Strain identifier
BacDive ID: 8589
Type strain: 
Species: Mycobacterium koreense
Strain Designation: 01-305
Strain history: <- BJ Kim, Seoul Natl. Univ. <- KIT(Korea Institute of Tuberculosis)
NCBI tax ID(s): 1069220 (species)
version 9.1 (current version)
General
@ref: 17668
BacDive-ID: 8589
DSM-Number: 45576
keywords: genome sequence, 16S sequence, Bacteria, aerobe, rod-shaped, human pathogen
description: Mycobacterium koreense 01-305 is an aerobe, rod-shaped human pathogen that was isolated from clinical isolate, human sputum.
NCBI tax id
- NCBI tax id: 1069220
- Matching level: species
strain history
| @ref | history |
|---|---|
| 17668 | <- B.-J. Kim, Seoul Natl. Univ., Republic of Korea; 01-305 |
| 67770 | KCTC 19819 <-- B.-J. Kim 01-305. |
| 67771 | <- BJ Kim, Seoul Natl. Univ. <- KIT(Korea Institute of Tuberculosis) |
doi: 10.13145/bacdive8589.20240916.9.1
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 koreense
- full scientific name: Mycobacterium koreense Kim et al. 2012
synonyms
- @ref: 20215
- synonym: Mycolicibacillus koreensis
@ref: 17668
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium koreense
full scientific name: Mycobacterium koreense Kim et al. 2012 emend. Nouioui et al. 2018
strain designation: 01-305
type strain: yes
Morphology
cell morphology
| @ref | cell shape | gram stain | motility | confidence |
|---|---|---|---|---|
| 30313 | rod-shaped | |||
| 67771 | positive | |||
| 69480 | no | 93 | ||
| 69480 | positive | 90.032 |
pigmentation
- @ref: 30313
- production: no
Culture and growth conditions
culture medium
- @ref: 17668
- 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 |
|---|---|---|---|
| 17668 | positive | growth | 37 |
| 30313 | positive | growth | 25-37 |
| 30313 | positive | optimum | 37 |
| 67770 | positive | growth | 37 |
| 67771 | positive | growth | 37 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30313 | no | |
| 69481 | no | 100 |
halophily
- @ref: 30313
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 5 %
observation
- @ref: 67770
- observation: quinones: MK-9(H2)
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30313 | catalase | + | 1.11.1.6 |
| 30313 | pyrazinamidase | + | 3.5.1.B15 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 17668 | clinical isolate, human sputum | Seoul | Republic of Korea | KOR | Asia |
| 67770 | Human sputum | Seoul | Republic of Korea | KOR | Asia |
| 67771 | Fromhuman sputum. | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Medical environment | #Clinic |
| #Host | #Human | |
| #Host Body Product | #Fluids | #Sputum |
Safety information
risk assessment
- @ref: 17668
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17668
- description: Mycobacterium koreense strain 01-305 16S ribosomal RNA gene, partial sequence
- accession: JF271826
- length: 1474
- database: nuccore
- NCBI tax ID: 1069220
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Mycolicibacillus koreensis JCM 19956 | GCA_010731835 | complete | ncbi | 1069220 |
| 66792 | Mycobacterium koreense strain KCTC 19819 | 1069220.3 | wgs | patric | 1069220 |
| 66792 | Mycolicibacillus koreensis strain JCM 19956 | 1069220.11 | complete | patric | 1069220 |
| 67770 | Mycolicibacillus koreensis KCTC 19819 | GCA_002104795 | contig | ncbi | 1069220 |
| 66792 | Mycolicibacillus koreensis DSM 45576 | GCA_025822715 | scaffold | ncbi | 1069220 |
GC content
- @ref: 67770
- GC-content: 69.4
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 90.032 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.988 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 77.582 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 70.128 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 94.88 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 93 | no |
External links
@ref: 17668
culture collection no.: DSM 45576, KCTC 19819, JCM 19956
straininfo link
- @ref: 77973
- straininfo: 401863
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21784962 | Mycobacterium koreense sp. nov., a slowly growing non-chromogenic species closely related to Mycobacterium triviale. | Kim BJ, Jeong J, Lee SH, Kim SR, Yu HK, Park YG, Kim KJ, Kook YH, Kim BJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.033274-0 | 2011 | Amino Acid Sequence, Bacterial Proteins/chemistry/genetics, DNA, Bacterial/genetics, Humans, Molecular Sequence Data, Mycobacterium/*classification/genetics/growth & development/*isolation & purification, Mycobacterium Infections/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Alignment | Pathogenicity |
| Phylogeny | 23159753 | Mycobacterium parakoreense sp. nov., a slowly growing non-chromogenic species related to Mycobacterium koreense, isolated from a human clinical specimen. | Kim BJ, Hong SH, Yu HK, Park YG, Jeong J, Lee SH, Kim SR, Kim K, Kook YH, Kim BJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.045070-0 | 2012 | DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Humans, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification, Mycobacterium Infections/microbiology, Mycolic Acids/analysis, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sputum/*microbiology | Pathogenicity |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17668 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45576) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45576 | |||
| 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 | |||
| 30313 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26654 | 28776041 | |
| 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/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 77973 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401863.1 | StrainInfo: A central database for resolving microbial strain identifiers |