Taxonomy of the canine Mollicutes by 16S rRNA gene and 16S/23S rRNA intergenic spacer region sequence comparison.
01 Mar 2004-International Journal of Systematic and Evolutionary Microbiology (Microbiology Society)-Vol. 54, Iss: 2, pp 537-542
TL;DR: The taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S r RNA intergenic spacer (IGS) region sequences, and the two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published myCoplasma 16S sRNA gene sequences.
Abstract: The taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S rRNA intergenic spacer (IGS) region sequences. The nucleotide sequences of the 16S rRNA gene of two untyped mycoplasmas and the IGS region of 11 Mycoplasma species were determined and used for phylogenetic analysis. The two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published mycoplasma 16S rRNA gene sequences.
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TL;DR: The development of a new diagnostic test based on PCR of the 16S rRNA gene with Mycoplasma-specific primers and separation of the PCR product according to primary sequence using denaturing gradient gel electrophoresis (DGGE).
Abstract: Diagnosis of Mycoplasma infection is normally based on culture and serological tests, which can be time-consuming and laborious. A number of specific PCRs have been developed but to date there has not been a single generic test capable of detecting and differentiating mycoplasmas to a species level. This report describes the development of a new diagnostic test based on PCR of the 16S rRNA gene with Mycoplasma-specific primers and separation of the PCR product according to primary sequence using denaturing gradient gel electrophoresis (DGGE). DGGE enabled the differentiation of 67 Mycoplasma species of human and veterinary origin and represents a significant improvement on current tests as diagnosis of Mycoplasma infection can be made directly from clinical samples in less than 24 h.
161 citations
Cites methods or result from "Taxonomy of the canine Mollicutes b..."
...This is not unexpected as previous analysis of full-length 16S sequences and 16S– 23S IGS sequences found that the species are highly similar (Chalker & Brownlie, 2004)....
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...Interestingly,M. cynos could be differentiated from all other canine Mycoplasma species whereas previous studies based on sequence analysis have shown it grouped closely with M. canis and M. edwardii (Chalker & Brownlie, 2004)....
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TL;DR: Revised standards for novel species of the class Mollicutes are proposed that reflect recent advances in molecular systematics and the species concept for prokaryotes.
Abstract: Minimal standards for novel species of the class Mollicutes (trivial term, mollicutes), last published in 1995, require revision. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes proposes herein revised standards that reflect recent advances in molecular systematics and the species concept for prokaryotes. The mandatory requirements are: (i) deposition of the type strain into two recognized culture collections, preferably located in different countries; (ii) deposition of the 16S rRNA gene sequence into a public database, and a phylogenetic analysis of the relationships among the 16S rRNA gene sequences of the novel species and its neighbours; (iii) deposition of antiserum against the type strain into a recognized collection; (iv) demonstration, by using the combination of 16S rRNA gene sequence analyses, serological analyses and supplementary phenotypic data, that the type strain differs significantly from all previously named species; and (v) assignment to an order, a family and a genus in the class, with an appropriate specific epithet. The 16S rRNA gene sequence provides the primary basis for assignment to hierarchical rank, and may also constitute evidence of species novelty, but serological and supplementary phenotypic data must be presented to substantiate this. Serological methods have been documented to be congruent with DNA–DNA hybridization data and with 16S rRNA gene placements. The novel species must be tested serologically to the greatest extent that the investigators deem feasible against all neighbouring species whose 16S rRNA gene sequences show >0.94 similarity. The investigator is responsible for justifying which characters are most meaningful for assignment to the part of the mollicute phylogenetic tree in which a novel species is located, and for providing the means by which novel species can be identified by other investigators. The publication of the description should appear in a journal having wide circulation. If the journal is not the International Journal of Systematic and Evolutionary Microbiology, copies of the publication must be submitted to that journal so that the name may be considered for inclusion in a Validation List as required by the International Code of Bacteriological Nomenclature (the Bacteriological Code). Updated informal descriptions of the class Mollicutes and some of its constituent higher taxa are available as supplementary material in IJSEM Online.
153 citations
Cites background from "Taxonomy of the canine Mollicutes b..."
...This region, because it is less highly conserved than the flanking genes, has the potential to resolve intraspecific relationships or relationships between closely related putative species (Harasawa et al., 2000; Chalker & Brownlie, 2004; Regassa et al., 2004)....
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TL;DR: The species of mycoplasma present throughout the respiratory tract of dogs with and without CIRD were determined and isolation of M. cynos was correlated with an increased severity of CIRD, younger age and a longer time in the kennel.
Abstract: Canine infectious respiratory disease (CIRD) is a complex infection that occurs worldwide predominantly in kennelled dogs, and several bacterial and viral micro-organisms have been associated with outbreaks of CIRD. However, few studies have comprehensively examined the species of mycoplasma present in healthy dogs and those with CIRD. As part of an extensive study investigating the micro-organisms involved in CIRD, the species of mycoplasma present throughout the respiratory tract of dogs with and without CIRD were determined. Mycoplasmas were cultured from tonsillar, tracheal and bronchial lavage samples, and identified to the species level by PCR and sequencing. Mycoplasma cynos was demonstrated on the ciliated tracheal epithelium by in situ hybridization and was the only mollicute found to be associated with CIRD, but only in the lower respiratory tract. Isolation of M. cynos was correlated with an increased severity of CIRD, younger age and a longer time in the kennel.
92 citations
Cites background or methods from "Taxonomy of the canine Mollicutes b..."
...Due to the high similarity of the 16S rRNA genes of canine Mycoplasma species (Chalker & Brownlie, 2004), PCR tests were developed for the species listed in Table 1 to species-specific regions identified in the 16S/23S rRNA intergenic spacer region....
