Strain identifier

BacDive ID: 13584

Type strain: No

Species: Agrobacterium radiobacter

Strain Designation: B 6, B6

Strain history: CIP <- 1967, P. Manigault <- A.C. Braun: strain B6

NCBI tax ID(s): 358 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9202

BacDive-ID: 13584

DSM-Number: 30205

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, human pathogen

description: Agrobacterium radiobacter B 6 is an aerobe, mesophilic, motile human pathogen that was isolated from Malus sp., crown gall of apple seedling.

NCBI tax id

  • NCBI tax id: 358
  • Matching level: species

strain history

@refhistory
9202<- DSM 60574 <- J. De Ley <- CIP <- A.C. Braun, B 6 (1934)
67770IAM 13129 <-- ATCC 23308 <-- M. P. Starr TT3 <-- A. C. Braun B6.
122121CIP <- 1967, P. Manigault <- A.C. Braun: strain B6

doi: 10.13145/bacdive13584.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Agrobacterium
  • species: Agrobacterium radiobacter
  • full scientific name: Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Bacillus radiobacter
    20215Rhizobium radiobacter
    20215Beijerinckia fluminensis

@ref: 9202

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Rhizobiaceae

genus: Agrobacterium

species: Agrobacterium radiobacter

full scientific name: Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 emend. Zhang et al. 2014

strain designation: B 6, B6

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes92.156
6948099.986negative
122121yesnegativerod-shaped

colony morphology

@refincubation period
92021-2 days
122121

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36619MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
9202NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
68368MacConkey mediumyes
122121CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122121CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
36619positivegrowth30mesophilic
9202positivegrowth26mesophilic
44253positivegrowth37mesophilic
67770positivegrowth25mesophilic
122121positivegrowth30-37mesophilic
122121nogrowth5psychrophilic
122121nogrowth10psychrophilic
122121nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44253aerobe
122121obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998
122121no

halophily

@refsaltgrowthtested relationconcentration
122121NaClpositivegrowth0-2 %
122121NaClnogrowth4 %
122121NaClnogrowth6 %
122121NaClnogrowth8 %
122121NaClnogrowth10 %

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
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836817632nitrate+reduction
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12212116947citrate-carbon source
1221214853esculin+hydrolysis
12212117632nitrate-builds gas from
12212117632nitrate-reduction
12212116301nitrite-builds gas from
12212116301nitrite+reduction
12212115792malonate-assimilation
12212117632nitrate-respiration

antibiotic resistance

  • @ref: 122121
  • 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
6836816301nitriteyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12212135581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
6836815688acetoin-
6836835581indole-
12212115688acetoin-
12212117234glucose+

enzymes

@refvalueactivityec
9202catalase+1.11.1.6
9202cytochrome-c oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369arginine dihydrolase-3.5.3.6
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
122121oxidase+
122121beta-galactosidase+3.2.1.23
122121alcohol dehydrogenase-1.1.1.1
122121gelatinase-
122121amylase-
122121catalase+1.11.1.6
122121lysine decarboxylase-4.1.1.18
122121ornithine decarboxylase-4.1.1.17
122121urease+3.5.1.5
68382esterase (C 4)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
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
    44253C16:09.116
    44253C14:0 3OH/C16:1 ISO I6.115.485
    44253C16:0 3OH2.217.52
    44253C16:1 ω7c1.515.819
    44253C18:1 ω7c /12t/9t77.617.824
    44253C19:0 CYCLO ω8c3.618.9
  • 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
44253--++-+----+----+++--
44253-++--+--+-++---+++--
122121-++--+----++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2MAC
9202+---+-++/------+--+/--+++++

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
9202+---++-++++++++--+--
9202+---+/-+-++++++++--+--+
9202+---++-++++++++--+--+
9202+---++-++++++++--+--
9202+---++-++++++++--+--
9202----++-++++++++--+--
9202----++-++++++++--+--
9202----+/-+-++++++++--+--
9202+---++-++++++++--+--
44253+---++-++++++++--+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122121++++++++++++++++++++++++++++++++++++++-+-+------++++--++++-++-+++------+-+-+---+++--+-+--+++-++-+-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
9202Malus sp., crown gall of apple seedlingMalus
44253Apple tree,tumour,'crown gall'
67770Apple seedling crown gallIAUSAUSANorth America
122121Plant, Apple tree, Crown gall

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant
#Infection#Plant infections#Gall

taxonmaps

  • @ref: 69479
  • File name: preview.99_6.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_6;97_6;98_6;99_6&stattab=map
  • Last taxonomy: Agrobacterium
  • 16S sequence: AB681869
  • Sequence Identity:
  • Total samples: 5894
  • soil counts: 595
  • aquatic counts: 822
  • animal counts: 3746
  • plant counts: 731

