"Vet Microbiol"},{"issue":"5","key":"ref4","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1111\/avj.12167","article-title":"Validation of ultrasonography in detecting structural disease of the urogenital tract of the koala, <italic>Phascolarctos cinereus<\/italic>","volume":"92","author":"C Marschner","year":"2014","journal-title":"Aust Vet J"},{"issue":"11","key":"ref5","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1111\/j.1751-0813.1987.tb06064.x","article-title":"Chlamydial disease in koalas","volume":"64","author":"AS Brown","year":"1987","journal-title":"Aust Vet J"},{"issue":"2","key":"ref6","doi-asserted-by":"crossref","first-page":"309","DOI":"10.7589\/2014-07-176","article-title":"The prevalence and clinical significance of <italic>Chlamydia<\/italic> infection in island and mainland populations of Victorian koalas (<italic>Phascolarctos cinereus<\/italic>)","volume":"51","author":"JLS Patterson","year":"2015","journal-title":"J Wildl Dis"},{"key":"ref7","article-title":"The koala: natural history, conservation and management","author":"RW Martin","year":"1999"},{"issue":"5","key":"ref8","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1099\/jmm.0.000241","article-title":"Identification of unusual <italic>Chlamydia pecorum<\/italic> genotypes in Victorian koalas (<italic>Phascolarctos cinereus<\/italic>) and clinical variables associated with infection","volume":"65","author":"AR Legione","year":"2016","journal-title":"J Med Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"5239","DOI":"10.1038\/s41598-017-05454-2","article-title":"Microbiota composition of the koala (<italic>Phascolarctos cinereus<\/italic>) ocular and urogenital sites, and their association with <italic>Chlamydia<\/italic> infection and disease","volume":"7","author":"ME Vidgen","year":"2017","journal-title":"Sci Rep"},{"key":"ref10","article-title":"Australian code for the care and use of animals for scientific purposes","year":"2013"},{"key":"ref11","unstructured":"Griffith JE. Studies into the diagnosis, treatment and management of chlamydiosis in koalas [PhD Thesis]. New South Wales, Australia: The University of Sydney; 2010."},{"issue":"6","key":"ref12","doi-asserted-by":"crossref","first-page":"2017","DOI":"10.1111\/j.1365-2672.2009.04388.x","article-title":"Characterization of <italic>Chlamydiaceae<\/italic> species using PCR and high resolution melt curve analysis of the 16S rRNA gene","volume":"107","author":"T Robertson","year":"2009","journal-title":"J Appl Microbiol"},{"issue":"2","key":"ref13","doi-asserted-by":"crossref","first-page":"426","DOI":"10.7589\/2015-10-276","article-title":"<italic>Chlamydia pecorum<\/italic> infection in free-ranging koalas (<italic>Phascolarctos cinereus<\/italic>) on French Island, Victoria, Australia","volume":"52","author":"AR Legione","year":"2016","journal-title":"J Wildl Dis"},{"issue":"5","key":"ref14","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"JG Caporaso","year":"2010","journal-title":"Nat Methods"},{"issue":"7","key":"ref15","doi-asserted-by":"crossref","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","volume":"72","author":"TZ DeSantis","year":"2006","journal-title":"Appl Environ Microbiol"},{"issue":"6","key":"ref16","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1002\/bit.20347","article-title":"Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction","volume":"89","author":"Y Yu","year":"2005","journal-title":"Biotechnol Bioeng"},{"key":"ref17","unstructured":"Illumina. 16S Metagenomic Sequencing Library Preparation 2013 [05\/11\/2015]. support.illumina.com\/downloads\/16s_metagenomic_sequencing_library_preparation.html."},{"issue":"19","key":"ref18","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"RC Edgar","year":"2010","journal-title":"Bioinformatics"},{"issue":"21","key":"ref19","doi-asserted-by":"crossref","first-page":"3476","DOI":"10.1093\/bioinformatics\/btv401","article-title":"Error filtering, pair assembly and error correction for next-generation sequencing reads","volume":"31","author":"RC Edgar","year":"2015","journal-title":"Bioinformatics"},{"issue":"10","key":"ref20","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"RC Edgar","year":"2013","journal-title":"Nat Methods"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"issue":"4","key":"ref22","doi-asserted-by":"crossref","first-page":"e1003531","DOI":"10.1371\/journal.pcbi.1003531","article-title":"Waste not, want not: why rarefying microbiome data is inadmissible","volume":"10","author":"PJ McMurdie","year":"2014","journal-title":"PLoS Comp Biol"},{"issue":"4","key":"ref23","first-page":"265","article-title":"Nonparametric estimation of the number of classes in a population","volume":"11","author":"A Chao","year":"1984","journal-title":"Scand J Stat"},{"issue":"1","key":"ref24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0006-3207(92)91201-3","article-title":"Conservation evaluation and phylogenetic diversity","volume":"61","author":"DP Faith","year":"1992","journal-title":"Biol Conserv"},{"issue":"3","key":"ref25","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"CE Shannon","year":"1948","journal-title":"Bell Syst Tech J"},{"issue":"12","key":"ref26","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"C Lozupone","year":"2005","journal-title":"Appl Environ Microbiol"},{"issue":"4","key":"ref27","doi-asserted-by":"crossref","first-page":"325","DOI":"10.2307\/1942268","article-title":"An