Chlamydiales – Taxonomy, Pathogenicity, and Zoonotic Potential

Abstract Changes in the taxonomy of the order Chlamydiales, after its separation from the order Rickettsiales, were presented. These changes resulted in the recognition of the following families: Chlamydiaceae, Chlavichlamydiaceae, Criblamydiaceae, Parachlamydiaceae, Piscichlamydiaceae, Rhabdochlamydiaceae, Simkaniaceae, and Waddliaceae. Other described changes concerned particularly the family Chlamydiaceae. Its genus Chlamydia was divided into Chlamydia and Chlamydophila. However, in the following years, a revision to the single original genus was made, based upon phylogenetic analysis of 16S and 23S rRNA genes of the strains belonging to these two taxonomic units. The review also discusses other families outside the family Chlamydiaceae, which contain so-called Chlamydia-related or Chlamydia-like organisms. Members of each family share a 16S rDNA gene sequence similarity >90%. Furthermore, characterisation of the pathogenecity is presented, focusing especially on the representatives of the family Chlamydiaceae, which cause animal infections, and describing their zoonotic potential. Available data on this topic, connected with the representatives of other families, were mentioned.

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Halomicrococcus hydrotolerans gen. nov., sp. nov., an extremely halophilic archaeon isolated from a subterranean salt deposit

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.003534 ◽

2020 ◽

Vol 70 (8) ◽

pp. 4425-4431 ◽

Cited By ~ 6

Author(s):

Shaoxing Chen ◽

Yao Xu ◽

Siqi Sun ◽

Jingwen Liu ◽

Feilong Chen

Keyword(s):

16S Rrna ◽

In Silico ◽

Gene Sequence ◽

Sequence Similarity ◽

Rrna Genes ◽

Salt Deposit ◽

Halophilic Archaeon ◽

Content Type ◽

Link Type ◽

The Family

A halophilic archaeon, strain H22T, was isolated from a subterranean salt deposit sampled at Yunnan salt mine, PR China. Colonies of strain H22T were light pink-pigmented. Cells were coccus, non-motile, Gram-stain-negative, and did not lyse in distilled water. The strain was aerobic and grew at 20–55 °C (optimum, 37 °C), in the presence of 10–30 % (w/v) NaCl (20 %) and at pH 6.5–9.0 (pH 7.0). Mg2+ was required for growth (optimum, 0.005 M). Major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and sulfated mannosyl-glucosyl-glycerol diether-1. Sequence similarity search based on the multiple 16S rRNA genes (rrnA, rrnB and rrnC) of strain H22T revealed that it was most closely related to species of the genera Haloarchaeobius , Haladaptatus , Halorussus and Halorubellus with relative low sequence similarities (91.9–93.7 %). The strain, however, shared highest rpoB′ gene sequence identities with Halorussus rarus TBN4T (90.8 % rpoB′ gene sequence similarity). Phylogenetic trees based on 16S rRNA and rpoB′ gene sequences revealed a robust lineage of the strain H22T with members of related genera of the family Halobacteriaceae . The DNA G+C content of strain H22T was 62.9 mol%. Genome-based analysis of average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) between strains H22T and its closest relative were equal or lower than 77.7 and 22.4 %, respectively, which were far below the threshold for delineation of a new species. Based on ANI values, in silico DDH, and distinct morphological and physiological differences from the previously described taxa, we suggest that strain H22T represents a novel species of a new genus within the family Halobacteriaceae , for which the name Halomicrococcus hydrotolerans gen. nov., sp. nov. is proposed. The type strain is H22T (=CGMCC 1.16291T=NBRC 113231T).

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rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira The GenBank accession numbers of the 16S rDNA gene sequences reported in this paper are AY038032–AY038037.

Microbiology ◽

10.1099/00221287-148-2-481 ◽

2002 ◽

Vol 148 (2) ◽

pp. 481-496 ◽

Cited By ~ 76

Author(s):

Isabelle Iteman ◽

Rosmarie Rippka ◽

Nicole Tandeau de Marsac ◽

Michael Herdman

Keyword(s):

16S Rrna ◽

16S Rdna ◽

Genomic Sequence ◽

Sequence Similarity ◽

16S Rrna Genes ◽

Rrna Genes ◽

23S Rrna ◽

Phylogenetic Position ◽

Rrna Gene ◽

Heterocystous Cyanobacteria

The taxonomic coherence and phylogenetic relationships of 11 planktonic heterocystous cyanobacterial isolates were examined by investigating two areas of the rRNA operon, the 16S rRNA gene (rrnS) and the internal transcribed spacer (ITS) located between the 16S rRNA and 23S rRNA genes. The rrnS sequences were determined for five strains, including representatives of Anabaena flos-aquae, Aphanizomenon flos-aquae, Nodularia sp. and two alkaliphilic planktonic members of the genera Anabaenopsis and Cyanospira, whose phylogenetic position was previously unknown. Comparison of the data with those previously published for individual groups of planktonic heterocystous cyanobacteria showed that, with the exception of members assigned to the genus Cylindrospermopsis, all the planktonic strains form a distinct subclade within the monophyletic clade of heterocystous cyanobacteria. Within this subclade five different phylogenetic clusters were distinguished. The phylogenetic groupings of Anabaena and Aphanizomenon strains within three of these clusters were not always consistent with their generic or specific assignments based on classical morphological definitions, and the high degree of sequence similarity between strains of Anabaenopsis and Cyanospira suggests that they may be assignable to a single genus. Ribotyping and additional studies performed on PCR amplicons of the 16S rDNA or the ITS for the 11 planktonic heterocystous strains demonstrated that they all contain multiple rrn operons and ITS regions of variable size. Finally, evidence is provided for intra-genomic sequence heterogeneity of the 16S rRNA genes within most of the individual isolates.

