Parachlamydia acanthamoebae are bacterium that fall into the category of host-associated microorganisms. This bacterium lives within free-living amoebae that are an intricate part of their reproduction. Originally named Candidatus Parachlamydia acanthamoebae, its current scientific name was introduced shortly after. This species has shown to have over eighty percent 16S rRNA gene sequencing identity with the class Chlamydiia. Parachlamydia acanthamoebae has the same family as the genus Neochlamydia with which it shares many similarities.
Discovery The isolation of Parachlamydia acanthamoebae is credited to Rolf Michel and Bärbel Hauröder-Philippczyk in Berlin in 1994. Using a nasal swab from volunteers, they were able to isolate coccoid-shaped bacteria that were present among other naturally-produced organisms. Although at least ten subsequent attempts at reisolation were tried, P. acanthamoebae was not isolated again until 1997 when the researchers Rudolf Amann, Nina Springer, and Wolfgang Ludwig isolated it with a strain of Acanthamoeba species. This sample was transferred to a non-nutrient agar plate and the parasitized trophozoite of the Acanthamoeba species multiplied. A trophozoite is an active stage in the Acanthamoeba species life cycle in which the protozoan grows and feeds. The researchers were able to isolate the infected trophozoites by this method only once, as subsequent tries were unsuccessful. The researchers then took small aliquots of the organism and filtered it to ensure the sample was pure. After running these samples through a centrifuge, a machine with a rapid rotating inner container, the samples were used to directly amplify the 16S rRNA gene to form a nearly full-length rRNA sequence by Polymerase Chain Reaction. The ribosomal DNA was sequenced using the T7 sequencing kit of Pharmacia. After analyzing the genome and confirming 86% 16S rRNA gene sequence identity to members of the genus Chlamydia, they proposed Parachlamydia acanthamoebae be classified under the order of Chlamydiales.
Phylogeny Amann et al. used a number of methods to analyze the phylogeny of Parachlamydia acanthamoebae. They were able to amplify rRNA fragments that covered almost all of the rRNA operon using PCR. A distance matrix was used to compare the attained 16S and 23S rRNA sequences with the 16S rRNA with other bacteria in the Chlamydia family as well as other bacteria from known phyla. The ARB Project and the FastDNAml tool were used to perform maximum parsimony and maximum likelihood analyses. The maximum likelihood analysis was performed by comparing the rRNA sequence from Parachlamydia acanthamoebae to rRNA sequences from the entire ARB Project database. The maximum likelihood analysis compared the P. acanthamoebae rRNA sequences with the same bacteria used in the distance matrix. Their analyses showed that P. acanthamoebae has an 86 to 87% sequence similarity with bacteria in the Chlamydia genus. It had a sequence similarity of 70 to 75% when compared to bacteria from other phyla in the same domain. From this information, they proposed that the bacteria are likely a novel member of a genus in the family Chlamydiaceae. Everett et al. set out to determine the characteristics that specifically distinguish all the families in the order Chlamydiales, and in doing so proposed that the formation of the family Parachlamydiaceae. They used Sequencher data analysis tools to accumulate 23S rRNA gene sequences from bacteria in all of the families within Chlamydiales. Sequence information for the 16S rRNA genes of these bacteria was collected from GenBank. They used the Clustal W program to align all of the 16S and 23S data that was collected. PAUP version 4.0 was used to create maximum parsimony and neighbor-joining phylogenetic trees. They found that P. acanthamoebae has a 16S rRNA sequence that is 15% different and a 23S rRNA sequence that is 17% different from members of the family Chlamydiaceae. From this, they proposed the formation of a new family, Parachlamydiaceae, where P. acanthamoebae is currently classified under.
Genomic information Greub et al. states that although there was a previous attempt to sequence the genome of P. acanthamoebae, the absence of a bridge element that helps with the assembly of the sequence and the repair of gaps made it difficult for researchers to completely sequence its genome. Pyrosequencing using the GS20 method and Solatex technology sequenced 1.6 Mbp of raw reads that each contained 36 bp, which were assembled into 95 contigs using GS20 reads. These reads were assembled in 8616 overlapping sequences that helped to further develop the genome. Through comparative genomics with the family Chlamydiaceae and the species Protochlamydia amoebophilia, a GC content of 35-36% and an approximate genome size of 2.4-3 Mbp were concluded. Further analysis of the genome of P. acanthamoebae shows that this bacterium has genes that encode a chemotaxis system that is similar to the system found in Escherichia coli. No other bacteria in Chlamydiales have been found to encode for a system similar to the one present in P. acanthamoebae. This chemotaxis system encodes for at least 15 proteins. Collingro et al. believe this system to be functional, as they found no mutations in the gene sequences for these proteins. The specific role of this chemotaxis system in P. acanthamoebae is unclear, however, since this bacterium is non-motile.
Physiology Parachlamydia acanthamoebae is widely distributed in nature, being found in aquatic as well as terrestrial environments. Due to this organism's symbiotic relationship with Acanthamoeba, it has the ability to survive a wide array of environmental stresses. It is a coccoid bacterium with a diameter of 0.5 um that has a variable reaction to gram staining. It is a mesophilic bacteria that can be grown on Vero cells.
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