| Extended Bibliography: |
Show bibliography
| Ref #: |
75210 |
| Author(s): |
Stone,B.B.;Nietupski,R.M.;Breton,G.L.;Weisburg,W.G. |
| Journal: |
Int J Syst Bacteriol |
| Title: |
Comparison of Mycobacterium 23S rRNA sequences by high-temperature reverse transcription and PCR |
| Volume: |
45 |
| Page(s): |
811-9 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/U24502
GENBANK/U24503
GENBANK/U24504
GENBANK/U24505
GENBANK/U24506
GENBANK/U24507
GENBANK/U24508
GENBANK/U24509
GENBANK/U24510
GENBANK/U24511
GENBANK/U24512
GENBANK/U24513
GENBANK/U24514
GENBANK/U24515
GENBANK/U24516
GENBANK/U24517
GENBANK/U24518
GENBANK/U24519
GENBANK/U24520
GENBANK/U24521
GENBANK/U24522
GENBANK/U24523
GENBANK/U24524
GENBANK/U24525
GENBANK/U24526
GENBANK/U24527
GENBANK/U24528
GENBANK/U24529
GENBANK/U24530
GENBANK/U24531
Base Sequence
Molecular Sequence Data
Mycobacterium/*genetics
Phylogeny
*Polymerase Chain Reaction
RNA, Bacterial/*chemistry
RNA, Ribosomal, 16S/chemistry
RNA, Ribosomal, 23S/*chemistry
Temperature
Transcription, Genetic
|
| Remarks: |
We describe a modified rRNA sequence analysis method which we used to determine the phylogenetic relationships among 58 species belonging to the genus Mycobacterium. We combined the sensitivity of the reverse transcriptase PCR for amplifying nanogram amounts of template rRNA material with the elevated extension temperatures used for the thermostable DNA polymerase from Thermus thermophilus. A 70 degrees C reverse transcription extension step permitted improved read-through of highly structured rRNA templates from members of the genus Mycobacterium, which have G+C contents of 66 to 71 mol%. The nucleic acid sequences of the amplified material were then determined by performing thermal cycle sequencing with alpha-33P-labeled primers, again with extension at 70 degrees C. Nonspecifically terminated bands were chased by using terminal deoxynucleotidyl transferase. Our method had a template requirement of nanogram amounts or less of purified RNA or 2,000 CFU of intact cells and had sufficient sensitivity so that lyophils obtained from the American Type Culture Collection could be used as source material. Sequences from a 250-nucleotide stretch of the 23S rRNA were aligned, and phylogenetic trees were evaluated by using the De Soete distance treeing algorithm and Rhodococcus bronchialis as the outgroup. Our 23S rRNA trees were compared with previously published 16S rRNA trees, including the comprehensive trees developed by the University of Illinois Ribosomal Database Project, and included 15 species not evaluated previously. Most of the groups were in general agreement and were consistent with relationships determined on the basis of biochemical characteristics, but some new relationships were also observed. |
| URL: |
7547304 |
|
| Ref #: |
65544 |
| Author(s): |
Goodfellow,M.;Chun,J.;Stubbs,S.;Tobili,A.S. |
| Journal: |
Lett Appl Microbiol |
| Title: |
Transfer of Nocardia amarae Lechevalier and Lechevalier 1974 to the genus Gordona as Gordona amarae comb. nov |
| Volume: |
19 |
| Page(s): |
401-5 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/X75902
Actinomycetales/*classification/genetics/metabolism
Genes, Bacterial/genetics
Lipids/analysis
Molecular Sequence Data
Nocardia/*classification/genetics/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Sequence Homology, Nucleic Acid
|
| Remarks: |
The taxonomic status of Nocardia amarae strains was examined using chemical, microbiological and nucleic acid sequencing methods. It was evident from the results of this and previous studies that Nocardia amarae has properties that are at variance with its classification in the genus Nocardia but consistent with its transfer to the genus Gordona. It is proposed that Nocardia amarae Lechevalier and Lechevalier 1974 be transferred to the genus Gordona as Gordona amarae comb. nov. |
| URL: |
7765703 |
|
| Ref #: |
65647 |
| Author(s): |
Patel,J.B.;Wallace RJ,J.r.;Brown-Elliott,B.A.;Taylor,T.;Imperatrice,C.;Leonard,D.G.;Wilson,R.W.;Mann,L.;Jost,K.C.;Nachamkin,I. |
| Journal: |
J Clin Microbiol |
| Title: |
Sequence-based identification of aerobic actinomycetes |
| Volume: |
42 |
| Page(s): |
2530-40 |
| Year: |
2004 |
| Keyword(s): |
Actinobacteria/classification/genetics/*isolation & purification
Aerobiosis
DNA, Ribosomal/chemistry
Nocardia/genetics/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
|
| Remarks: |
