Strain identifier
BacDive ID: 8401
Type strain: 
Species: Mycobacterium gilvum
Strain Designation: Spyr1
Strain history: <- A. Kallimanis, Univ. Ioannina, Dept. Of Chemistry; Spyr1
NCBI tax ID(s): 1804 (species)
version 9.1 (current version)
General
@ref: 15648
BacDive-ID: 8401
DSM-Number: 45189
keywords: genome sequence, 16S sequence, Bacteria
description: Mycobacterium gilvum Spyr1 is a bacterium that was isolated from soil from a creosote contaminated site.
NCBI tax id
- NCBI tax id: 1804
- Matching level: species
strain history
- @ref: 15648
- history: <- A. Kallimanis, Univ. Ioannina, Dept. Of Chemistry; Spyr1
doi: 10.13145/bacdive8401.20240916.9.1
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 gilvum
- full scientific name: Mycobacterium gilvum Stanford and Gunthorpe 1971 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Mycolicibacterium gilvum
@ref: 15648
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium gilvum
full scientific name: Mycobacterium gilvum Stanford and Gunthorpe 1971
strain designation: Spyr1
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 90.069
multimedia
- @ref: 15648
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45189.jpg
- caption: Medium 250 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 15648 | MIDDLEBROOK MEDIUM (DSMZ Medium 645) | yes | https://mediadive.dsmz.de/medium/645 | Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water |
| 15648 | PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250) | yes | https://mediadive.dsmz.de/medium/250 | Name: PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250) Composition: Agar 20.0 g/l Proteose peptone no. 3 5.0 g/l Meat extract 3.0 g/l Glycerol Distilled water |
culture temp
- @ref: 15648
- growth: positive
- type: growth
- temperature: 37
Isolation, sampling and environmental information
isolation
- @ref: 15648
- sample type: soil from a creosote contaminated site
- geographic location: Ioannina NW
- country: Greece
- origin.country: GRC
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 15648
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15648
- description: Mycobacterium gilvum Spyr1 16S rRNA gene, strain Spyr1
- accession: AJ699170
- length: 1283
- database: nuccore
- NCBI tax ID: 278137
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Mycobacterium gilvum Spyr1 | 278137.19 | plasmid | patric | 278137 |
| 66792 | Mycobacterium gilvum Spyr1 | 278137.18 | plasmid | patric | 278137 |
| 66792 | Mycobacterium gilvum Spyr1 | 278137.3 | complete | patric | 278137 |
GC content
- @ref: 15648
- GC-content: 67
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 90.069 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.587 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 56.778 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.333 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 96 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 87 | no |
External links
@ref: 15648
culture collection no.: DSM 45189, LMG 24558
straininfo link
- @ref: 77800
- straininfo: 402964
literature
- topic: Genetics
- Pubmed-ID: 22180818
- title: Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1.
- authors: Kallimanis A, Karabika E, Mavromatis K, Lapidus A, Labutti KM, Liolios K, Ivanova N, Goodwin L, Woyke T, Velentzas AD, Perisynakis A, Ouzounis CC, Kyrpides NC, Koukkou AI, Drainas C
- journal: Stand Genomic Sci
- DOI: 10.4056/sigs.2265047
- year: 2011
- topic2: Phylogeny
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 15648 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45189) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45189 | |
| 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 | |
| 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) | |
| 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) | |
| 77800 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402964.1 | StrainInfo: A central database for resolving microbial strain identifiers |