Strain identifier
BacDive ID: 8555
Type strain: 
Species: Mycobacterium kumamotonense
Strain history: T. Ezaki CST 7247.
NCBI tax ID(s): 354243 (species)
version 8.1 (current version)
General
@ref: 12335
BacDive-ID: 8555
DSM-Number: 45093
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, human pathogen
description: Mycobacterium kumamotonense DSM 45093 is an aerobe, mesophilic human pathogen that was isolated from sputa of a 57-year old Japanes woman.
NCBI tax id
- NCBI tax id: 354243
- Matching level: species
strain history
| @ref | history |
|---|---|
| 12335 | <- JCM <- T. Ezaki; CST 7247 |
| 67770 | T. Ezaki CST 7247. |
doi: 10.13145/bacdive8555.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Mycobacteriaceae
- genus: Mycobacterium
- species: Mycobacterium kumamotonense
- full scientific name: Mycobacterium kumamotonense Masaki et al. 2007
synonyms
- @ref: 20215
- synonym: Mycolicibacter kumamotonensis
@ref: 12335
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium kumamotonense
full scientific name: Mycobacterium kumamotonense Masaki et al. 2007 emend. Nouioui et al. 2018
type strain: yes
Morphology
colony morphology
- @ref: 59384
- incubation period: 7-10 days
multimedia
- @ref: 12335
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45093.jpg
- caption: Medium 645 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 12335
- name: MIDDLEBROOK MEDIUM (DSMZ Medium 645)
- growth: yes
- link: https://mediadive.dsmz.de/medium/645
- composition: Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 12335 | positive | growth | 37 | mesophilic |
| 59384 | positive | growth | 35 | mesophilic |
| 67770 | positive | growth | 35 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 59384 | aerobe |
| 59384 | microaerophile |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 12335 | sputa of a 57-year old Japanes woman | Kumamoto Prefecture | Japan | JPN | Asia | |
| 59384 | Human sputum,57-yr-old female Japanese | Kumamoto | Japan | JPN | Asia | 2001 |
| 67770 | Sputum of a 57-year-old Japanese woman with abnormal shadow by indirect X-ray |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Human | #Female |
| #Host Body Product | #Fluids | #Sputum |
taxonmaps
- @ref: 69479
- File name: preview.99_3552.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_312;97_346;98_980;99_3552&stattab=map
- Last taxonomy: Mycolicibacter
- 16S sequence: AB239925
- Sequence Identity:
- Total samples: 2741
- soil counts: 1498
- aquatic counts: 718
- animal counts: 445
- plant counts: 80
Safety information
risk assessment
- @ref: 12335
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Mycobacterium kumamotonense strain CCUG 51961 16S ribosomal RNA gene, partial sequence | EU191911 | 471 | ena | 354243 |
| 20218 | Mycobacterium kumamotonense strain DSM45093 16S ribosomal RNA gene, partial sequence | JN571176 | 479 | ena | 354243 |
| 12335 | Mycobacterium kumamotonense gene for 16S rRNA, partial sequence, strain:CST7274 (= GTC2729) | AB239925 | 1434 | ena | 354243 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Mycobacterium kumamotonense strain DSM 45093 | 354243.4 | wgs | patric | 354243 |
| 66792 | Mycolicibacter kumamotonensis strain CST 7247 | 354243.11 | wgs | patric | 354243 |
| 67770 | Mycolicibacter kumamotonensis CST 7247 | GCA_010093495 | scaffold | ncbi | 354243 |
| 67770 | Mycolicibacter kumamotonensis DSM 45093 | GCA_002086285 | contig | ncbi | 354243 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 12335 | 51.19 | |
| 67770 | 67.4 | high performance liquid chromatography (HPLC) |
| 67770 | 68.1 | genome sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | yes | 94.522 | no |
| anaerobic | no | 99.349 | no |
| halophile | no | 91.48 | no |
| spore-forming | no | 87.855 | no |
| glucose-util | yes | 53.116 | no |
| motile | no | 95.014 | no |
| flagellated | no | 98.873 | no |
| aerobic | yes | 90.101 | no |
| thermophile | no | 97.043 | yes |
| glucose-ferment | no | 92.177 | no |
External links
@ref: 12335
culture collection no.: DSM 45093, CCUG 51961, GTC 2729, JCM 13453, CST 7247
straininfo link
- @ref: 77938
- straininfo: 297259
literature
- topic: Phylogeny
- Pubmed-ID: 17116985
- title: Mycobacterium kumamotonense Sp. Nov. recovered from clinical specimen and the first isolation report of Mycobacterium arupense in Japan: Novel slowly growing, nonchromogenic clinical isolates related to Mycobacterium terrae complex.
- authors: Masaki T, Ohkusu K, Hata H, Fujiwara N, Iihara H, Yamada-Noda M, Nhung PH, Hayashi M, Asano Y, Kawamura Y, Ezaki T
- journal: Microbiol Immunol
- DOI: 10.1111/j.1348-0421.2006.tb03865.x
- year: 2006
- mesh: Bacterial Proteins/genetics, Humans, Japan, Molecular Sequence Data, Mycobacterium/chemistry/*classification/genetics/*isolation & purification, Mycobacterium Infections/*microbiology, Mycolic Acids/analysis, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Pathogenicity
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 12335 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45093) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45093 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 59384 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 51961) | https://www.ccug.se/strain?id=51961 | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 77938 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297259.1 | StrainInfo: A central database for resolving microbial strain identifiers |