Strain identifier

BacDive ID: 4307

Type strain: Yes

Species: Brenneria rubrifaciens

Strain Designation: 533c

Strain history: CIP <- 1997, CFBP <- E. Wilson: strain 533C

NCBI tax ID(s): 55213 (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 2:
version 1:
version 8.1 (current version)

General

@ref: 1696

BacDive-ID: 4307

DSM-Number: 4483

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, plant pathogen

description: Brenneria rubrifaciens 533c is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from persian walnut tree.

NCBI tax id

  • NCBI tax id: 55213
  • Matching level: species

strain history

@refhistory
1696<- ATCC <- M.P. Starr, ICPB <- E. Wilson; 533c
122289CIP <- 1997, CFBP <- E. Wilson: strain 533C

doi: 10.13145/bacdive4307.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Pectobacteriaceae
  • genus: Brenneria
  • species: Brenneria rubrifaciens
  • full scientific name: Brenneria rubrifaciens (Wilson et al. 1967) Hauben et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Erwinia rubrifaciens

@ref: 1696

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Pectobacteriaceae

genus: Brenneria

species: Brenneria rubrifaciens

full scientific name: Brenneria rubrifaciens (Wilson et al. 1967) Hauben et al. 1999

strain designation: 533c

type strain: yes

Morphology

cell morphology

  • @ref: 122289
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1696NUTRIENT 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
38539MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122289CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1696positivegrowth30mesophilic
38539positivegrowth25mesophilic
122289positivegrowth5-37
122289nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122289
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
122289mannitol+fermentation29864
122289citrate-carbon source16947
122289glucose+fermentation17234
122289lactose+fermentation17716
122289nitrate-reduction17632
122289nitrite-reduction16301
122289malonate-assimilation15792
122289sodium thiosulfate-builds gas from132112
122289glucose+degradation17234

antibiotic resistance

  • @ref: 122289
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122289
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12228915688acetoin-
12228917234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
122289oxidase-
122289beta-galactosidase+3.2.1.23
122289alcohol dehydrogenase-1.1.1.1
122289gelatinase-
122289catalase+1.11.1.6
122289lysine decarboxylase-4.1.1.18
122289ornithine decarboxylase-4.1.1.17
122289phenylalanine ammonia-lyase-4.3.1.24
122289tryptophan deaminase-
122289urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122289--+--+--+-++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122289+/---++----+/-+++-------+/-+--------+-------+/-----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122289+++++--+--+-----++-++-+--------+-+++-----+-------+---------++--------------+---++-----+--++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
1696persian walnut tree
122289Plant, Persian walnut tree, Juglans regiaTracy, CaliforniaUnited States of AmericaUSANorth America1963

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_30087.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_1313;97_1877;98_22383;99_30087&stattab=map
  • Last taxonomy: Brenneria rubrifaciens subclade
  • 16S sequence: Z96098
  • Sequence Identity:
  • Total samples: 132
  • soil counts: 5
  • aquatic counts: 35
  • animal counts: 81
  • plant counts: 11

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
1696yes1Risk group (German classification)
1222891Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Erwinia rubrifaciens 16S ribosomal RNA gene, partial sequenceU802071457ena55213
20218Erwinia rubrifaciens 16S rRNA gene (strain DSM 4483)AJ2334181491ena55213
20218Brenneria rubrifaciens strain LMG 2709 16S ribosomal RNA gene, partial sequenceFJ6118851387ena55213
20218Erwinia rubrifaciens LMG 2709 16S ribosomal RNAZ960981484ena55213

External links

@ref: 1696

culture collection no.: DSM 4483, ATCC 29291, ICPB ER 103, NCPPB 2020, PDDCC 1915, CIP 105203, CFBP 3619, ICMP 1915, LMG 2709

straininfo link

  • @ref: 73799
  • straininfo: 264324

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1696Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4483)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4483
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
38539Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17196
68371Automatically annotated from API 50CH acid
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
73799Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264324.1StrainInfo: A central database for resolving microbial strain identifiers
122289Curators of the CIPCollection of Institut Pasteur (CIP 105203)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105203