Extended Bibliography: |
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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 #: |
59414 |
Author(s): |
Pitulle,C.;Dorsch,M.;Kazda,J.;Wolters,J.;Stackebrandt,E. |
Journal: |
Int J Syst Bacteriol |
Title: |
Phylogeny of rapidly growing members of the genus Mycobacterium |
Volume: |
42 |
Page(s): |
337-43 |
Year: |
1992 |
Keyword(s): |
GENBANK/X55593
GENBANK/X55594
GENBANK/X55595
GENBANK/X55596
GENBANK/X55597
GENBANK/X55598
GENBANK/X55599
GENBANK/X55600
GENBANK/X55601
GENBANK/X55602
Base Sequence
Molecular Sequence Data
Mycobacteria, Atypical/classification/*genetics
Mycobacterium/classification/*genetics
*Phylogeny
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Sequence Homology, Nucleic Acid
|
Remarks: |
The 16S rRNAs from nine rapidly growing Mycobacterium species were partially sequenced by using the dideoxynucleotide-terminated, primer extension method with cDNA generated by reverse transcriptase. The sequences were aligned with 47 16S rRNA or DNA sequences that represented 30 previously described and 5 undescribed species of the genus Mycobacterium, and a dendrogram was constructed by using equally weighted distance values. Our results confirmed the phylogenetic separation of the rapidly and slowly growing mycobacteria and showed that the majority of the slowly growing members of the genus represent the most recently evolved organisms. The 24 strains which represented 21 rapidly growing species constituted several sublines, which were defined by the following taxa: (i) Mycobacterium neoaurum and M. diernhoferi, (ii) M. gadium, (iii) the M. chubuense cluster, (iv) the M. fortuitum cluster, (v) M. kommossense, (vi) M. sphagni, (vii) M. fallax and M. chitae, (viii) M. aurum and M. vaccae, (ix) the M. flavescens cluster, and (x) M. chelonae subsp. abscessus. Our phylogenetic analysis confirmed the validity of the phenotypically defined species mentioned above, but our conclusions disagree with most of the conclusions about intrageneric relationships derived from numerical phenetic analyses. |
URL: |
1380284 |
|
Ref #: |
95455 |
Author(s): |
Devulder,G.;Perouse de Montclos,M.;Flandrois,J.P. |
Journal: |
Int J Syst Evol Microbiol |
Title: |
A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model |
Volume: |
55 |
Page(s): |
293-302 |
Year: |
2005 |
Keyword(s): |
Animals
Bacterial Proteins/*genetics
*Bacterial Typing Techniques
Chaperonins/genetics
DNA, Bacterial/analysis
DNA-Directed RNA Polymerases/genetics
Genes, rRNA
Humans
Mycobacterium/*classification/*genetics
*Phylogeny
Polymerase Chain Reaction
RNA, Ribosomal, 16S/genetics
*Sequence Analysis, DNA
Superoxide Dismutase/genetics
|
Remarks: |
Advances in DNA sequencing and the increasing number of sequences available in databases have greatly enhanced the bacterial identification process. Several species within the genus Mycobacterium cause serious human and animal diseases. In order to assess their relative positions in the evolutionary process, four gene fragments, from the 16S rRNA (564 bp), hsp65 (420 bp), rpoB (396 bp) and sod (408 bp) genes, were sequenced from 97 strains, including all available type strains of the genus Mycobacterium. The results demonstrate that, in this case, the concatenation of different genes allows significant increases in the power of discrimination and the robustness of the phylogenetic tree. The sequential and/or combined use of sequences of several genes makes it possible to refine the phylogenetic approach and provides a molecular basis for accurate species identification. |
URL: |
15653890 |
|
Ref #: |
13155 |
Author(s): |
Pitulle,C.;Dorsch,M.;Kazda,J.;Wolters,J.;Stackebrandt,E. |
Journal: |
Int J Syst Bacteriol |
Title: |
Phylogeny of rapidly growing members of the genus Mycobacterium |
Volume: |
42 |
Page(s): |
337-43 |
Year: |
1992 |
Keyword(s): |
GENBANK/X55593
GENBANK/X55594
GENBANK/X55595
GENBANK/X55596
GENBANK/X55597
GENBANK/X55598
GENBANK/X55599
GENBANK/X55600
GENBANK/X55601
GENBANK/X55602
Base Sequence
Molecular Sequence Data
Mycobacteria, Atypical/classification/*genetics
Mycobacterium/classification/*genetics
*Phylogeny
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Sequence Homology, Nucleic Acid
Support, Non-U.S. Gov't
|
Remarks: |
The 16S rRNAs from nine rapidly growing Mycobacterium species were partially sequenced by using the dideoxynucleotide-terminated, primer extension method with cDNA generated by reverse transcriptase. The sequences were aligned with 47 16S rRNA or DNA sequences that represented 30 previously described and 5 undescribed species of the genus Mycobacterium, and a dendrogram was constructed by using equally weighted distance values. Our results confirmed the phylogenetic separation of the rapidly and slowly growing mycobacteria and showed that the majority of the slowly growing members of the genus represent the most recently evolved organisms. The 24 strains which represented 21 rapidly growing species constituted several sublines, which were defined by the following taxa: (i) Mycobacterium neoaurum and M. diernhoferi, (ii) M. gadium, (iii) the M. chubuense cluster, (iv) the M. fortuitum cluster, (v) M. kommossense, (vi) M. sphagni, (vii) M. fallax and M. chitae, (viii) M. aurum and M. vaccae, (ix) the M. flavescens cluster, and (x) M. chelonae subsp. abscessus. Our phylogenetic analysis confirmed the validity of the phenotypically defined species mentioned above, but our conclusions disagree with most of the conclusions about intrageneric relationships derived from numerical phenetic analyses. |
URL: |
92368931 |
|
Ref #: |
5147 |
Author(s): |
Tsukamura,M.;Mizuno,S.;Tsukamura,S. |
Journal: |
Int. J. Syst. Bacteriol. |
Title: |
Numerical analysis of rapidly growing scotochromogenic mycobacteria, including Mycobacterium obusense sp. nov., nom. rev., Mycobacterium rhodesiae sp. nov., nom. rev., Mycobacterium aichiense sp. nov., nom. rev., Mycobacterium chubuense sp. nov., nom. re |
Volume: |
31 |
Page(s): |
263-275 |
Year: |
1981 |
|
Ref #: |
6097 |
Journal: |
Med. Biol. |
Volume: |
86 |
Page(s): |
16 |
Year: |
1973 |
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