The untold diversity of chlamydiae was first revealed in 1990s when a chlamydia-like bacteria was recognized with free-living amoeba as endosymbiont. Since then, they have been considered as novel members of the order Chlamydiales. This discovery led to the reorganization of the chlamydial taxonomy as three new families were added (Collingro et al. Initially, the phylum Chlamydiae is composed of a single class which is Chlamydiae which is composed of the order Chlamydiales. With the addition of the three new families, this order is now composed of four families including the Chlamydiaceae, which contains all of the traditional chlamydiae species and the novel chlamydia species (Griffiths et al. These novel chlamydiae were proposed to be classified as Parachlamydiaceae, Simkaniaceae and Waddliaceae (Collingro et al.Since chlamydia-like species are found mostly in non-culturable sources, it is difficult to obtain information regarding it sequences. The only way to do so however, is through PCR amplification using primers based on 16S rRNA sequences and the clustering of any amplified sequence with the known chlamydiae species in the rRNA trees (Griffiths, 2005). To assign the symbionts to their evolutionary lineages, the application of the full cycle rRNA approach which included 16S rRNA sequencing and fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes was used (Horn et al. Fritsche et al. (2000) however used neighbor-joining, parsimony and distance matrix methods in analyzing the 16S rRNA gene sequences of acanthamoeba isolates with their aim to uncover the diversity of Chlamydiales. They further used fluorescently labeled oligonucleotide probes to target 16S rRNA to differentiate the two groups of intra-amoebal endosymbionts.Studies have shown that at some point in the evolutionary history, the Chlamydiales diverged which resulted to the present families. In spite of this divergence, all families under order Chlamydiales share common characteristics. The 16S rRNA of all families is about 80 to 90% related to each other. Except for endosymbionts of Parachlamydiaceae, all are obligate intracellular parasites. Only the elementary bodies of Parachlamydia acanthamoeba retain the Gram stain which may be explained by the thick cell envelopes. All the rest are Gram-negative. Pelomorphism is another distinct
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