ordination of the upland forest communities of southern Wisconsin","volume":"27","author":"JR Bray","year":"1957","journal-title":"Ecol Monogr"},{"issue":"2","key":"ref28","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1093\/bioinformatics\/btp636","article-title":"PyNAST: a flexible tool for aligning sequences to a template alignment","volume":"26","author":"JG Caporaso","year":"2010","journal-title":"Bioinformatics"},{"issue":"7","key":"ref29","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/molbev\/msp077","article-title":"FastTree: computing large minimum evolution trees with profiles instead of a distance matrix","volume":"26","author":"MN Price","year":"2009","journal-title":"Mol Biol Evol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/2047-217X-2-16","article-title":"EMPeror: a tool for visualizing high-throughput microbial community data","volume":"2","author":"Y V\u00e1zquez-Baeza","year":"2013","journal-title":"GigaScience"},{"issue":"1","key":"ref31","first-page":"32","article-title":"A new method for non-parametric multivariate analysis of variance","volume":"26","author":"MJ Anderson","year":"2001","journal-title":"Austral Ecol"},{"issue":"1","key":"ref32","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J Roy Stat Soc Ser B (Stat Method)"},{"issue":"Database issue","key":"ref33","doi-asserted-by":"crossref","first-page":"D67","DOI":"10.1093\/nar\/gkv1276","article-title":"GenBank","volume":"44","author":"K Clark","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"16","key":"ref34","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1093\/bioinformatics\/btn322","article-title":"Database indexing for production MegaBLAST searches","volume":"24","author":"A Morgulis","year":"2008","journal-title":"Bioinformatics"},{"issue":"3\u20134","key":"ref35","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/j.vetmic.2013.08.025","article-title":"Investigation of the koala (<italic>Phascolarctos cinereus<\/italic>) hindgut microbiome via 16S pyrosequencing","volume":"167","author":"CJ Barker","year":"2013","journal-title":"Vet Microbiol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"10189","DOI":"10.1038\/srep10189","article-title":"Variation in koala microbiomes within and between individuals: effect of body region and captivity status","volume":"5","author":"N Alfano","year":"2015","journal-title":"Sci Rep"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1099\/00207713-51-4-1521","article-title":"Proposal of the genera <italic>Anaerococcus<\/italic> gen. nov., <italic>Peptoniphilus<\/italic> gen. nov. and <italic>Gallicola<\/italic> gen. nov. for members of the genus <italic>Peptostreptococcus<\/italic>","volume":"51","author":"T Ezaki","year":"2001","journal-title":"Int J Syst Evol Microbiol"},{"issue":"4","key":"ref38","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/0378-1135(90)90018-Q","article-title":"Summer mastitis in heifers: a bacteriological examination of secretions from clinical cases of summer mastitis in Denmark","volume":"22","author":"M Madsen","year":"1990","journal-title":"Vet Microbiol"},{"issue":"2","key":"ref39","first-page":"161","article-title":"The bacterial pathogenesis of acute pelvic inflammatory disease","volume":"52","author":"FG Cunningham","year":"1978","journal-title":"Obstet Gynecol"},{"issue":"2","key":"ref40","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/ismej.2007.12","article-title":"Differences in the composition of vaginal microbial communities found in healthy caucasian and black women","volume":"1","author":"X Zhou","year":"2007","journal-title":"ISME J"},{"issue":"2","key":"ref41","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1099\/jmm.0.000416","article-title":"Koala retrovirus genotyping analyses reveal a low prevalence of KoRV-A in Victorian koalas and an association with clinical disease","volume":"66","author":"AR Legione","year":"2017","journal-title":"J Med Microbiol"},{"issue":"Supplement 1","key":"ref42","doi-asserted-by":"crossref","first-page":"4680","DOI":"10.1073\/pnas.1002611107","article-title":"Vaginal microbiome of reproductive-age women","volume":"108","author":"J Ravel","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"R79","DOI":"10.1186\/gb-2012-13-9-r79","article-title":"Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment","volume":"13","author":"XC Morgan","year":"2012","journal-title":"Genome Biol"},{"issue":"5","key":"ref44","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1099\/mic.0.2007\/014803-0","article-title":"The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, <italic>Macropus eugenii<\/italic>","volume":"154","author":"K-L Chhour","year":"2008","journal-title":"Microbiology"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0194881","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T05:56:12Z","timestamp":1719899772000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0194881"}},"subtitle":[],"editor":[{"given":"Ashlesh K","family":"Murthy","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,3,26]]},"references-count":44,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2018,3,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0194881","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/099945","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,3,26]]}}}