Abstract
Advances in culture-independent methods have meant that we can more readily detect and diagnose emerging infectious disease threats in humans and animals. 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 Chlamydiae that require labour-intensive culturing. We have used this tool to investigate the microbial metagenomes of Chlamydia-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, Ca. 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 Ca. C. corallus and two putative novel species in the genus Chlamydia. 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 Chlamydiae.
Highlights
Recent advances in culture-independent molecular methods and diagnostics, coupled with an increased breadth and depth of sampling, have played a significant role in detecting emerging disease threats in humans and animals[1,2,3,4]
This species is closely related to Chlamydia pneumoniae and its genome encodes several chlamydial virulence markers such as a type three secretion system, translocated actin-recruiting phosphoprotein (Tarp) and chlamydial protease-like activity factor (CPAF)[8]
We showed that metagenomics analysis is useful for novel chlamydial species discovery but that it reveals key genomic differences between a novel chlamydial taxon and established species
Summary
Most abundant bacterial Serratia marcescens taxon (coverage of 16S (~125x) rRNA sequence) (Phylum) (Proteobacteria). We showed that metagenomics analysis is useful for novel chlamydial species discovery but that it reveals key genomic differences between a novel chlamydial taxon and established species
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