Strain identifier

BacDive ID: 1882

Type strain: Yes

Species: Brucella grignonensis

Strain Designation: OgA9a

Strain history: CIP <- 2002, A. Hartmann, Helmholz Center, Munich-Neuherberg, Germany: strain OgA9a <- M. Lebuhn

NCBI tax ID(s): 94627 (species)

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General

@ref: 5001

BacDive-ID: 1882

DSM-Number: 13338

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Brucella grignonensis OgA9a is an obligate aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from soil.

NCBI tax id

  • NCBI tax id: 94627
  • Matching level: species

strain history

@refhistory
5001<- M. Lebuhn; OgA9a
119740CIP <- 2002, A. Hartmann, Helmholz Center, Munich-Neuherberg, Germany: strain OgA9a <- M. Lebuhn

doi: 10.13145/bacdive1882.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Brucellaceae
  • genus: Brucella
  • species: Brucella grignonensis
  • full scientific name: Brucella grignonensis (Lebuhn et al. 2000) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Ochrobactrum grignonense

@ref: 5001

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Brucellaceae

genus: Brucella

species: Brucella grignonensis

full scientific name: Brucella grignonensis (Lebuhn et al. 2000) Hördt et al. 2020

strain designation: OgA9a

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
23335negative0.6-1.2 µm0.4 µmrod-shapedyesperitrichous
119740negativerod-shapedno

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium usedhemolysis ability
233351 mmmilky opaquecircular1 dayNA
1197401

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5001NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
23335Nutrient agar (NA)yes
33779MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119740CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5001positivegrowth30mesophilic
23335positivegrowth4-40
23335positiveoptimum30mesophilic
33779positivegrowth30mesophilic
119740positivegrowth15-37
119740nogrowth5psychrophilic
119740nogrowth41thermophilic
119740nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
23335positivegrowth3.0-9.0alkaliphile
23335positiveoptimum6.0-7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 119740
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119740NaClpositivegrowth0-4 %
119740NaClnogrowth6 %
119740NaClnogrowth8 %
119740NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2333517521(-)-quinic acid-assimilation
2333515963ribitol-assimilation
2333517784D-glucosaminic acid-assimilation
2333516551D-trehalose-assimilation
2333517306maltose-assimilation
2333541865sebacic acid-assimilation
23335645522-hydroxybutyrate+assimilation
2333516947citrate+assimilation
2333517754glycerol+assimilation
2333515792malonate+assimilation
2333537684mannose+assimilation
2333528053melibiose+assimilation
2333516704uridine+assimilation
2333522599arabinose+builds acid from
2333528053melibiose+builds acid from
2333522599arabinose+/-assimilation
2333517057cellobiose+/-assimilation
2333517126DL-carnitine+/-assimilation
2333528066gentiobiose+/-assimilation
2333524265gluconate+/-assimilation
2333514336glycerol 1-phosphate+/-assimilation
2333517151xylitol+/-assimilation
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
11974016947citrate+carbon source
1197404853esculin-hydrolysis
119740606565hippurate+hydrolysis
11974017632nitrate+reduction
11974016301nitrite+reduction
11974015792malonate+assimilation
11974017632nitrate+respiration
6837717634D-glucose+builds acid from
6837717306maltose-builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis intermediateis sensitive
2333537943colistinyesyes
233358309polymyxin byesyes
2333517698chloramphenicolyesyes
1197400129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesyesno

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11974035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
11974015688acetoin-
11974017234glucose-

enzymes

@refvalueactivityec
23335urease-3.5.1.5
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
68377beta-galactosidase-3.2.1.23
68377alkaline phosphatase-3.1.3.1
68377beta-lactamase+3.5.2.6
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
119740oxidase+
119740beta-galactosidase-3.2.1.23
119740alcohol dehydrogenase-1.1.1.1
119740gelatinase-
119740amylase-
119740DNase-
119740caseinase-3.4.21.50
119740catalase+1.11.1.6
119740tween esterase-
119740gamma-glutamyltransferase+2.3.2.2
119740lecithinase-
119740lipase-
119740lysine decarboxylase-4.1.1.18
119740ornithine decarboxylase-4.1.1.17
119740phenylalanine ammonia-lyase-4.3.1.24
119740tryptophan deaminase-
119740urease+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
119740-++--+--+-+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5001+-------++++/-+-++-++-
5001+-------+++-+-++-++-+

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
5001++--++/-+---+-+
5001+++--++/-+---+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119740+++-+--------------+++-++-+--++++------++----+--+++--++++--++-+--+-----+-+-+---++++---+-++++--+++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
5001soilFranceFRAEurope
23335soil of the Grignon Experimental Station
57167SoilFranceFRAEuropeGrignon
119740Environment, Soil samples and wheat rootsFranceFRAEuropeGrignon1998

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_45821.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_45;97_1426;98_1736;99_45821&stattab=map
  • Last taxonomy: Ochrobactrum
  • 16S sequence: AM490619
  • Sequence Identity:
  • Total samples: 33
  • soil counts: 8
  • aquatic counts: 2
  • animal counts: 21
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
50011Risk group (German classification)
1197401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ochrobactrum grignonense gene for 16S rRNA, partial sequence, strain: NBRC 102586AB6818661407ena94627
20218Ochrobactrum grignonense partial 16S rRNA gene, strain Oga9aAM4906191387ena94627
23335Ochrobactrum grignonense 16S rRNA gene (partial), 23S rRNA gene (partial), tRNA-Ile gene, tRNA-Ala gene and ITS1, type strain OgA9aAJ2425812349nuccore94627

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brucella grignonensis OgA9aGCA_002252505contigncbi94627
66792Brucella grignonensis LMG 18954GCA_012103085contigncbi94627
66792Ochrobactrum grignonense strain LMG 1895494627.15wgspatric94627
66792Brucella grignonensis OgA9a2834567989draftimg94627

GC content

  • @ref: 23335
  • GC-content: 58.00
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes76.366no
flagellatedno83.924no
gram-positiveno98.431no
anaerobicno96.751no
halophileno93.993no
spore-formingno96.863no
thermophileno98.452yes
glucose-utilyes90.776yes
aerobicyes89.631no
glucose-fermentno90.56yes

External links

@ref: 5001

culture collection no.: DSM 13338, NBRC 102586, CCUG 46362, CIP 107373, LMG 18954

straininfo link

  • @ref: 71526
  • straininfo: 13105

literature

  • topic: Phylogeny
  • Pubmed-ID: 11155998
  • title: Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov.
  • authors: Lebuhn M, Achouak W, Schloter M, Berge O, Meier H, Barakat M, Hartmann A, Heulin T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-6-2207
  • year: 2000
  • mesh: Alphaproteobacteria/*classification/genetics/immunology/isolation & purification/metabolism, Antibodies, Bacterial/immunology, Antibodies, Monoclonal/immunology, Bacterial Typing Techniques, DNA, Ribosomal/analysis, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Triticum/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5001Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13338)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13338
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
23335M Lebuhn, W Achouak, M Schloter, O Berge, H Meier, M Barakat, A Hartmann, T Heulin10.1099/00207713-50-6-2207Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov.IJSEM 50: 2207-2223 200011155998
33779Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4801
57167Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46362)https://www.ccug.se/strain?id=46362
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)
68369Automatically annotated from API 20NE
68377Automatically annotated from API NH
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
71526Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13105.1StrainInfo: A central database for resolving microbial strain identifiers
119740Curators of the CIPCollection of Institut Pasteur (CIP 107373)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107373