Strain identifier
BacDive ID: 133873
Type strain:
Species: Brevundimonas abyssalis
Strain Designation: TAR-001
Strain history: CIP <- 2013, CECT
NCBI tax ID(s): 1125965 (species)
General
@ref: 30734
BacDive-ID: 133873
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile
description: Brevundimonas abyssalis TAR-001 is an aerobe, Gram-negative, motile bacterium that was isolated from Deep-subsea floor sediment at a depth of 11 m below the sea floor off the Shimokita Peninsula of Japan.
NCBI tax id
- NCBI tax id: 1125965
- Matching level: species
strain history
@ref | history |
---|---|
36195 | 2013, CECT |
67770 | T. Tsubouchi TAR-001. |
115983 | CIP <- 2013, CECT |
doi: 10.13145/bacdive133873.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Caulobacterales
- family: Caulobacteraceae
- genus: Brevundimonas
- species: Brevundimonas abyssalis
- full scientific name: Brevundimonas abyssalis Tsubouchi et al. 2013
@ref: 30734
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Caulobacterales
family: Caulobacteraceae
genus: Brevundimonas
species: Brevundimonas abyssalis
strain designation: TAR-001
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | motility | cell shape |
---|---|---|---|---|---|
30734 | negative | 2.75 µm | 0.4 µm | yes | |
115983 | negative | yes | rod-shaped |
pigmentation
- @ref: 30734
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
36195 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
115983 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
30734 | positive | growth | 02-41 | |
30734 | positive | optimum | 20 | psychrophilic |
36195 | positive | growth | 20 | psychrophilic |
67770 | positive | growth | 20 | psychrophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30734 | positive | growth | 6.5-10.0 | alkaliphile |
30734 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30734
- oxygen tolerance: aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30734 | NaCl | positive | growth | 01-04 % |
30734 | NaCl | positive | optimum | 1.5 % |
metabolite utilization
- @ref: 30734
- Chebi-ID: 4853
- metabolite: esculin
- utilization activity: +
- kind of utilization tested: hydrolysis
enzymes
@ref | value | activity | ec |
---|---|---|---|
30734 | acid phosphatase | + | 3.1.3.2 |
30734 | alkaline phosphatase | + | 3.1.3.1 |
30734 | alpha-galactosidase | + | 3.2.1.22 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
67770 | Deep-subsea floor sediment at a depth of 11 m below the sea floor off the Shimokita Peninsula of Japan | |||
115983 | Environment, Deep see floor sediment | Japan | JPN | Asia |
taxonmaps
- @ref: 69479
- File name: preview.99_6975.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_73;96_3275;97_4016;98_5122;99_6975&stattab=map
- Last taxonomy: Brevundimonas abyssalis
- 16S sequence: AB688113
- Sequence Identity:
- Total samples: 1342
- soil counts: 459
- aquatic counts: 526
- animal counts: 288
- plant counts: 69
Safety information
risk assessment
- @ref: 115983
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
16S sequences
- @ref: 30734
- description: Brevundimonas abyssalis gene for 16S ribosomal RNA, partial sequence
- accession: AB688113
- length: 1406
- database: nuccore
- NCBI tax ID: 1391729
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Brevundimonas abyssalis TAR-001 | 1391729.3 | wgs | patric | 1391729 |
66792 | Brevundimonas abyssalis TAR-001 | 2574180166 | draft | img | 1391729 |
67770 | Brevundimonas abyssalis TAR-001 | GCA_000466985 | contig | ncbi | 1391729 |
GC content
- @ref: 30734
- GC-content: 67.6
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 87.379 | yes |
gram-positive | no | 97.964 | yes |
anaerobic | no | 98.656 | no |
halophile | no | 89.591 | yes |
spore-forming | no | 96.22 | no |
thermophile | no | 98.685 | no |
glucose-util | yes | 77.02 | no |
aerobic | yes | 89.563 | yes |
flagellated | no | 91.87 | no |
glucose-ferment | no | 93.314 | no |
External links
@ref: 30734
culture collection no.: JCM 18150, CECT 8073, CIP 110627
straininfo link
- @ref: 91625
- straininfo: 388598
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23041635 | Brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment. | Tsubouchi T, Shimane Y, Usui K, Shimamura S, Mori K, Hiraki T, Tame A, Uematsu K, Maruyama T, Hatada Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.043364-0 | 2012 | Bacterial Typing Techniques, Base Composition, Caulobacteraceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/analysis | Genetics |
Genetics | 24136847 | Draft Genome Sequence of the Dimorphic Prosthecate Bacterium Brevundimonas abyssalis TAR-001T. | Tsubouchi T, Nishi S, Usui K, Shimane Y, Takaki Y, Maruyama T, Hatada Y | Genome Announc | 10.1128/genomeA.00826-13 | 2013 |
Reference
@id | authors | title | doi/url | ID_cross_reference | pubmed | 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 | |||
30734 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27065 | 28776041 | |
36195 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/30429 | ||||
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 | |||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
91625 | 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-ID388598.1 | |||
115983 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110627 | Collection of Institut Pasteur (CIP 110627) |