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Metagenomics is fast becoming a popular tool for detection and characterisation of novel bacterial pathogens in their environment, and is particularly useful for obligate intracellular bacteria such as <jats:italic>Chlamydiae<\/jats:italic> that require labour-intensive culturing. We have used this tool to investigate the microbial metagenomes of <jats:italic>Chlamydia<\/jats:italic>-positive cloaca and choana samples from snakes. The microbial complexity within these anatomical sites meant that despite previous detection of chlamydial 16S rRNA sequences by single-gene broad-range PCR, only a chlamydial plasmid could be detected in all samples, and a chlamydial chromosome in one sample. Comparative genomic analysis of the latter revealed it represented a novel taxon, <jats:italic>Ca<\/jats:italic>. Chlamydia corallus, with genetic differences in regards to purine and pyrimidine metabolism. Utilising statistical methods to relate plasmid phylogeny to the phylogeny of chromosomal sequences showed that the samples also contain additional novel strains of <jats:italic>Ca<\/jats:italic>. C. corallus and two putative novel species in the genus <jats:italic>Chlamydia<\/jats:italic>. This study highlights the value of metagenomics methods for rapid novel bacterial discovery and the insights it can provide into the biology of uncultivable intracellular bacteria such as <jats:italic>Chlamydiae<\/jats:italic>.<\/jats:p>","DOI":"10.1038\/s41598-017-10757-5","type":"journal-article","created":{"date-parts":[[2017,8,31]],"date-time":"2017-08-31T11:01:52Z","timestamp":1504177312000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":58,"title":["Culture-independent metagenomics supports discovery of uncultivable bacteria within the genus Chlamydia"],"prefix":"10.1038","volume":"7","author":[{"given":"Alyce","family":"Taylor-Brown","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Labolina","family":"Spang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Borel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Polkinghorne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,9,6]]},"reference":[{"issue":"81","key":"10757_CR1","doi-asserted-by":"publisher","DOI":"10.1186\/gm485","volume":"5","author":"RR Miller","year":"2013","unstructured":"Miller, R. 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