Culture Collections

Bacteria and Mycoplasmas detail

Conditions of Supply of Microbial Pathogens: Safety





Bacteria Collection: Mycobacterium phlei

NCTC Number: NCTC 8151
Current Name: Mycobacterium phlei
Original Strain Reference: Timoteo
Other Collection No: ATCC 19249; ATCC 11758; DSM 43239; TIMOTEO
Previous Catalogue Name: Mycobacterium phlei
Type Strain: Yes
Family: Mycobacteriaceae
Hazard Group (ACDP): 2
Release Restrictions: Terms & Conditions of Supply of Microbial Pathogens: Safety
Conditions for growth on solid media: Nutrient agar, 48 hours, 37°C, aerobic
Conditions for growth on liquid media: 7h9,37, aerobic
Whole Genome Sequence: http://www.ebi.ac.uk/ena/data/view/ERS1211594
16S rRNA Gene Sequence: >gb|AF480603|ATCC 11758|Mycobacterium phlei 16S ribosomal RNA gene, partial sequence.| gacgaacgctggcgg...
23S rRNA Gene Sequence: >gb|U24540|ATCC 11758|Mycobacterium phlei 23S rRNA, partial sequence.| tgtgcctacaatccg...
Extended Bibliography: showhide Show bibliography
Ref #: 60196
Author(s): Kim,B.J.;Lee,S.H.;Lyu,M.A.;Kim,S.J.;Bai,G.H.;Chae,G.T.;Kim,E.C.;Cha,C.Y.;Kook,Y.H.
Journal: J Clin Microbiol
Title: Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB)
Volume: 37
Page(s): 1714-20
Year: 1999
Keyword(s): GENBANK/AF057449 GENBANK/AF057450 GENBANK/AF057451 GENBANK/AF057452 GENBANK/AF057453 GENBANK/AF057454 GENBANK/AF057455 GENBANK/AF057456 GENBANK/AF057457 GENBANK/AF057458 GENBANK/AF057459 GENBANK/AF057460 GENBANK/AF057461 GENBANK/AF057462 GENBANK/AF057463 GENBANK/AF057464 GENBANK/AF057465 GENBANK/AF057466 GENBANK/AF057467 GENBANK/AF057468 GENBANK/AF057469 GENBANK/AF057470 GENBANK/AF057471 GENBANK/AF057472 GENBANK/AF057473 GENBANK/AF057474 GENBANK/AF057475 GENBANK/AF057476 GENBANK/AF057477 GENBANK/AF057478 etc. Amino Acid Sequence DNA-Directed RNA Polymerases/chemistry/*genetics Humans Molecular Sequence Data Mycobacterium/*classification/enzymology/genetics Mycobacterium Infections/microbiology Phylogeny Restriction Mapping Sequence Alignment Sequence Homology, Amino Acid
Remarks: For the differentiation and identification of mycobacterial species, the rpoB gene, encoding the beta subunit of RNA polymerase, was investigated. rpoB DNAs (342 bp) were amplified from 44 reference strains of mycobacteria and clinical isolates (107 strains) by PCR. The nucleotide sequences were directly determined (306 bp) and aligned by using the multiple alignment algorithm in the MegAlign package (DNASTAR) and the MEGA program. A phylogenetic tree was constructed by the neighbor-joining method. Comparative sequence analysis of rpoB DNAs provided the basis for species differentiation within the genus Mycobacterium. Slowly and rapidly growing groups of mycobacteria were clearly separated, and each mycobacterial species was differentiated as a distinct entity in the phylogenetic tree. Pathogenic Mycobacterium kansasii was easily differentiated from nonpathogenic M. gastri; this differentiation cannot be achieved by using 16S rRNA gene (rDNA) sequences. By being grouped into species-specific clusters with low-level sequence divergence among strains of the same species, all of the clinical isolates could be easily identified. These results suggest that comparative sequence analysis of amplified rpoB DNAs can be used efficiently to identify clinical isolates of mycobacteria in parallel with traditional culture methods and as a supplement to 16S rDNA gene analysis. Furthermore, in the case of M. tuberculosis, rifampin resistance can be simultaneously determined.
URL: 10325313
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 #: 60037
Author(s): Hamid,M.E.;Roth,A.;Landt,O.;Kroppenstedt,R.M.;Goodfellow,M.;Mauch,H.
Journal: J Clin Microbiol
