Strain identifier

BacDive ID: 4402

Type strain: Yes

Species: Erwinia persicina

Strain Designation: HK 204, 9108-82

Strain history: CIP <- 1997, CFBP, Erwinia persicinus <- ATCC <- D.J. Brenner, CDC: strain 9108-82 <- K. Komagata and N. Okada: strain HK 204

NCBI tax ID(s): 1219360 (strain), 55211 (species)

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General

@ref: 8048

BacDive-ID: 4402

DSM-Number: 19328

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

description: Erwinia persicina HK 204 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from tomato plant.

NCBI tax id

NCBI tax idMatching level
1219360strain
55211species

strain history

@refhistory
8048<- IAM <- M. V. Hao and K. Komagata; HK 204
67770K. Komagata HK 204.
121688CIP <- 1997, CFBP, Erwinia persicinus <- ATCC <- D.J. Brenner, CDC: strain 9108-82 <- K. Komagata and N. Okada: strain HK 204

doi: 10.13145/bacdive4402.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Erwiniaceae
  • genus: Erwinia
  • species: Erwinia persicina
  • full scientific name: Erwinia persicina corrig. Hao et al. 1990

  • synonyms

    • @ref: 20215
    • synonym: Erwinia persicinus

@ref: 8048

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Erwinia

species: Erwinia persicina

full scientific name: Erwinia persicina Hao et al. 1990

strain designation: HK 204, 9108-82

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121688negativerod-shapedyes
125439negative99.3
125438negative99.5

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8048NUTRIENT 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
39228MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8048TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
121688CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
8048positivegrowth30
39228positivegrowth25
67770positivegrowth37
121688positivegrowth5-30
121688nogrowth37
121688nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
121688facultative anaerobe
125439aerobe97.2

spore formation

@refspore formationconfidence
125439no96.4
125438no90.265

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12168829864mannitol+fermentation
12168816947citrate+carbon source
12168817234glucose+fermentation
12168817716lactose-fermentation
12168817632nitrate+reduction
12168816301nitrite-reduction
12168815792malonate+assimilation
121688132112sodium thiosulfate-builds gas from
12168817234glucose+degradation
68371Potassium 5-ketogluconate+builds acid from
6837127613amygdalin+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837112936D-galactose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
68371Potassium 2-ketogluconate-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
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+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
6836817632nitrate+reduction
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+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

antibiotic resistance

  • @ref: 121688
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
12168835581indoleno
6836817997dinitrogenno
6836816301nitriteyes
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
12168815688acetoin+
12168817234glucose-
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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
121688oxidase-
121688beta-galactosidase+3.2.1.23
121688alcohol dehydrogenase-1.1.1.1
121688gelatinase-
121688catalase+1.11.1.6
121688lysine decarboxylase-4.1.1.18
121688ornithine decarboxylase-4.1.1.17
121688phenylalanine ammonia-lyase-4.3.1.24
121688tryptophan deaminase-
121688urease-3.5.1.5
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121688-+---+----++-+------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
8048+---+----+-+++++++++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121688+/-+/--++----++++-+/--+/-++---++++++-+/-+/-+/---+---+-------+/--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121688+++++-++++++++++-++++--+-------+++--++--+--------+++-+++++-++--------------+--+++-----+--++++++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8048tomato plantJapanJPNAsia
67770Tomato
121688Tomato, Lycopersicon esculentumJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4284.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_502;98_2340;99_4284&stattab=map
  • Last taxonomy: Erwinia
  • 16S sequence: Z96086
  • Sequence Identity:
  • Total samples: 12606
  • soil counts: 935
  • aquatic counts: 1231
  • animal counts: 9059
  • plant counts: 1381

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
8048yes1Risk group (German classification)
1216881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8048Erwinia persicinus 16S ribosomal RNA gene, partial sequenceU802051456nuccore55211
67770Erwinia persicinus LMG 11254 16S ribosomal RNAZ960861496nuccore55211
124043Erwinia persicina gene for 16S rRNA, partial sequence, strain: NBRC 102418.AB6817741469nuccore55211
124043Erwinia persicina gene for 16S ribosomal RNA, partial sequence, strain: IAM 12843.AB9077781491nuccore55211

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erwinia persicina NBRC 1024181219360.3wgspatric1219360
66792Erwinia persicina NBRC 1024182731957625draftimg1219360
67770Erwinia persicina NBRC 102418GCA_001571305contigncbi1219360

GC content

  • @ref: 67770
  • GC-content: 54
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.5no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.764yes
125438spore-formingspore-formingAbility to form endo- or exosporesno90.265no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no66.718no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes71.683no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.4
125439BacteriaNetmotilityAbility to perform movementyes78.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe97.2

External links

@ref: 8048

culture collection no.: DSM 19328, ATCC 35998, CDC 9108-82, IAM 12843, JCM 3704, AJ 2716, CFBP 3622, CIP 105199, ICMP 12532, LMG 11254, NBRC 102418, NCIMB 13181, NCPPB 3774

straininfo link

  • @ref: 73893
  • straininfo: 11848

literature

topicPubmed-IDtitleauthorsjournalDOIyearmesh
Phylogeny2275853Erwinia persicinus, a new species isolated from plants.Hao MV, Brenner DJ, Steigerwalt AG, Kosako Y, Komagata KInt J Syst Bacteriol10.1099/00207713-40-4-3791990Base Composition, DNA, Bacterial/analysis, Erwinia/*classification/genetics, Nucleic Acid Hybridization, Phylogeny, Plants/*microbiology, Species Specificity
30727103First Report of Erwinia persicinus Causing Wilting of Medicago sativa Sprouts in China.Zhang ZF, Nan ZBPlant Dis10.1094/PDIS-10-11-09092012
30781193Erwinia persicina Causing Chlorosis and Necrotic Spots in Leaves and Tendrils of Pisum sativum in Southeastern Spain.Gonzalez AJ, Tello JC, Rodicio MRPlant Dis10.1094/PDIS-91-4-0460A2007

Reference

@idauthorscataloguedoi/urltitle
8048Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19328)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19328
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
39228Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17192
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
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
73893Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11848.1StrainInfo: A central database for resolving microbial strain identifiers
121688Curators of the CIPCollection of Institut Pasteur (CIP 105199)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105199
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1