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...…other canine mycoplasmas have been isolated that do not cross-react with antisera to any of the known species, have distinct 16S rRNA genes, and have not yet been fully characterized (Mycoplasma sp. strains HRC 689 and VJC 358; Barile et al., 1970; Kirchner et al., 1990; Chalker & Brownlie, 2004)....
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...…from which products were not amplified by any of the above PCRs, were speciated by sequencing a partial sequence of the 16S rRNA gene or the intergenic spacer region using methods described previously (Chalker & Brownlie, 2004), and by comparison of the resulting sequence data to known species....
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...The last 145 bp of the 16S rRNA genes, the entire 16S/23S rRNA spacer region, and the first 36 bp of the 23S rRNA gene of M. cynos were amplified as a single amplicon using the PCR reaction described by Chalker & Brownlie (2004)....
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TL;DR: Three-target sequence analysis was demonstrated to be a reliable and useful taxonomic tool for the species differentiation within the family Mycoplasmataceae based on their phylogenetic relatedness and pairwise sequence similarities.
72 citations
Cites background from "Taxonomy of the canine Mollicutes b..."
...For example, the 16S– 23S ITS was demonstrated to be a useful target for genetic analysis of mycoplasmas due to its high inter-species diversity and low intra-species polymorphism (Chalker and Brownlie, 2004; Harasawa et al., 2004; Ramirez et al., 2008; Volokhov et al., 2006, 2007)....
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TL;DR: The multilocus phylogenetic analysis of Acholeplasma multilocale sequence data strongly indicated that this organism is most closely related to the genera Mesoplasma and Entomoplasma (family entomoplasmataceae) and form the branch with mesoplasma seiffertii, Mesopl plasma syrphidae, and Mesoplasia photuris.
40 citations
References
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TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Abstract: CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.
38,522 citations
Additional excerpts
...Sequences were aligned with CLUSTAL X (Thompson et al., 1997)....
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4,301 citations
"Taxonomy of the canine Mollicutes b..." refers methods in this paper
...1; the same tree was obtained with parsimony analyses that were generated by the phylogenetic analysis package PHYLIP (Felsenstein, 1993)....
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TL;DR: FASTA and FASTP were designed to identify protein sequences that have descended from a common ancestor and they have proved very useful for this task, but it is not clear that NWS-based programs would be more successful in finding distantly related members of the G-protein-coupled receptor family.
Abstract: The FASTA program can search the NBRF protein sequence library (2.5 million residues) in less than 20 min on an IBM-PC microcomputer and unambiguously detect proteins that shared a common ancestor billions of years in the past. FASTA is both fast and selective because it initially considers only amino acid identities. Its sensitivity is increased not only by using the PAM250 matrix to score and rescore regions with large numbers of identities but also by joining initial regions. The results of searches with FASTA compare favorably with results using NWS-based programs that are 100 times slower. FASTA is slightly less sensitive but considerably more selective. It is not clear that NWS-based programs would be more successful in finding distantly related members of the G-protein-coupled receptor family. The joining step by FASTA to calculate the initn score is especially useful for sequences that share regions of sequence similarity that are separated by variable-length loops. FASTP and FASTA were designed to identify protein sequences that have descended from a common ancestor, and they have proved very useful for this task. In many cases, a FASTA sequence search will result in a list of high scoring library sequences that are homologous to the query sequence, or the search will result in a list of sequences with similarity scores that cannot be distinguished from the bulk of the library. In either case, the question of whether there are sequences in the library that are clearly related to the query sequence has been answered unambiguously. Unfortunately, the results often will not be so clear-cut, and careful analysis of similarity scores, statistical significance, the actual aligned residues, and the biological context are required. In the course of analyzing the G-protein-coupled receptor family, several proteins were found that, because of a high initn score and a low init1 score that increased almost 2-fold with optimization, appeared to be members of this family which were not previously recognized. RDF2 analysis showed borderline z values, and only a careful examination of the sequence alignments that focused on the conserved residues provided convincing evidence that the high scores were fortuitous. As sequence comparison methods become more powerful by becoming more sensitive, they become more likely to mislead, and even greater care is required.
2,334 citations
"Taxonomy of the canine Mollicutes b..." refers background in this paper
...Comparison of the 16S rRNA gene of strains to all available prokaryotic 16S rRNA gene sequences by FASTA analysis (Pearson, 1990) indicated that all high-scoring matches of both untyped strains are with Mycoplasma species and, in addition, these strains are distinct from all known available mycoplasma sequences....
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...Comparison of the 16S rRNA gene of strains to all available prokaryotic 16S rRNA gene sequences by FASTA analysis (Pearson, 1990) indicated that all high-scoring matches of both untyped strains are with Mycoplasma species and, in addition, these strains are distinct from all known available…...
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TL;DR: A graphical method, likelihood-mapping, is introduced, to visualize the phylogenetic content of a set of aligned sequences, based on an analysis of the maximum likelihoods for the three fully resolved tree topologies that can be computed for four sequences.
Abstract: We introduce a graphical method, likelihood-mapping, to visualize the phylogenetic content of a set of aligned sequences. The method is based on an analysis of the maximum likelihoods for the three fully resolved tree topologies that can be computed for four sequences. The three likelihoods are represented as one point inside an equilateral triangle. The triangle is partitioned in different regions. One region represents star-like evolution, three regions represent a well-resolved phylogeny, and three regions reflect the situation where it is difficult to distinguish between two of the three trees. The location of the likelihoods in the triangle defines the mode of sequence evolution. If n sequences are analyzed, then the likelihoods for each subset of four sequences are mapped onto the triangle. The resulting distribution of points shows whether the data are suitable for a phylogenetic reconstruction or not.
854 citations