Strain identifier
BacDive ID: 8587
Type strain: 
Species: Mycobacterium shinjukuense
Strain history: T. Ezaki GTC 2738.
NCBI tax ID(s): 398694 (species)
version 8.1 (current version)
General
@ref: 18021
BacDive-ID: 8587
DSM-Number: 45663
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Mycobacterium shinjukuense DSM 45663 is an aerobe, mesophilic bacterium that was isolated from sputum.
NCBI tax id
- NCBI tax id: 398694
- Matching level: species
strain history
| @ref | history |
|---|---|
| 18021 | <- JCM; JCM 14233 <- T. Ezaki; GTC 2738 |
| 67770 | T. Ezaki GTC 2738. |
doi: 10.13145/bacdive8587.20230509.8.1
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 shinjukuense
- full scientific name: Mycobacterium shinjukuense Saito et al. 2011
@ref: 18021
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium shinjukuense
full scientific name: Mycobacterium shinjukuense Saito et al. 2011 emend. Nouioui et al. 2018
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 93.989 | |
| 69480 | 100 | positive |
colony morphology
- @ref: 59937
- incubation period: 7-10 days
multimedia
- @ref: 18021
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45663.jpg
- caption: Medium 645 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 18021
- 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 |
|---|---|---|---|---|
| 18021 | positive | growth | 37 | mesophilic |
| 59937 | positive | growth | 35 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 59937 | aerobe |
| 59937 | microaerophile |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.936
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 18021 | sputum | Tokyo | Japan | JPN | Asia | |
| 59937 | Human sputum,75-yr-old female Japanese | Tokyo | Japan | JPN | Asia | 2004 |
| 67770 | Sputum | Tokyo | Japan | JPN | Asia |
isolation source categories
- Cat1: #Host Body Product
- Cat2: #Fluids
- Cat3: #Sputum
Safety information
risk assessment
- @ref: 18021
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18021
- description: Mycobacterium shinjukuense gene for 16S rRNA, partial sequence, strain: GTC 2738
- accession: AB268503
- length: 1505
- database: ena
- NCBI tax ID: 398694
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Mycobacterium shinjukuense JCM 14233 | GCA_010730055 | complete | ncbi | 398694 |
| 66792 | Mycobacterium shinjukuense strain CCUG 53584 | 398694.3 | wgs | patric | 398694 |
| 66792 | Mycobacterium shinjukuense strain JCM 14233 | 398694.15 | complete | patric | 398694 |
| 66792 | Mycobacterium shinjukuense CCUG 53584 | 2865597299 | draft | img | 398694 |
| 67770 | Mycobacterium shinjukuense CCUG 53584 | GCA_002086755 | contig | ncbi | 398694 |
| 66792 | Mycobacterium shinjukuense DSM 45663 | GCA_025822285 | scaffold | ncbi | 398694 |
GC content
- @ref: 67770
- GC-content: 67.8
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 52 | no |
| motile | no | 96.246 | no |
| flagellated | no | 99.023 | no |
| gram-positive | yes | 88.364 | no |
| anaerobic | no | 98.372 | no |
| aerobic | yes | 87.828 | no |
| halophile | no | 87.093 | no |
| spore-forming | no | 89.33 | no |
| glucose-util | yes | 60.528 | no |
| thermophile | no | 91.381 | yes |
| glucose-ferment | no | 91.157 | no |
External links
@ref: 18021
culture collection no.: DSM 45663, CCUG 53584, JCM 14233, GTC 2738
straininfo link
- @ref: 77971
- straininfo: 406773
literature
- topic: Phylogeny
- Pubmed-ID: 20833878
- title: Mycobacterium shinjukuense sp. nov., a slowly growing, non-chromogenic species isolated from human clinical specimens.
- authors: Saito H, Iwamoto T, Ohkusu K, Otsuka Y, Akiyama Y, Sato S, Taguchi O, Sueyasu Y, Kawabe Y, Fujimoto H, Ezaki T, Butler R
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.025478-0
- year: 2010
- mesh: Aged, Aged, 80 and over, Bacterial Proteins/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Female, Humans, Male, Middle Aged, Molecular Sequence Data, Mycobacterium/*classification/genetics/growth & development/*isolation & purification, Mycobacterium Infections/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics
- topic2: Pathogenicity
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 18021 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45663) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45663 | |||
| 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 | |||
| 59937 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 53584) | https://www.ccug.se/strain?id=53584 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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) | |||
| 77971 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406773.1 | StrainInfo: A central database for resolving microbial strain identifiers |