Title: Differentiation between Mycobacterium farcinogenes and Mycobacterium senegalense strains based on 16S-23S ribosomal DNA internal transcribed spacer sequences
Volume: 40
Page(s): 707-11
Year: 2002
Keyword(s): GENBANK/AJ291580 GENBANK/AJ291581 GENBANK/AJ291582 GENBANK/AJ291583 GENBANK/AJ291584 GENBANK/AJ291585 GENBANK/AJ291586 GENBANK/AJ291587 GENBANK/AJ291588 GENBANK/AJ291589 GENBANK/AJ291590 GENBANK/AJ291591 GENBANK/AJ291592 GENBANK/AJ291593 GENBANK/AJ291594 GENBANK/AJ291595 GENBANK/AJ291596 GENBANK/AJ291597 GENBANK/AJ291598 GENBANK/AJ291599 GENBANK/AJ291600 GENBANK/Y10384 GENBANK/Y10385 GENBANK/Y11581 GENBANK/Y11582 Animals Base Sequence Cattle Cattle Diseases/*microbiology DNA, Ribosomal Spacer/*genetics Molecular Sequence Data Mycobacterium/*classification/genetics Mycobacterium Infections/microbiology/*veterinary Phylogeny Polymerase Chain Reaction/*methods RNA, Ribosomal, 16S/*genetics RNA, Ribosomal, 23S/*genetics Sequence Analysis, DNA
Remarks: 16S ribosomal DNA (rDNA) and 16S-23S internal transcribed spacer rDNA sequence analyses were performed on Mycobacterium farcinogenes and M. senegalense strains and 26 strains of other rapidly growing mycobacteria to investigate the phylogenetic structure of bovine farcy mycobacteria within the M. fortuitum complex. M. farcinogenes and M. senegalense were indistinguishable in their 5"-end 16S rDNA but showed both considerable interspecies spacer sequence divergence and a high level of intraspecies sequence stability. A rapid detection assay using PCR and hybridization with species-specific probes was developed. The assay was specific among 46 species other than M. farcinogenes and M. senegalense and correctly identified all M. farcinogenes and M. senegalense strains. PCR- and 16S-23S rDNA sequence-based detection will be a valuable approach for diagnosis of the causal agents of African bovine farcy in cattle.
URL: 11826003
Ref #: 95496
Author(s): Turenne,C.Y.;Tschetter,L.;Wolfe,J.;Kabani,A.
Journal: J Clin Microbiol
Title: Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species
Volume: 39
Page(s): 3637-48
Year: 2001
Keyword(s): *Databases, Nucleic Acid *Genes, rRNA Humans Internet Mycobacterium/*classification/genetics Mycobacterium Infections/*microbiology Phylogeny Quality Control RNA, Ribosomal, 16S/*genetics Reference Standards *Sequence Analysis, DNA Species Specificity
Remarks: The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing approximately 440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1- to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species.
URL: 11574585
Ref #: 13682
Author(s): Hamid,M.E.;Roth,A.;Landt,O.;Kroppenstedt,R.M.;Goodfellow,M.;Mauch,H.
Journal: J Clin Microbiol
Title: Differentiation between Mycobacterium farcinogenes and Mycobacterium
Volume: 40
Page(s): 707-711
Year: 2002
Keyword(s): 0 (DNA, Ribosomal Spacer) 0 (RNA, Ribosomal, 16S) 0 (RNA, Ribosomal, 23S) Animal Base Sequence Cattle Cattle Diseases/*microbiology DNA, Ribosomal Spacer/*genetics Molecular Sequence Data Mycobacterium/*classification/genetics Mycobacterium Infections/microbiology/*veterinary Phylogeny Polymerase Chain Reaction/*methods RNA, Ribosomal, 16S/*genetics RNA, Ribosomal, 23S/*genetics Sequence Analysis, DNA Support, Non-U.S. Gov't
Remarks: 16S ribosomal DNA (rDNA) and 16S-23S internal transcribed spacer rDNA
URL: 21683667
Ref #: 13151
Author(s): Turenne,C.Y.;Tschetter,L.;Wolfe,J.;Kabani,A.
Journal: J Clin Microbiol
Title: Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species
Volume: 39
Page(s): 3637-48
Year: 2001
Keyword(s): *Databases, Nucleic Acid *Genes, rRNA Human Internet Mycobacterium/*classification/genetics Mycobacterium Infections/*microbiology Phylogeny Quality Control RNA, Ribosomal, 16S/*genetics Reference Standards *Sequence Analysis, DNA Species Specificity
