Strain identifier

BacDive ID: 1892

Type strain: Yes

Species: Brucella pseudogrignonensis

Strain history: 2007, CCUG

NCBI tax ID(s): 419475 (species)

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General

@ref: 16310

BacDive-ID: 1892

DSM-Number: 22354

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped, colony-forming, human pathogen

description: Brucella pseudogrignonensis DSM 22354 is a mesophilic, Gram-negative, rod-shaped human pathogen that forms circular colonies and was isolated from blood of a 28-year-old man.

NCBI tax id

  • NCBI tax id: 419475
  • Matching level: species

strain history

@refhistory
16310<- CIP <- CCUG <- ?
375602007, CCUG

doi: 10.13145/bacdive1892.20230509.8.1

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 pseudogrignonensis
  • full scientific name: Brucella pseudogrignonensis (Kämpfer et al. 2007) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Ochrobactrum pseudogrignonense

@ref: 16310

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Brucellaceae

genus: Brucella

species: Brucella pseudogrignonensis

full scientific name: Brucella pseudogrignonensis (Kämpfer et al. 2007) Hördt et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
23341negative2 µmrod-shapedno
69480negative99.977

colony morphology

  • @ref: 23341
  • colony size: 2 mm
  • colony color: beige, translucent
  • colony shape: circular
  • incubation period: 1 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16310CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
23341MacConkeyyes
23341Nutrient agar (NA)yes
23341PYE agaryes
23341Reasoner's 2A agar (R2A)yes
23341Trypticase Soy Agar (TSA)yes
37560MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
16310positivegrowth30mesophilic
23341positivegrowth28-30mesophilic
23341positivegrowth4psychrophilic
23341nogrowth42thermophilic
37560positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
23341no
69481no100
69480no99.993

halophily

  • @ref: 23341
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
23341178794-hydroxybenzoate-assimilation
2334117057cellobiose-assimilation
2334117306maltose-assimilation
2334168428maltitol-assimilation
23341506227N-acetylglucosamine-assimilation
233419300suberic acid-assimilation
23341gamma-L-glutamate-4-nitroanilide-hydrolysis
2334116865gamma-aminobutyric acid+assimilation
2334115963ribitol+assimilation
2334116958beta-alanine+assimilation
2334116383cis-aconitate+assimilation
2334116947citrate+assimilation
2334115824D-fructose+assimilation
2334117924D-sorbitol+assimilation
23341370543-hydroxybutyrate+assimilation
2334129991L-aspartate+assimilation
2334115971L-histidine+assimilation
2334115603L-leucine+assimilation
2334162345L-rhamnose+assimilation
2334117268myo-inositol+assimilation
2334128037N-acetylgalactosamine+assimilation
2334117992sucrose+assimilation
2334115708trans-aconitate+assimilation
2334127082trehalose+assimilation
23341L-proline-4-nitroanilide+hydrolysis
2334191050p-nitrophenyl phenyl phosphonate+/-hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
16310cytochrome-c oxidase+1.9.3.1
23341cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16310+-------++++/-+/-----++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16310blood of a 28-year-old manGöteborgSwedenSWEEurope
50239Human blood,28-yr-old manGöteborgSwedenSWEEurope1992-10-28

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Fluids#Blood
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_5001.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_45;97_1426;98_1736;99_5001&stattab=map
  • Last taxonomy: Ochrobactrum
  • 16S sequence: AM422371
  • Sequence Identity:
  • Total samples: 4519
  • soil counts: 503
  • aquatic counts: 738
  • animal counts: 2153
  • plant counts: 1125

Safety information

risk assessment

  • @ref: 16310
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16310
  • description: Ochrobactrum pseudogrignonense partial 16S rRNA gene, type strain CCUG 30717T
  • accession: AM422371
  • length: 1387
  • database: ena
  • NCBI tax ID: 419475

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brucella pseudogrignonensis CCUG 30717GCA_002252525contigncbi419475
66792Brucella pseudogrignonensis CIP 109451GCA_012395205contigncbi419475
66792Ochrobactrum pseudogrignonense strain CCUG 30717419475.13wgspatric419475
66792Ochrobactrum pseudogrignonense strain CIP 109451419475.20wgspatric419475
66792Ochrobactrum pseudogrignonense CCUG 307172854890933draftimg419475

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.659yes
anaerobicno97.131no
halophileno92.556no
spore-formingno96.322yes
glucose-utilyes93.998no
aerobicyes90.603no
flagellatedno86.206yes
motileyes72.909yes
thermophileno99.508no
glucose-fermentno91.514yes

External links

@ref: 16310

culture collection no.: DSM 22354, CCUG 30717, CIP 109451

straininfo link

  • @ref: 71536
  • straininfo: 57055

literature

  • topic: Phylogeny
  • Pubmed-ID: 17978211
  • title: Ochrobactrum haematophilum sp. nov. and Ochrobactrum pseudogrignonense sp. nov., isolated from human clinical specimens.
  • authors: Kampfer P, Scholz HC, Huber B, Falsen E, Busse HJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65066-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Gram-Negative Bacterial Infections/microbiology, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Ochrobactrum/chemistry/*classification/genetics/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16310Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22354)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22354
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
23341Peter Kämpfer, Holger C. Scholz, Birgit Huber, Enevold Falsen, Hans-Jürgen Busse10.1099/ijs.0.65066-0Ochrobactrum haematophilum sp. nov. and Ochrobactrum pseudogrignonense sp. nov., isolated from human clinical specimensIJSEM 57: 2513-2518 200717978211
37560Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7196
50239Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30717)https://www.ccug.se/strain?id=30717
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
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
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
71536Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID57055.1StrainInfo: A central database for resolving microbial strain identifiers