Strain identifier
BacDive ID: 159652
Type strain: 
Species: Abditibacterium utsteinense
Strain Designation: R-68213
Strain history: <- A. Willems, Lab. Microbiology, Ghent Univ., Belgium <- G. Tahon, Laboratory of Microbiology, Ghent University, Gent, Belgium
NCBI tax ID(s): 1960156 (species)
version 9.3 (current version)
General
@ref: 66502
BacDive-ID: 159652
DSM-Number: 105287
keywords: genome sequence, 16S sequence, Bacteria, psychrophilic
description: Abditibacterium utsteinense R-68213 is a psychrophilic bacterium that was isolated from Top surface sample consisting of weathered granite parent material, elevation 1382 m.
NCBI tax id
- NCBI tax id: 1960156
- Matching level: species
strain history
- @ref: 66502
- history: <- A. Willems, Lab. Microbiology, Ghent Univ., Belgium <- G. Tahon, Laboratory of Microbiology, Ghent University, Gent, Belgium
doi: 10.13145/bacdive159652.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/abditibacteriota
- domain: Bacteria
- phylum: Abditibacteriota
- class: Abditibacteriia
- order: Abditibacteriales
- family: Abditibacteriaceae
- genus: Abditibacterium
- species: Abditibacterium utsteinense
- full scientific name: Abditibacterium utsteinense Tahon et al. 2018
@ref: 66502
domain: Bacteria
phylum: Abditibacteriota
class: Abditibacteria
order: Abditibacteriales
family: Abditibacteriaceae
genus: Abditibacterium
species: Abditibacterium utsteinense
full scientific name: Abditibacterium utsteinense Tahon et al. 2018
strain designation: R-68213
type strain: yes
Morphology
cell morphology
- @ref: 125439
- gram stain: negative
- confidence: 99.7
multimedia
- @ref: 66502
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_105287.jpg
- caption: DSM 105287 on medium 830 at 20 °C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 66502
- 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: 66502
- growth: positive
- type: growth
- temperature: 20
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 99.6
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98
Isolation, sampling and environmental information
isolation
- @ref: 66502
- sample type: Top surface sample consisting of weathered granite parent material, elevation 1382 m
- geographic location: East Antarctica, Utsteinen, near Belgian Princess Elisabeth Station (71° 57' S, 23° 20' E)
- country: Antarctica
- origin.country: ATA
- continent: Australia and Oceania
- latitude: -71.9465
- longitude: 23.3457
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Climate | #Cold | #Alpine |
| #Environmental | #Terrestrial | #Geologic |
Sequence information
16S sequences
- @ref: 66502
- description: Abditibacterium utsteinense strain R-68213 16S ribosomal RNA gene, partial sequence
- accession: KY386500
- length: 1473
- database: nuccore
- NCBI tax ID: 1960156
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Abditibacterium utsteinense LMG 29911 | GCA_002973605 | contig | ncbi | 1960156 |
| 66792 | Abditibacterium utsteinense strain LMG 29911 | 1960156.3 | wgs | patric | 1960156 |
GC content
- @ref: 66502
- GC-content: 54.27
- method: sequence analysis
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 79.348 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 86.284 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 73.54 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 71.009 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 89.465 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 75.712 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 68.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.7 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.6 |
External links
@ref: 66502
culture collection no.: DSM 105287, LMG 29911
straininfo link
- @ref: 112126
- straininfo: 404846
literature
- topic: Phylogeny
- Pubmed-ID: 29475572
- title: Abditibacterium utsteinense sp. nov., the first cultivated member of candidate phylum FBP, isolated from ice-free Antarctic soil samples.
- authors: Tahon G, Tytgat B, Lebbe L, Carlier A, Willems A
- journal: Syst Appl Microbiol
- DOI: 10.1016/j.syapm.2018.01.009
- year: 2018
- mesh: Antarctic Regions, Bacterial Typing Techniques, Base Composition, Base Sequence, DNA, Bacterial/genetics, Drug Resistance, Multiple, Bacterial/genetics, Fatty Acids/analysis, Genome, Bacterial/*genetics, *Gram-Negative Anaerobic Bacteria/classification/genetics/isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology
- topic2: Genetics
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 | |
| 66502 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-105287 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105287) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 112126 | 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-ID404846.1 | |
| 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 |