Strain identifier

BacDive ID: 135927

Type strain: No

Species: Acidovorax oryzae

Strain history: CIP <- 2000, CCUG <- 1984, LMG <- NCPPB, Pseudomonas setariae <- K. Ohata

NCBI tax ID(s): 1408420 (strain), 862720 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 8.1 (current version)

General

@ref: 35204

BacDive-ID: 135927

keywords: genome sequence, Bacteria, obligate aerobe, mesophilic, motile

description: Acidovorax oryzae CIP 106433 is an obligate aerobe, mesophilic, motile bacterium of the family Comamonadaceae.

NCBI tax id

NCBI tax idMatching level
1408420strain
862720species

strain history

  • @ref: 35204
  • history: CIP <- 2000, CCUG <- 1984, LMG <- NCPPB, Pseudomonas setariae <- K. Ohata

doi: 10.13145/bacdive135927.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Acidovorax
  • species: Acidovorax oryzae
  • full scientific name: Acidovorax oryzae Schaad et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Paracidovorax oryzae

@ref: 35204

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Acidovorax

species: Acidovorax oryzae

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.37
6948099.997negative
35204yesnegativerod-shaped

pigmentation

  • @ref: 35204
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
35204MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
35204CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
35204CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
35204positivegrowth25mesophilic
35204positivegrowth25-41
35204nogrowth5psychrophilic
35204nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 35204
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.973

halophily

@refsaltgrowthtested relationconcentration
35204NaClpositivegrowth0-2 %
35204NaClnogrowth4 %
35204NaClnogrowth6 %
35204NaClnogrowth8 %
35204NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
3520416947citrate+carbon source
352044853esculin-hydrolysis
3520417632nitrate+reduction
3520416301nitrite-reduction
3520417632nitrate-respiration

antibiotic resistance

  • @ref: 35204
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
3520435581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
35204oxidase-
35204beta-galactosidase-3.2.1.23
35204alcohol dehydrogenase-1.1.1.1
35204gelatinase-
35204amylase-
35204DNase-
35204caseinase+3.4.21.50
35204catalase+1.11.1.6
35204tween esterase+
35204lecithinase-
35204lipase+
35204lysine decarboxylase-4.1.1.18
35204ornithine decarboxylase-4.1.1.17
35204protease+
35204tryptophan deaminase-
35204urease+3.5.1.5
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46357C12:03.312
    46357C14:03.214
    46357C16:028.316
    46357C10:0 3OH4.411.423
    46357C16:1 ω7c48.315.819
    46357C18:1 ω7c /12t/9t12.517.824
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
46357---+-+--------------
35204-+++++----+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
46357+---+---+++++++++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
35204+++---------------++++----+----+-+--+------++-+-+++++++-+---+----+-------+-++--+++--+---+++++++-+++

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typesampling dateisolation date
35204JapanJPNAsia
46357JapanJPNAsiaOryza sativa1955
35204JapanJPNAsiaOryza sativa1955

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

Safety information

risk assessment

  • @ref: 35204
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracidovorax oryzae ATCC 19882GCA_000687165scaffoldncbi1408420
66792Acidovorax oryzae ATCC 198821408420.3wgspatric1408420
66792Acidovorax oryzae ATCC 198822563366540draftimg1408420

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.319no
flagellatedyes67.056no
gram-positiveno98.526no
anaerobicno98.239no
halophileno95.536no
spore-formingno92.802no
glucose-utilyes74.003yes
aerobicyes95.238no
thermophileno99.203yes
glucose-fermentno89.484yes

External links

@ref: 35204

culture collection no.: CIP 106433, CCUG 15836, LMG 1806, NCPPB 1392, ATCC 19882, ICMP 3960, CFBP 2426

straininfo link

  • @ref: 93191
  • straininfo: 96

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
35204Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106433Collection of Institut Pasteur (CIP 106433)
46357Curators of the CCUGhttps://www.ccug.se/strain?id=15836Culture Collection University of Gothenburg (CCUG) (CCUG 15836)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
93191Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID96.1