Strain identifier

BacDive ID: 4397

Type strain: Yes

Species: Erwinia psidii

Strain history: CIP <- 1997, CFBP

NCBI tax ID(s): 69224 (species)

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General

@ref: 7080

BacDive-ID: 4397

DSM-Number: 17597

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, plant pathogen

description: Erwinia psidii DSM 17597 is an aerobe, Gram-negative, rod-shaped plant pathogen that was isolated from Psidium guajava.

NCBI tax id

  • NCBI tax id: 69224
  • Matching level: species

strain history

@refhistory
7080<- NCPPB <- ? <- C. F. Robbs, Brazil
357911997, CFBP
122011CIP <- 1997, CFBP

doi: 10.13145/bacdive4397.20240916.9.1

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 psidii
  • full scientific name: Erwinia psidii Rodrigues Neto et al. 1988

@ref: 7080

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Erwinia

species: Erwinia psidii

full scientific name: Erwinia psidii Rodrigues Neto et al. 1988

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122011negativerod-shapedno
69480negative99.494

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7080TRYPTICASE 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
35791MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122011CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
7080positivegrowth30
35791positivegrowth25
122011positivegrowth10-30
122011nogrowth5
122011nogrowth37
122011nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7080aerobe
122011facultative anaerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 98

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
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
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
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
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
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
68371glycerol-builds acid from17754
122011mannitol+fermentation29864
122011citrate-carbon source16947
122011glucose+fermentation17234
122011lactose+fermentation17716
122011nitrate-reduction17632
122011nitrite-reduction16301
122011malonate-assimilation15792
122011sodium thiosulfate-builds gas from132112
122011glucose+degradation17234

antibiotic resistance

  • @ref: 122011
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122011
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12201115688acetoin-
12201117234glucose+

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
122011oxidase-
122011beta-galactosidase+3.2.1.23
122011alcohol dehydrogenase-1.1.1.1
122011gelatinase-
122011catalase+1.11.1.6
122011lysine decarboxylase-4.1.1.18
122011ornithine decarboxylase-4.1.1.17
122011phenylalanine ammonia-lyase-4.3.1.24
122011tryptophan deaminase-
122011urease-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
122011-+---+----++-+--++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122011---------+/-+/-+/-+/-----+/-+/---+/---------+/-+/--------+/-------+/--+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122011+++++--+---------++++--+-------+++---------++----+---------++------------------++-----+--++--------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
7080Psidium guajavaPsidium guajavaBrazilBRAMiddle and South America
122011Psidium guajavaBrazilBRAMiddle and South America

isolation source categories

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

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
7080yes1Risk group (German classification)
1220111Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7080Erwinia psidii LMG 7034 16S ribosomal RNAZ960851496nuccore69224
124043Erwinia psidii strain LMG 7039 16S ribosomal RNA gene, partial sequence.JQ8096961494nuccore69224
124043Erwinia psidii strain IBSBF 435 16S ribosomal RNA gene, partial sequence.KC2012971130nuccore69224

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erwinia psidii IBSBF 435GCA_003846135scaffoldncbi69224
66792Erwinia psidii strain IBSBF 43569224.3wgspatric69224
66792Erwinia psidii IBSBF 4352898987143draftimg69224

GC content

  • @ref: 7080
  • GC-content: 52

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno98no
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.494no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.612yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no62.437no
69480spore-formingspore-formingAbility to form endo- or exosporesno86.882no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.75yes
69480flagellatedmotile2+Ability to perform flagellated movementyes81.166no

External links

@ref: 7080

culture collection no.: DSM 17597, LMG 7039, NCPPB 3555, IBSBF 435, PDDCC 8426, CIP 105200, CFBP 3627, ICMP 8426

straininfo link

  • @ref: 73888
  • straininfo: 2668

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism16076103Acyl-homoserine lactones from Erwinia psidii R. IBSBF 435T, a guava phytopathogen (Psidium guajava L.).Pomini AM, Manfio GP, Araujo WL, Marsaioli AJJ Agric Food Chem10.1021/jf050586e20054-Butyrolactone/*analogs & derivatives/analysis/chemistry, Erwinia/*metabolism, Molecular Structure, Plant Diseases/*microbiology, Psidium/*drug effectsPathogenicity
Genetics30714036Draft Genome Sequence of Erwinia psidii, Causal Agent of Bacterial Blight of Guava (Psidium guava) and Dieback of Eucalypt (Eucalyptus spp.).Hermenegildo PDS, Santos SA, Guimaraes LMS, Pereira IC, Vidigal PMP, Badel JL, Alfenas-Zerbini P, Mafia RG, Ferreira MASV, Alfenas ACMicrobiol Resour Announc10.1128/MRA.01598-182019

Reference

@idauthorscataloguedoi/urltitle
7080Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17597)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17597
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
35791Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17193
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
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
73888Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2668.1StrainInfo: A central database for resolving microbial strain identifiers
122011Curators of the CIPCollection of Institut Pasteur (CIP 105200)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105200
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy