Strain identifier
BacDive ID: 131463
Type strain: 
Species: Domibacillus tundrae
Strain history: H. R. Gyeong; KOPRI, South Korea; PAMC 80007.
NCBI tax ID(s): 1587527 (species)
version 9.3 (current version)
General
@ref: 22690
BacDive-ID: 131463
DSM-Number: 29572
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Domibacillus tundrae DSM 29572 is a mesophilic bacterium that was isolated from active layer soil from moist acidic tussock tundra.
NCBI tax id
- NCBI tax id: 1587527
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22690 | <- HyeRyeon Gyeong, Korea Polar Research Institute, Incheon; PAMC 80007 |
| 67770 | H. R. Gyeong; KOPRI, South Korea; PAMC 80007. |
doi: 10.13145/bacdive131463.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Bacillaceae
- genus: Domibacillus
- species: Domibacillus tundrae
- full scientific name: Domibacillus tundrae Gyeong et al. 2015
@ref: 22690
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Bacillaceae
genus: Domibacillus
species: Domibacillus tundrae
full scientific name: Domibacillus tundrae Gyeong et al. 2015
type strain: yes
Culture and growth conditions
culture medium
- @ref: 22690
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 22690 | positive | growth | 30 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 97.5
spore formation
- @ref: 125439
- spore formation: yes
- confidence: 95.1
observation
- @ref: 67770
- observation: quinones: MK-6, MK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 22690 | active layer soil from moist acidic tussock tundra | Alaska, Council (64.50765° N 163.42696° W) | USA | USA | North America | 64.5076 | -163.427 |
| 67770 | Active layer soil of Council | Alaska | USA | USA | North America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Condition | #Acidic | |
| #Condition | #Psychrophilic (<10°C) | |
| #Climate | #Cold | #Tundra |
Safety information
risk assessment
- @ref: 22690
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22690
- description: Domibacillus tundrae strain PAMC 80007 16S ribosomal RNA gene, partial sequence
- accession: KM657429
- length: 1482
- database: nuccore
- NCBI tax ID: 1587527
Genome sequences
- @ref: 67770
- description: Domibacillus tundrae PAMC 80007
- accession: GCA_000970675
- assembly level: contig
- database: ncbi
- NCBI tax ID: 1587527
GC content
| @ref | GC-content | method |
|---|---|---|
| 22690 | 43.5 | sequence analysis |
| 67770 | 43.5 | genome sequence analysis |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 76.727 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.036 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 77.95 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 89.658 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 87.779 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 77.65 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 95.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 87.6 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | variable | 85.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97.5 |
External links
@ref: 22690
culture collection no.: DSM 29572, JCM 30371, KCTC 33549, PAMC 80007
straininfo link
- @ref: 89882
- straininfo: 400438
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26296675 | Domibacillus tundrae sp. nov., isolated from active layer soil of tussock tundra in Alaska, and emended description of the genus Domibacillus. | Gyeong HR, Baek K, Hwang CY, Park KH, Kim HM, Lee HK, Lee YK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000429 | 2015 | Alaska, Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Tundra, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 27073919 | Domibacillus antri sp. nov., isolated from the soil of a cave. | Xu D, Wang L, Wang G, Zheng S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001080 | 2016 | Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 22690 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29572 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29572) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 89882 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID400438.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |