Strain identifier

BacDive ID: 1887

Type strain: Yes

Species: Brucella oryzae

Strain history: <- M. Schloter <- A. K. Tripathi et al.

NCBI tax ID(s): 335286 (species)

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General

@ref: 7006

BacDive-ID: 1887

DSM-Number: 17471

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

description: Brucella oryzae CCUG 54940 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from deep water rice roots .

NCBI tax id

  • NCBI tax id: 335286
  • Matching level: species

strain history

  • @ref: 7006
  • history: <- M. Schloter <- A. K. Tripathi et al.

doi: 10.13145/bacdive1887.20230509.8.1

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 oryzae
  • full scientific name: Brucella oryzae (Tripathi et al. 2006) Hördt et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Ochrobactrum oryzae

@ref: 7006

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Brucellaceae

genus: Brucella

species: Brucella oryzae

full scientific name: Brucella oryzae (Tripathi et al. 2006) Hördt et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
23337negative1.4 µm0.8 µmrod-shapedyesmonotrichous, polar
69480yes90.497
69480negative99.994

colony morphology

  • @ref: 23337
  • colony color: milky white, translucent
  • colony shape: circular
  • medium used: Nutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7006NUTRIENT 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
23337Nutrient agar (NA)yes

culture temp

@refgrowthtypetemperaturerange
7006positivegrowth28mesophilic
23337positivegrowth10-37
23337positiveoptimum30mesophilic
60400positivegrowth30-37mesophilic

culture pH

@refabilitytypepHPH range
23337positivegrowth4.0-9.0alkaliphile
23337positiveoptimum6.0-7.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23337aerobe
60400aerobe

spore formation

@refspore formationconfidence
23337no
69481no100
69480no99.996

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2333716947citrate-
2333717992sucrose-
2333716000ethanolamine-
2333717240itaconate-
2333717295L-phenylalanine-
2333750048phenylethylamine-
2333728037N-acetylgalactosamine+respiration
23337182404-hydroxy-L-proline+
2333715963ribitol+
2333773706bromosuccinate+
2333716383cis-aconitate+
2333715895D-galactonic acid lactone+
2333717784D-glucosaminic acid+
2333716523D-serine+
2333717113erythritol+
2333716865gamma-aminobutyric acid+
2333773804glycyl L-aspartic acid+
2333729991L-aspartate+
2333715971L-histidine+
2333715603L-leucine+
2333715729L-ornithine+
2333716857L-threonine+
2333724996lactate+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate+builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol+builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose+builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol+builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol+builds acid from
6837117754glycerol-builds acid from
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
23337catalase+1.11.1.6
23337cytochrome 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
7006+---+---+++-+++/---+--

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7006--+++---+-++++-+------+-----+---+-------+-+--+--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7006deep water rice roots (endophyte)Suraha Tal LakeIndiaINDAsia
23337surface-sterilized seeds and plant tissue from deep-water rice (Oryza sativa)

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Host Body-Site#Plant#Root (Rhizome)
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Fruit (Seed)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_34292.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_4733;97_5743;98_25339;99_34292&stattab=map
  • Last taxonomy: Ochrobactrum oryzae subclade
  • 16S sequence: AB681868
  • Sequence Identity:
  • Total samples: 207
  • soil counts: 28
  • aquatic counts: 55
  • animal counts: 94
  • plant counts: 30

Safety information

risk assessment

  • @ref: 7006
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ochrobactrum oryzae gene for 16S rRNA, partial sequence, strain: NBRC 102588AB6818681412ena335286
7006Ochrobactrum oryzae partial 16S rRNA gene, strain MTCC 4195TAM0412471477ena335286

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brucella oryzae NBRC 102588GCA_012103035contigncbi335286
66792Ochrobactrum oryzae strain NBRC 102588335286.8wgspatric335286

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.492no
anaerobicno97.445yes
halophileno94.929no
spore-formingno96.758yes
glucose-utilyes91.479yes
motileyes62.091yes
flagellatedno94.646no
thermophileno98.819no
aerobicyes87.144yes
glucose-fermentno91.277yes

External links

@ref: 7006

culture collection no.: CCUG 54940, DSM 17471, MTCC 4195, NBRC 102588

straininfo link

  • @ref: 71531
  • straininfo: 292771

literature

  • topic: Phylogeny
  • Pubmed-ID: 16825649
  • title: Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India.
  • authors: Tripathi AK, Verma SC, Chowdhury SP, Lebuhn M, Gattinger A, Schloter M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63934-0
  • year: 2006
  • mesh: Carbohydrate Metabolism, Carboxylic Acids/metabolism, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, Ochrobactrum/*classification/genetics/*isolation & purification/physiology, Oryza/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Water Microbiology
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7006Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17471)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17471
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
23337Anil K. Tripathi, Subhash C. Verma, Soumitra Paul Chowdhury, Michael Lebuhn, Andreas Gattinger, Michael Schloter10.1099/ijs.0.63934-0Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in IndiaIJSEM 56: 1677-1680 200616825649
60400Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54940)https://www.ccug.se/strain?id=54940
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
68371Automatically annotated from API 50CH acid
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
71531Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292771.1StrainInfo: A central database for resolving microbial strain identifiers