Strain identifier

BacDive ID: 2306

Type strain: Yes

Species: Brevundimonas variabilis

Strain history: CIP <- 2000, W.R. Abraham, GBF, Braunschweig, Germany <- ATCC <- J.S. Poindexter: strain CB 17

NCBI tax ID(s): 74312 (species)

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General

@ref: 1743

BacDive-ID: 2306

DSM-Number: 4737

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Brevundimonas variabilis CCUG 48882 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from pond water.

NCBI tax id

  • NCBI tax id: 74312
  • Matching level: species

strain history

@refhistory
1743<- ATCC <- J.S. Poindexter, CB 17
123797CIP <- 2000, W.R. Abraham, GBF, Braunschweig, Germany <- ATCC <- J.S. Poindexter: strain CB 17

doi: 10.13145/bacdive2306.20230509.8.1

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 variabilis
  • full scientific name: Brevundimonas variabilis (Poindexter 1989 ex Poindexter 1964) Abraham et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Caulobacter variabilis

@ref: 1743

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Caulobacteraceae

genus: Brevundimonas

species: Brevundimonas variabilis

full scientific name: Brevundimonas variabilis (Poindexter 1989) Abraham et al. 1999

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.999
123797negativerod-shapedno

pigmentation

  • @ref: 123797
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1743CAULOBACTER MEDIUM (DSMZ Medium 595)yeshttps://mediadive.dsmz.de/medium/595Name: CAULOBACTER MEDIUM (DSMZ Medium 595) Composition: Agar 15.0 g/l Bacto peptone 2.0 g/l Yeast extract 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Tap water
40322MEDIUM 341 - for Caulobacter and BrevundimonasyesDistilled water make up to (995.000 ml);Magnesium sulphate heptahydrate (0.200 g);Calcium chloride dihydrate (0.100 g);Agar (15.000 g);Yeast extract (1.000 g);Peptone (2.000 g);Vitamin solution - M0655 (5.000 ml)
123797CIP Medium 341yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=341

culture temp

@refgrowthtypetemperaturerange
1743positivegrowth30mesophilic
40322positivegrowth30mesophilic
58379positivegrowth30mesophilic
123797positivegrowth10-37
123797nogrowth5psychrophilic
123797nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 58379
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
123797NaClpositivegrowth0 %
123797NaClnogrowth2 %
123797NaClnogrowth4 %
123797NaClnogrowth6 %
123797NaClnogrowth8 %
123797NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12379716947citrate-carbon source
1237974853esculin+hydrolysis
12379717632nitrate-reduction
12379716301nitrite-reduction

antibiotic resistance

  • @ref: 123797
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123797
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 123797
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123797oxidase-
123797beta-galactosidase+3.2.1.23
123797alcohol dehydrogenase-1.1.1.1
123797gelatinase-
123797catalase+1.11.1.6
123797lysine decarboxylase-4.1.1.18
123797ornithine decarboxylase-4.1.1.17
123797tryptophan deaminase-
123797urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123797-+++-++-+--+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123797+-++---+--+-------+-----------------------------------------+--------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
1743pond water
58379Water,pond
123797Environment, Pond water

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Pond (small)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17431Risk group (German classification)
1237971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Caulobacter variabilis 16S rRNA geneAJ0078081391ena74312
1743Brevundimonas variabilis DNA for 16S ribosomal RNA, strain ATCC 15255 (T)AJ2277831416ena74312

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brevundimonas variabilis DSM 4737GCA_014199945contigncbi74312
66792Brevundimonas variabilis strain DSM 473774312.3wgspatric74312
66792Brevundimonas variabilis DSM 47372829757494draftimg74312

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileyes87.232no
flagellatedno79.854no
gram-positiveno97.724no
anaerobicno98.91yes
aerobicyes92.542yes
halophileno95.209no
spore-formingno94.858no
thermophileno98.55yes
glucose-utilyes79.339no
glucose-fermentno92.462no

External links

@ref: 1743

culture collection no.: CCUG 48882, CIP 106445, DSM 4737, ATCC 15255, CB 17, KCTC 12443

straininfo link

  • @ref: 71863
  • straininfo: 11938

literature

  • topic: Phylogeny
  • Pubmed-ID: 19671711
  • title: Brevundimonas basaltis sp. nov., isolated from black sand.
  • authors: Choi JH, Kim MS, Roh SW, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.013557-0
  • year: 2009
  • mesh: Base Sequence, Caulobacteraceae/*classification/genetics/isolation & purification/physiology, Fatty Acids/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1743Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4737)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4737
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40322Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18576
58379Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48882)https://www.ccug.se/strain?id=48882
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71863Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11938.1StrainInfo: A central database for resolving microbial strain identifiers
123797Curators of the CIPCollection of Institut Pasteur (CIP 106445)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106445