Remarks: The use of the 16S rRNA gene for identification of nontuberculous mycobacteria (NTM) provides a faster and better ability to accurately identify them in addition to contributing significantly in the discovery of new species. Despite their associated problems, many rely on the use of public sequence databases for sequence comparisons. To best evaluate the taxonomic status of NTM species submitted to our reference laboratory, we have created a 16S rRNA sequence database by sequencing 121 American Type Culture Collection strains encompassing 92 species of mycobacteria, and have also included chosen unique mycobacterial sequences from public sequence repositories. In addition, the Ribosomal Differentiation of Medical Microorganisms (RIDOM) service has made freely available on the Internet mycobacterial identification by 16S rRNA analysis. We have evaluated 122 clinical NTM species using our database, comparing >1,400 bp of the 16S gene, and the RIDOM database, comparing approximately 440 bp. The breakdown of analysis was as follows: 61 strains had a sequence with 100% similarity to the type strain of an established species, 19 strains showed a 1- to 5-bp divergence from an established species, 11 strains had sequences corresponding to uncharacterized strain sequences in public databases, and 31 strains represented unique sequences. Our experience with analysis of the 16S rRNA gene of patient strains has shown that clear-cut results are not the rule. As many clinical, research, and environmental laboratories currently employ 16S-based identification of bacteria, including mycobacteria, a freely available quality-controlled database such as that provided by RIDOM is essential to accurately identify species or detect true sequence variations leading to the discovery of new species.
URL: 21458757
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 #: 150
Author(s): Gordon,R.E.;Smith,M.M.
Journal: J. Bacteriol.
Title: Rapidly growing, acid fast bacteria. I. Species description of Mycobacterium phlei Lehmann and Neumann and Mycobacterium smegmatis (Trevisan) Lehmann and Neumann.
Volume: 66
Page(s): 41-48
Year: 1953
Ref #: 6924
Author(s): DeutschesInstitutfürNormungDIN.NormenausschußMedizin(NAMed)
Title: DIN 58959-7. Qualitätsmanagement in der medizinischen Mikrobiologie. Teil 7: Allgemeine Anforderungen an das Mitführen von Kontrollstämmen. Beiblatt 2: ATCC- und DSM-Nummern häufig verwendeter Kontrollstämme.
Year: 1997
Data: (ATCC 19249, ATCC 11758, JCM 5865) Type strain / G. Penso, Rome in 1949
Accession Date: 01/01/1949
History: PENSO G, INSTITUTO SUPERIORE DI SANITA, ROME
Authority: Lehmann and Neumann 1899 (AL)
Depositor: PENSO G
Taxonomy: TaxLink: S1971 (Mycobacterium phlei Lehmann and Neumann 1899) - Date of change: 5/02/2003
Biosafety Responsibility: It is the responsibility of the customer to ensure that their facilities comply with biosafety regulations for their own country

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The Culture Collections hold cell cultures, bacteria, fungi and virus strains from worldwide sources. Our scientists ensure that the identification of the cultures is correct and they remain unchanged from when they are first deposited with the Collection. Nevertheless, some of the data we provide about the cultures is supplied by the person depositing the strains and, although we have multiple checking procedures in place, we cannot always verify all their data. Please note that the Culture Collections cannot be held responsible for any inaccuracies in the data provided by the depositors.

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