Sequencing of the genome of a new Rhabdochlamydia species from tick samples

The Rhabdochlamydiaceae is one of the most widely distributed families of the order Chlamydiales. A recent study of the prevalence of Chlamydiae in ticks in Switzerland reported the presence of Rhabdochlamydia 16S ribosomal sequences in more than 2% of the 8534 analyzed pools of ticks. Nevertheless, Rhabdochlamydia remains uncultivated and poorly studied. To investigate the evolution and biology of Chlamydiae in ticks, shotgun metagenomics was performed on a pool of ticks presenting a high concentration of bacterial DNA and more than 97% of 16S rRNA identity to the cockroach parasite Rhabdochlamydia crassificans. Read assembly with different software yielded consistent contigs that likely belong to a single Rhabdochlamydia spp. present in one of the ticks. This Rhabdochlamydia spp. exhibits a smaller genome (1.8Mbp) as compared to other Chlamydia-related bacteria, with reduced metabolic capabilities but numerous parasitic transporters and a coding density similar to the compact Chlamydiaceae genomes. Detailed comparative analyses of representative genomes of six families belonging to the Chlamydiales order highlighted important variations in energy metabolism, with some lineages exhibiting evidences of ongoing genome decay.