Strain identifier

BacDive ID: 1897

Type strain: Yes

Species: Brucella ciceri

Strain Designation: CA-34

Strain history: <- A. Imran, Natl. Inst. Biotechnol. & Genetic Engineering, Faisalabad, Pakistan; CA-34 <- F. Y. Hafeez and Irfan-ul-Haq

NCBI tax ID(s): 391287 (species)

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General

@ref: 16178

BacDive-ID: 1897

DSM-Number: 22292

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

description: Brucella ciceri CA-34 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from root nodules of chickpea, Cicer arietinum.

NCBI tax id

  • NCBI tax id: 391287
  • Matching level: species

strain history

  • @ref: 16178
  • history: <- A. Imran, Natl. Inst. Biotechnol. & Genetic Engineering, Faisalabad, Pakistan; CA-34 <- F. Y. Hafeez and Irfan-ul-Haq

doi: 10.13145/bacdive1897.20230509.8.1

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 ciceri
  • full scientific name: Brucella ciceri (Imran et al. 2010) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Ochrobactrum ciceri

@ref: 16178

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Brucellaceae

genus: Brucella

species: Brucella ciceri

full scientific name: Brucella ciceri (Imran et al. 2010) Hördt et al. 2020

strain designation: CA-34

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
23344negativedumbbell-shapedyes
69480negative99.984

colony morphology

@refcolony sizecolony colorcolony shapeincubation period
233442-3 mmoff-white, translucentcircular
615021 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16178R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
23344LB (Luria-Bertani) MEDIUMyes
23344Nutrient agar (NA)yes
23344YEM agaryes

culture temp

@refgrowthtypetemperaturerange
16178positivegrowth30mesophilic
23344positivegrowth28-37mesophilic
61502positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23344aerobe
61502aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
233445291gelatin+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol-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

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.
2334428971ampicillinyesyes10 µg
23344161680aztreonamyesyes30 µg
233443547cephradineyesyes30 µg
23344472657cefiximeyesyes5 µg

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
23344catalase+1.11.1.6
23344cytochrome 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
16178+----+--+++-++-+-++-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentsampling dategeographic location
16178root nodules of chickpea, Cicer arietinumCicer arietinumPakistanPAKAsia
23344chickpea nodules1996NIBGE
61502Chickpea nodule (Cicer arietinum)PakistanPAKAsia1996Punjab,Faisalabad

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_63846.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_640;97_2602;98_3225;99_63846&stattab=map
  • Last taxonomy: Brucella
  • 16S sequence: DQ647056
  • Sequence Identity:
  • Total samples: 49
  • soil counts: 8
  • aquatic counts: 20
  • animal counts: 18
  • plant counts: 3

Safety information

risk assessment

  • @ref: 16178
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16178
  • description: Ochrobactrum ciceri strain Ca-34 16S ribosomal RNA gene, complete sequence
  • accession: DQ647056
  • length: 1492
  • database: ena
  • NCBI tax ID: 391287

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brucella ciceri DSM 22292GCA_012103155contigncbi391287
66792Ochrobactrum ciceri strain DSM 22292391287.4wgspatric391287

GC content

  • @ref: 16178
  • GC-content: 58.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.416yes
anaerobicno97.732yes
halophileno91.699no
spore-formingno96.809no
glucose-utilyes91.888yes
aerobicyes94.113yes
motileyes85.999yes
flagellatedno86.157no
thermophileno98.27yes
glucose-fermentno91.471yes

External links

@ref: 16178

culture collection no.: DSM 22292, CCUG 57879

straininfo link

  • @ref: 71541
  • straininfo: 401642

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19684324Ochrobactrum ciceri sp. nov., isolated from nodules of Cicer arietinum.Imran A, Hafeez FY, Fruhling A, Schumann P, Malik KA, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.013987-02009Base Sequence, Cicer/*microbiology, Fatty Acids/analysis, Molecular Sequence Data, Ochrobactrum/*classification/genetics/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationGenetics
Phylogeny21169456Ochrobactrum daejeonense sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant.Woo SG, Ten LN, Park J, Lee MInt J Syst Evol Microbiol10.1099/ijs.0.025510-02010Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Nitrates/*metabolism, Ochrobactrum/*classification/genetics/*isolation & purification/metabolism, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sewage/*microbiology, Waste Disposal, FluidMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16178Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22292)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22292
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
23344A. Imran, F. Y. Hafeez, A. Frühling, P. Schumann, K. A. Malik, E. Stackebrandt10.1099/ijs.0.013987-0Ochrobactrum ciceri sp. nov., isolated from nodules of Cicer arietinumIJSEM 60: 1548-1553 201019684324
61502Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57879)https://www.ccug.se/strain?id=57879
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
71541Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401642.1StrainInfo: A central database for resolving microbial strain identifiers