Strain identifier
BacDive ID: 1553
Type strain: 
Species: Tumebacillus permanentifrigoris
Strain Designation: Eur1 9.5
Strain history: L. Whyte Eur1 9.5.
NCBI tax ID(s): 378543 (species)
version 9.3 (current version)
General
@ref: 7690
BacDive-ID: 1553
DSM-Number: 18773
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Tumebacillus permanentifrigoris Eur1 9.5 is an aerobe, spore-forming, mesophilic bacterium that was isolated from 9-m-deep permafrost sample.
NCBI tax id
- NCBI tax id: 378543
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7690 | <- L.G. White; Eur1 9.5 |
| 67770 | L. Whyte Eur1 9.5. |
doi: 10.13145/bacdive1553.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Alicyclobacillaceae
- genus: Tumebacillus
- species: Tumebacillus permanentifrigoris
- full scientific name: Tumebacillus permanentifrigoris Steven et al. 2008
@ref: 7690
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Alicyclobacillaceae
genus: Tumebacillus
species: Tumebacillus permanentifrigoris
full scientific name: Tumebacillus permanentifrigoris Steven et al. 2008
strain designation: Eur1 9.5
type strain: yes
Morphology
cell morphology
- @ref: 32193
- gram stain: positive
- cell length: 3.25 µm
- cell width: 0.5 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 32193
- production: yes
Culture and growth conditions
culture medium
- @ref: 7690
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 7690 | positive | growth | 25 |
| 32193 | positive | growth | 05-37 |
| 32193 | positive | optimum | 27.5 |
| 67770 | positive | growth | 25 |
Physiology and metabolism
oxygen tolerance
- @ref: 32193
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32193 | yes | |
| 125438 | yes | 92.131 |
observation
- @ref: 67770
- observation: quinones: MK-7
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32193 | 17057 | cellobiose | + | carbon source |
| 32193 | 28260 | galactose | + | carbon source |
| 32193 | 17234 | glucose | + | carbon source |
| 32193 | 17716 | lactose | + | carbon source |
| 32193 | 17306 | maltose | + | carbon source |
| 32193 | 29864 | mannitol | + | carbon source |
| 32193 | 27082 | trehalose | + | carbon source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 7690 | 9-m-deep permafrost sample | High Arctic | Canada | CAN | North America |
| 67770 | 9-m-deep permafrost sample from the Canadian high Arctic |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Permafrost |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_31536.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1221;96_15361;97_18791;98_23427;99_31536&stattab=map
- Last taxonomy: Tumebacillus permanentifrigoris subclade
- 16S sequence: DQ444975
- Sequence Identity:
- Total samples: 14295
- soil counts: 9892
- aquatic counts: 1571
- animal counts: 651
- plant counts: 2181
Safety information
risk assessment
- @ref: 7690
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7690
- description: Tumebacillus permanentifrigoris strain Eur1 9.5 16S ribosomal RNA gene, partial sequence
- accession: DQ444975
- length: 1407
- database: nuccore
- NCBI tax ID: 378543
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Tumebacillus permanentifrigoris strain DSM 18773 | 378543.3 | wgs | patric | 378543 |
| 66792 | Tumebacillus permanentifrigoris DSM 18773 | 2756170254 | draft | img | 378543 |
| 67770 | Tumebacillus permanentifrigoris DSM 18773 | GCA_003148565 | scaffold | ncbi | 378543 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7690 | 53.1 | |
| 67770 | 53.1 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 66.73 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 86.193 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 92.131 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 72.464 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 80.93 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 75.261 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 87.9 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 76.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 78.8 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | anaerobe | 83.4 |
External links
@ref: 7690
culture collection no.: DSM 18773, JCM 14557, CGMCC 1.10982
straininfo link
- @ref: 71198
- straininfo: 407982
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18523202 | Tumebacillus permanentifrigoris gen. nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost. | Steven B, Chen MQ, Greer CW, Whyte LG, Niederberger TD | Int J Syst Evol Microbiol | 10.1099/ijs.0.65101-0 | 2008 | Aerobiosis, Arctic Regions, Bacillaceae/*classification/genetics/isolation & purification/*physiology, Bacterial Typing Techniques, Base Composition, Canada, Culture Media/chemistry, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Ice Cover/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Spores, Bacterial/physiology | Genetics |
| Phylogeny | 20802062 | Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field. | Baek SH, Cui Y, Kim SC, Cui CH, Yin C, Lee ST, Im WT | Int J Syst Evol Microbiol | 10.1099/ijs.0.023358-0 | 2010 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification, Molecular Sequence Data, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 23435245 | Tumebacillus flagellatus sp. nov., an alpha-amylase/pullulanase-producing bacterium isolated from cassava wastewater. | Wang Q, Xie N, Qin Y, Shen N, Zhu J, Mi H, Huang R | Int J Syst Evol Microbiol | 10.1099/ijs.0.045351-0 | 2013 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Glycoside Hydrolases/*biosynthesis, Gram-Positive Rods/*classification/genetics/isolation & purification, Manihot, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Waste Water/*microbiology, alpha-Amylases/*biosynthesis | Genetics |
| Phylogeny | 25858243 | Tumebacillus algifaecis sp. nov., isolated from decomposing algal scum. | Wu YF, Zhang B, Xing P, Wu QL, Liu SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.000240 | 2015 | Alicyclobacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, *Eutrophication, Fatty Acids/chemistry, Lakes, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 35580016 | Tumebacillus amylolyticus sp. nov., isolated from garden soil in Korea. | Kang M, Chhetri G, Kim J, Kim I, So Y, Seo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005376 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gardens, Humans, *Peptidoglycan/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Vitamin K 2/chemistry | Pathogenicity |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 7690 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18773) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18773 | |||
| 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 | |||
| 32193 | 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 | 28435 | 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/ | ||||
| 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 | |||
| 71198 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407982.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |