Strain identifier

BacDive ID: 4306

Type strain: Yes

Species: Brenneria nigrifluens

Strain Designation: EN 101, WC1

Strain history: CIP <- 1997, CFBP <- J.A. Berger, USA: strain WC1

NCBI tax ID(s): 1121120 (strain), 55210 (species)

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General

@ref: 9180

BacDive-ID: 4306

DSM-Number: 30175

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

description: Brenneria nigrifluens EN 101 is an aerobe, mesophilic, motile plant pathogen that was isolated from bark canker in Persian walnut tree.

NCBI tax id

NCBI tax idMatching level
1121120strain
55210species

strain history

@refhistory
9180<- ATCC <- M.P. Starr; EN 101
121299CIP <- 1997, CFBP <- J.A. Berger, USA: strain WC1

doi: 10.13145/bacdive4306.20230509.8.1

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 nigrifluens
  • full scientific name: Brenneria nigrifluens (Wilson et al. 1957) Hauben et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Erwinia nigrifluens

@ref: 9180

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Pectobacteriaceae

genus: Brenneria

species: Brenneria nigrifluens

full scientific name: Brenneria nigrifluens (Wilson et al. 1957) Hauben et al. 1999

strain designation: EN 101, WC1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.091
6948099.905negative
121299nonegativerod-shaped

multimedia

  • @ref: 9180
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_30175.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9180NUTRIENT 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
39227MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121299CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
9180positivegrowth26mesophilic
39227positivegrowth25mesophilic
58361positivegrowth30mesophilic
121299positivegrowth5-30
121299nogrowth37mesophilic
121299nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58361aerobe
121299facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.854

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
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
68371melibiose+builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
121299mannitol-fermentation29864
121299citrate+carbon source16947
121299glucose-fermentation17234
121299lactose-fermentation17716
121299nitrate-reduction17632
121299nitrite-reduction16301
121299malonate-assimilation15792
121299sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 121299
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 121299
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12129915688acetoin+
12129917234glucose-

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
121299oxidase-
121299beta-galactosidase+3.2.1.23
121299alcohol dehydrogenase-1.1.1.1
121299gelatinase-
121299catalase+1.11.1.6
121299lysine decarboxylase-4.1.1.18
121299ornithine decarboxylase-4.1.1.17
121299phenylalanine ammonia-lyase-4.3.1.24
121299tryptophan deaminase-
121299urease+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
121299-----+-++--++-+---+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121299+/---+/-+/-+/----++++-+/--+/-+/------+/-+/-+/--+/--++/----+---------+/--+/-+/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121299+++++-+++++-++++++++++++-+-----+++++---------+--++++-++-++-++++++++--+-+++-+--+++-+---+-++++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
9180bark canker in Persian (English) walnut treeCaliforniaUSAUSANorth America
58361Bark canker in Persian walnutCaliforniaUSAUSANorth America1955
121299Bark canker in Persian walnutCaliforniaUnited States of AmericaUSANorth America1955

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Bark

taxonmaps

  • @ref: 69479
  • File name: preview.99_2429.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_1313;97_1560;98_1897;99_2429&stattab=map
  • Last taxonomy: Brenneria nigrifluens subclade
  • 16S sequence: Z96095
  • Sequence Identity:
  • Total samples: 348
  • soil counts: 8
  • aquatic counts: 77
  • animal counts: 250
  • plant counts: 13

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
9180yes1Risk group (German classification)
1212991Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Erwinia nigrifluens 16S ribosomal RNA gene, partial sequenceU802031456ena55210
20218Erwinia nigrifluens 16S rRNA gene (strain DSM 30175)AJ2334151500ena55210
20218Brenneria nigrifluens strain LMG 2694 16S ribosomal RNA gene, partial sequenceFJ6118841387ena55210
20218Erwinia nigrifluens LMG 2694 16S ribosomal RNAZ960951484ena55210

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Brenneria nigrifluens DSM 30175 = ATCC 13028GCA_005484965completencbi1121120
66792Brenneria nigrifluens DSM 30175 = ATCC 13028 LMG 2694GCA_003115835scaffoldncbi1121120
66792Brenneria nigrifluens strain ATCC 1302855210.5completepatric55210
66792Brenneria nigrifluens strain LMG 269455210.4wgspatric55210
66792Brenneria nigrifluens DSM 301752574179731draftimg1121120

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.905no
flagellatedyes73.701no
gram-positiveno98.173no
anaerobicno94.864yes
aerobicno55.176no
halophileno91.011no
spore-formingno93.382no
thermophileno98.694yes
glucose-utilyes94.896no
glucose-fermentyes89.359no

External links

@ref: 9180

culture collection no.: CCUG 48853, NCPPB 564, CIP 105198, LMG 2694, CFBP 3616, ICMP 1578, DSM 30175, ATCC 13028

straininfo link

  • @ref: 73798
  • straininfo: 2656

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny30403583Brenneria corticis sp. nov., isolated from symptomatic bark of Populusxeuramericana canker.Li Y, Zheng MH, Wang HM, Lin CL, Wang XZInt J Syst Evol Microbiol10.1099/ijsem.0.0030772018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/isolation & purification, Fatty Acids/chemistry, *Phylogeny, Plant Bark/*microbiology, Plant Diseases/*microbiology, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Genetics31515335Complete Genome Sequences of Brenneria rubrifaciens Strain 6D370 and Brenneria nigrifluens Strain ATCC 13028, Causative Agents of Bark Cankers in Walnut.Poret-Peterson AT, McClean AE, Chen L, Kluepfel DAMicrobiol Resour Announc10.1128/MRA.00597-192019

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9180Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30175)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30175
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
39227Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17191
58361Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48853)https://www.ccug.se/strain?id=48853
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)
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
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
73798Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2656.1StrainInfo: A central database for resolving microbial strain identifiers
121299Curators of the CIPCollection of Institut Pasteur (CIP 105198)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105198