Molecular studies have revealed considerably more diversity in the phylum Chlamydiae than was previously thought. A significant barrier to characterising these novel chlamydiae is the requirement for culturing. We recently identified a range of novel uncultured chlamydiae in captive snakes in Switzerland, however, nothing is known about their biology.
Using a metagenomics approach, the aim of this study was characterise the genome of a novel chlamydial species (Uncultured Chlamydia sp. 2742-308) from a captive snake, to expand our knowledge of the additional diversity and biology of the genus Chlamydia.
Total genomic DNA extracted from a choana swab from a captive snake underwent host methylated DNA depletion. The selectively enriched DNA was then subjected to multiple displacement amplification. Whole genome sequencing was carried out on the resulting enriched DNA sample on an Illumina MiSeq using 150 bp paired-end reads. Reads were filtered using Trimmomatic prior to de novo assembly using SPAdes. BLASTx analysis was conducted to identify chlamydial contigs. Automated and manual annotation was carried out using RAST and Artemis, respectively. Phylogenetic relationships were assessed based on concatenation of 40 conserved proteins.
We identified two genomic contigs: a 1,113,133 bp contig, and a 7,504 bp contig, representing the chromosome and plasmid of Chlamydia sp. 2742-308, respectively. The 998 predicted coding regions include an expanded repertoire of outer membrane proteins (pmps and omps), some of which exhibited frameshift mutations, as well as several chlamydial virulence factors such as Tarp and mip. Notably, no evidence of a traditional chlamydial plasticity zone was identified. Phylogenetically, Chlamydia sp. 2742-308 forms a clade with C. pneumoniae and C. pecorum, distinct from former Chlamydophila spp.
Genomic characterisation of a novel uncultured chlamydiae from a reptilian host has expanded our understanding of the diversity and biology of a genus that was thought to be the most well-characterised in this unique phylum. It is anticipated that this method will be suitable for characterisation of other novel chlamydiae.