We investigated the utility of 500-bp 16S rRNA gene sequencing for identifying clinically significant species of aerobic actinomycetes. A total of 28 reference strains and 71 clinical isolates that included members of the genera Streptomyces, Gordonia, and Tsukamurella and 10 taxa of Nocardia were studied. Methods of nonsequencing analyses included growth and biochemical analysis, PCR-restriction enzyme analysis of the 439-bp Telenti fragment of the 65 hsp gene, susceptibility testing, and, for selected isolates, high-performance liquid chromatography. Many of the isolates were included in prior taxonomic studies. Sequencing of Nocardia species revealed that members of the group were generally most closely related to the American Type Culture Collection (ATCC) type strains. However, the sequences of Nocardia transvalensis, N. otitidiscaviarum, and N. nova isolates were highly variable; and it is likely that each of these species contains multiple species. We propose that these three species be designated complexes until they are more taxonomically defined. The sequences of several taxa did not match any recognized species. Among other aerobic actinomycetes, each group most closely resembled the associated reference strain, but with some divergence. The study demonstrates the ability of partial 16S rRNA gene sequencing to identify members of the aerobic actinomycetes, but the study also shows that a high degree of sequence divergence exists within many species and that many taxa within the Nocardia spp. are unnamed at present. A major unresolved issue is the type strain of N. asteroides, as the present one (ATCC 19247), chosen before the availability of molecular analysis, does not represent any of the common taxa associated with clinical nocardiosis. |
| URL: |
15184431 |
|
| Ref #: |
95449 |
| Author(s): |
Shen,F.T.;Lu,H.L.;Lin,J.L.;Huang,W.S.;Arun,A.B.;Young,C.C. |
| Journal: |
Res Microbiol |
| Title: |
Phylogenetic analysis of members of the metabolically diverse genus Gordonia based on proteins encoding the gyrB gene |
| Volume: |
157 |
| Page(s): |
367-75 |
| Year: |
2006 |
| Keyword(s): |
Amino Acid Sequence
DNA Gyrase/genetics/*metabolism
DNA Primers
Gordonia Bacterium/*classification/enzymology
Molecular Sequence Data
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Homology, Amino Acid
|
| Remarks: |
Members of the metabolically diverse genus Gordonia were isolated from various biotopes including pristine and polluted sites around Taiwan. Identification, comparison and diversity assessment based on the gyrB gene were carried out using a newly developed primer pair for gyrB. The 16S rRNA gene was also sequenced for comparison. A 1.2-kb fragment of the gyrB gene of 17 Gordonia strains including type strains was determined by direct sequencing of PCR amplified fragments. A total of 25 strains (8 of which were retrieved from a public database) of the genus Gordonia form a distinct phyletic line in the GyrB-based tree and are separated from other closely related species of genera of the suborder Corynebacterineae. Sequence similarity of the gyrB sequence from twelve Gordonia type strains ranged from 79.3 to 97.2%, corresponding to between 270 and 41 nucleotide differences, while there was only a 0.3-3.8% difference in 16S rRNA gene sequence similarity at the interspecies level. Phylogenetic analysis based on the GyrB sequence deduced from the gyrB gene is consistent with that of DNA-DNA hybridization results and provides a better discrimination within the species of Gordonia compared to the 16S rRNA gene. The present study demonstrates that gyrB gene analysis will aid in describing novel species belonging to the genus Gordonia. |
| URL: |
16310344 |
|
| Ref #: |
12782 |
| Author(s): |
Goodfellow,M.;Chun,J.;Stubbs,S.;Tobili,A.S. |
| Journal: |
Lett Appl Microbiol |
| Title: |
Transfer of Nocardia amarae Lechevalier and Lechevalier 1974 to the genus Gordona as Gordona amarae comb. nov |
| Volume: |
19 |
| Page(s): |
401-5 |
| Year: |
1995 |
| Keyword(s): |
GENBANK/X75902
Actinomycetales/*classification/genetics/metabolism
Genes, Bacterial/genetics
Lipids/analysis
Molecular Sequence Data
Nocardia/*classification/genetics/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Sequence Homology, Nucleic Acid
Support, Non-U.S. Gov't
|
| Remarks: |
The taxonomic status of Nocardia amarae strains was examined using chemical, microbiological and nucleic acid sequencing methods. It was evident from the results of this and previous studies that Nocardia amarae has properties that are at variance with its classification in the genus Nocardia but consistent with its transfer to the genus Gordona. It is proposed that Nocardia amarae Lechevalier and Lechevalier 1974 be transferred to the genus Gordona as Gordona amarae comb. nov. |
| URL: |
95118578 |
|
| Ref #: |
1300 |
| Author(s): |
Skerman,V.B.D.;McGowan,V.;Sneath,P.H.A.(ed) |
| Journal: |
Int. J. Syst. Bacteriol. |
| Title: |
Approved Lists of Bacterial Names. |
| Volume: |
30 |
| Page(s): |
225-420 |
| Year: |
1980 |
|
| Ref #: |
2184 |
| Author(s): |
Goodfellow,M.;Alderson,G. |
| Journal: |
J. Gen. Microbiol. |
| Title: |
The actinomycete-genus Rhodococcus: a home for the "rhodochrous" complex. |
| Volume: |
100 |
| Page(s): |
99-122 |
| Year: |
1977 |
|
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