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Sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.018218-0 ◽

2010 ◽

Vol 60 (11) ◽

pp. 2618-2622 ◽

Cited By ~ 27

Author(s):

De-Chao Zhang ◽

Hong-Can Liu ◽

Yu-Hua Xin ◽

Yu-Guang Zhou ◽

Franz Schinner ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Gene Sequence ◽

Sequence Similarity ◽

Rrna Gene ◽

Aerobic Bacterium ◽

Psychrophilic Bacterium ◽

Phenotypic Characteristics ◽

The Family ◽

Type Strains ◽

Sequence Similarities

Strain BZ30T was isolated from hydrocarbon-contaminated soil. The Gram-negative, aerobic bacterium was psychrophilic and able to grow at temperatures ranging from 1 to 30 °C. The predominant cellular fatty acids of strain BZ30T were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) (37.4 %), C18 : 1 ω7c (19.6 %), C16 : 0 (8.2 %), C14 : 0 2-OH (8.0 %) and C16 : 0 2-OH (5.0 %). The predominant ubiquinone was Q-10. Major polar lipids were sphingoglycolipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Spermidine was the major polyamine. The genomic DNA G+C content was 64.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain BZ30T belonged to the family Sphingomonadaceae of the α-4 group of the phylum Proteobacteria, and was related to the members of the genus Sphingopyxis, sharing the highest sequence similarities with the type strains of Sphingopyxis chilensis (98.3 %), S. witflariensis (98.2 %), S. taejonensis (97.4 %) and S. ginsengisoli (97.2 %). On the basis of the phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain BZ30T represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis bauzanensis is proposed. The type strain is BZ30T (=DSM 22271T =CGMCC 1.8959T =CIP 110136T).

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Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter: Implications for Phylogenetic Inference and Systematics

Journal of Bacteriology ◽

10.1128/jb.187.17.6106-6118.2005 ◽

2005 ◽

Vol 187 (17) ◽

pp. 6106-6118 ◽

Cited By ~ 91

Author(s):

Floyd E. Dewhirst ◽

Zeli Shen ◽

Michael S. Scimeca ◽

Lauren N. Stokes ◽

Tahani Boumenna ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Sequence Data ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

23S Rrna Gene ◽

23S Rrna Genes

ABSTRACT Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31′ and 27′. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.

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Phylogenetic Analysis of the Archaeal Order of Sulfolobales Based on Sequences of 23S rRNA Genes and 16S/23S rDNA Spacers

Systematic and Applied Microbiology ◽

10.1016/s0723-2020(96)80010-5 ◽

1996 ◽

Vol 19 (1) ◽

pp. 61-65 ◽

Cited By ~ 7

Author(s):

Siro I. Trevisanato ◽

Niels Larsen ◽

Andreas H. Segerer ◽

Karl O. Stetter ◽

Roger A. Garrett

Keyword(s):

Phylogenetic Analysis ◽

Rrna Genes ◽

23S Rrna ◽

23S Rrna Genes

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Phylogenetic analysis by 16S rDNA gene sequence comparison of avian taxa of Bisgaard and characterization and description of two new taxa of Pasteurellaceae

Journal of Applied Microbiology ◽

10.1046/j.1365-2672.2003.01986.x ◽

2003 ◽

Vol 95 (2) ◽

pp. 354-363 ◽

Cited By ~ 34

Author(s):

H. Christensen ◽

G. Foster ◽

J.P. Christensen ◽

T. Pennycott ◽

J.E. Olsen ◽

...

Keyword(s):

Phylogenetic Analysis ◽

16S Rdna ◽

New Taxa ◽

Sequence Comparison ◽

Gene Sequence ◽

16S Rdna Gene ◽

Rdna Gene

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Nucleotide sequences of the 23S rRNA genes fromBordetella pertussis, B.parapertussis, B.bronchisepticaandB.avium, and their implications for phylogenetic analysis

Nucleic Acids Research ◽

10.1093/nar/21.14.3320 ◽

1993 ◽

Vol 21 (14) ◽

pp. 3320-3320 ◽

Cited By ~ 22

Author(s):

Michael Müller ◽

Armin Hildebrandt

Keyword(s):

Phylogenetic Analysis ◽

Nucleotide Sequences ◽

Rrna Genes ◽

23S Rrna ◽

23S Rrna Genes

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The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis

Plants ◽

10.3390/plants9121692 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1692

Author(s):

Li Gu ◽

Ting Su ◽

Ming-Tai An ◽

Guo-Xiong Hu

Keyword(s):

Phylogenetic Analysis ◽

Sequence Similarity ◽

Single Copy ◽

Structural Features ◽

Rrna Genes ◽

Trna Genes ◽

Sequencing Data ◽

High Sequence Similarity ◽

Plastid Genomes ◽

Cp Genome

Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.

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