Safety information

risk assessment

@refpathogenicity humanpathogenicity plantbiosafety levelbiosafety level comment
9202yes, in single casesyes1Risk group (German classification)
1221211Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Agrobacterium tumefaciens gene for 16S rRNA, partial sequence, strain: NBRC 102589AB6818691410ena358
20218Agrobacterium tumefaciens strain DSM 30205 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequenceAF3452741087ena358
67770Bifidobacterium longum subsp. infantis strain BIC1401212621a, whole genome shotgun sequenceD01256239227ena1682
67770Agrobacterium tumefaciens gene for 16S rRNA, strain: IAM 13129D127841438ena358

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agrobacterium tumefaciens strain NCTC13543358.254wgspatric358
67770Agrobacterium tumefaciens NCTC13543GCA_900455815contigncbi358

GC content

  • @ref: 9202
  • GC-content: 60.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.545no
anaerobicno96.943yes
halophileno92.641no
spore-formingno97.216no
glucose-utilyes94.033no
motileyes86.618no
flagellatedno78.718no
thermophileno99.654yes
aerobicyes93.927yes
glucose-fermentno89.28yes

External links

@ref: 9202

culture collection no.: DSM 30205, ATCC 23308, CCM 1040, CIP B6, DSM 60574, ICPB TT 3, NBRC 102589, NCPPB 397, CCUG 725, CIP 67.1, LMG 187, IAM 13129, JCM 20845, CCEB 758, HAMBI 1811, ICMP 5856, ICPB TT3, LMG 28, NCPPB 2437, NCTC 13543

straininfo link

  • @ref: 82771
  • straininfo: 419

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism12071951Structural determination of the O-chain polysaccharide from Agrobacterium tumefaciens, strain DSM 30205.De Castro C, De Castro O, Molinaro A, Parrilli MEur J Biochem10.1046/j.1432-1033.2002.02955.x2002Agrobacterium tumefaciens/*chemistry/pathogenicity, Carbohydrate Conformation, Lipopolysaccharides/*chemistry/metabolism, Plant Diseases/*microbiology, Plants/microbiology
Phylogeny16897296Endophytic occupation of root nodules and roots of Melilotus dentatus by Agrobacterium tumefaciens.Wang LL, Wang ET, Liu J, Li Y, Chen WXMicrob Ecol10.1007/s00248-006-9116-y2006Agrobacterium tumefaciens/classification/*genetics/*growth & development, Electrophoresis, Polyacrylamide Gel/methods, Gene Amplification, Melilotus/growth & development/*microbiology, Phylogeny, Plant Roots/*microbiology, Plant Tumors/microbiology, Polymerase Chain Reaction/methods, *Soil Microbiology, SymbiosisEnzymology
Phylogeny18979058Characterization of copper-resistant agrobacterium isolated from legume nodule in mining tailings.Yu J, Fan L, Yang S, Tang M, Yang W, Li H, Wei GBull Environ Contam Toxicol10.1007/s00128-008-9598-z2008Base Sequence, Copper/*pharmacology, DNA Primers, *Drug Resistance, Microbial, Fabaceae/*microbiology, *Mining, Phylogeny, Polymerase Chain Reaction, Rhizobium/drug effects/genetics/*isolation & purificationEnzymology
Phylogeny21148676Rhizobium pusense sp. nov., isolated from the rhizosphere of chickpea (Cicer arietinum L.).Panday D, Schumann P, Das SKInt J Syst Evol Microbiol10.1099/ijs.0.028407-02010Base Composition, Cicer/*microbiology, DNA, Bacterial/genetics, Fatty Acids/metabolism, India, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/*isolation & purification/metabolism, *Rhizosphere, *Soil MicrobiologyMetabolism
Pathogenicity30867394Chemical Composition and in vivo Efficacy of the Essential Oil of Mentha piperita L. in the Suppression of Crown Gall Disease on Tomato Plants.Hsouna AB, Touj N, Hammami I, Dridi K, Al-Ayed AS, Hamdi NJ Oleo Sci10.5650/jos.ess182612019Agrobacterium tumefaciens/drug effects/pathogenicity, *Anti-Bacterial Agents, Dose-Response Relationship, Drug, Drug Resistance, Bacterial, Gas Chromatography-Mass Spectrometry, *Lycopersicon esculentum, Mentha piperita/*chemistry, Menthol, Oils, Volatile/administration & dosage/*chemistry/*pharmacology, Plant Diseases/*microbiology/prevention & control/*therapy
Enzymology32109569Purification and characterization of seven bioactive compounds from the newly isolated Streptomyces cavourensis TN638 strain via solid-state fermentation.Kaaniche F, Hamed A, Elleuch L, Chakchouk-Mtibaa A, Smaoui S, Karray-Rebai I, Koubaa I, Arcile G, Allouche N, Mellouli LMicrob Pathog10.1016/j.micpath.2020.1041062020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9202Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30205)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30205
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
36619Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10280
44253Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 725)https://www.ccug.se/strain?id=725
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
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
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
82771Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID419.1StrainInfo: A central database for resolving microbial strain identifiers
122121Curators of the CIPCollection of Institut Pasteur (CIP 67.1)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2067.1