Strain identifier
BacDive ID: 1862
Type strain: 
Species: Brevibacterium antiquum
Strain history: LMG 22206 <-- VKM Ac-2118 <-- S. G. Karasev.
NCBI tax ID(s): 234835 (species)
version 9.3 (current version)
General
@ref: 15784
BacDive-ID: 1862
DSM-Number: 21545
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic
description: Brevibacterium antiquum DSM 21545 is an aerobe, mesophilic bacterium that was isolated from 1.8- to 3-Million-year-old ancient permafrost sediments.
NCBI tax id
- NCBI tax id: 234835
- Matching level: species
strain history
| @ref | history |
|---|---|
| 15784 | <- JCM <- LMG <- VKM <- S. G. Karasev |
| 67770 | LMG 22206 <-- VKM Ac-2118 <-- S. G. Karasev. |
doi: 10.13145/bacdive1862.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Brevibacteriaceae
- genus: Brevibacterium
- species: Brevibacterium antiquum
- full scientific name: Brevibacterium antiquum Gavrish et al. 2005
@ref: 15784
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Brevibacteriaceae
genus: Brevibacterium
species: Brevibacterium antiquum
full scientific name: Brevibacterium antiquum Gavrish et al. 2005
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 125438 | no | 90.267 | |
| 125438 | 92.642 | positive |
Culture and growth conditions
culture medium
- @ref: 15784
- 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 |
|---|---|---|---|
| 15784 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 125438 | aerobe | 92.077 |
| 125439 | obligate aerobe | 90.3 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 94.6
observation
- @ref: 67770
- observation: quinones: MK-8(H2)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 15784 | 1.8- to 3-Million-year-old ancient permafrost sediments | Kolyma Lowland, East Siberia | Russia | RUS | Asia |
| 67770 | 1.8- to 3-Million-year-old ancient permafrost sediments | Kolyma Lowland, East Siberia | Russia | RUS |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Permafrost |
| #Environmental | #Terrestrial | #Sediment |
Safety information
risk assessment
- @ref: 15784
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15784
- description: Brevibacterium antiquum strain VKM Ac-2118 16S ribosomal RNA gene, partial sequence
- accession: AY243344
- length: 1501
- database: nuccore
- NCBI tax ID: 234835
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Brevibacterium antiquum DSM 21545 | GCA_016107655 | contig | ncbi | 234835 |
| 66792 | Brevibacterium antiquum strain DSM 21545 | 234835.13 | wgs | patric | 234835 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 92.642 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.233 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 68.651 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 92.077 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.471 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 90.267 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 94.6 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 54.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 80 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 90.3 |
External links
@ref: 15784
culture collection no.: DSM 21545, JCM 13317, LMG 22206, UCM Ac-411, VKM Ac-2118
straininfo link
- @ref: 71507
- straininfo: 127961
literature
| topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15198034 | [Three new species of brevibacteria--Brevibacterium antiquum sp. nov., Brevibacterium aurantiacum sp. nov. and Brevibacterium permense sp. nov]. | Gavrish EIu, Krauzova VI, Potekhina NV, Karasev SG, Plotnikova EG, Altyntseva OV, Korosteleva LA, Evtushenko LI | Mikrobiologiia | 2004 | Brevibacterium/chemistry/*classification/physiology, DNA, Bacterial/genetics, *Genome, Bacterial, Molecular Sequence Data, Phylogeny, Pigments, Biological, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/chemistry/genetics, Russia, Sequence Analysis, *Soil Microbiology, Soil Pollutants, Teichoic Acids/chemistry | Genetics | |
| Phylogeny | 25843055 | Increase in Bacterial Colony Formation from a Permafrost Ice Wedge Dosed with a Tomitella biformata Recombinant Resuscitation-Promoting Factor Protein. | Puspita ID, Kitagawa W, Kamagata Y, Tanaka M, Nakatsu CH | Microbes Environ | 2015 | Actinobacteria/*isolation & purification/*metabolism, Bacteria/*growth & development/*isolation & purification, Bacterial Proteins/genetics/*metabolism, Cluster Analysis, Colony Count, Microbial, Cytokines/genetics/*metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Microbial Viability/*drug effects, Molecular Sequence Data, Permafrost/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Recombinant Proteins/genetics/metabolism, Sequence Analysis, DNA, Time Factors | Metabolism | 10.1264/jsme2.ME14119 |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 15784 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21545) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21545 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 71507 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID127961.1 | 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 |