Strain identifier

BacDive ID: 133873

Type strain: Yes

Species: Brevundimonas abyssalis

Strain Designation: TAR-001

Strain history: CIP <- 2013, CECT

NCBI tax ID(s): 1125965 (species)

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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

@refhistory
361952013, CECT
67770T. Tsubouchi TAR-001.
115983CIP <- 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

@refgram staincell lengthcell widthmotilitycell shape
30734negative2.75 µm0.4 µmyes
115983negativeyesrod-shaped

pigmentation

  • @ref: 30734
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36195MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
115983CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
30734positivegrowth02-41
30734positiveoptimum20psychrophilic
36195positivegrowth20psychrophilic
67770positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
30734positivegrowth6.5-10.0alkaliphile
30734positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30734
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
30734NaClpositivegrowth01-04 %
30734NaClpositiveoptimum1.5 %

metabolite utilization

  • @ref: 30734
  • Chebi-ID: 4853
  • metabolite: esculin
  • utilization activity: +
  • kind of utilization tested: hydrolysis

enzymes

@refvalueactivityec
30734acid phosphatase+3.1.3.2
30734alkaline phosphatase+3.1.3.1
30734alpha-galactosidase+3.2.1.22

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
67770Deep-subsea floor sediment at a depth of 11 m below the sea floor off the Shimokita Peninsula of Japan
115983Environment, Deep see floor sedimentJapanJPNAsia

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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevundimonas abyssalis TAR-0011391729.3wgspatric1391729
66792Brevundimonas abyssalis TAR-0012574180166draftimg1391729
67770Brevundimonas abyssalis TAR-001GCA_000466985contigncbi1391729

GC content

  • @ref: 30734
  • GC-content: 67.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.379yes
gram-positiveno97.964yes
anaerobicno98.656no
halophileno89.591yes
spore-formingno96.22no
thermophileno98.685no
glucose-utilyes77.02no
aerobicyes89.563yes
flagellatedno91.87no
glucose-fermentno93.314no

External links

@ref: 30734

culture collection no.: JCM 18150, CECT 8073, CIP 110627

straininfo link

  • @ref: 91625
  • straininfo: 388598

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23041635Brevundimonas 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 YInt J Syst Evol Microbiol10.1099/ijs.0.043364-02012Bacterial 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/analysisGenetics
Genetics24136847Draft Genome Sequence of the Dimorphic Prosthecate Bacterium Brevundimonas abyssalis TAR-001T.Tsubouchi T, Nishi S, Usui K, Shimane Y, Takaki Y, Maruyama T, Hatada YGenome Announc10.1128/genomeA.00826-132013

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
30734Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172706528776041
36195Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30429
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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 betahttps://microbeatlas.org/
91625Reimer, 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 identifiers10.60712/SI-ID388598.1
115983Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110627Collection of Institut Pasteur (CIP 110627)