Strain identifier

BacDive ID: 133135

Type strain: Yes

Species: Clavibacter capsici

Strain Designation: PF008

NCBI tax ID(s): 1874630 (subspecies)

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General

@ref: 24897

BacDive-ID: 133135

keywords: genome sequence, Bacteria, aerobe, mesophilic, Gram-positive

description: Clavibacter capsici PF008 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from pepper showing bacterial canker disease.

NCBI tax id

  • NCBI tax id: 1874630
  • Matching level: subspecies

doi: 10.13145/bacdive133135.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Clavibacter
  • species: Clavibacter capsici
  • full scientific name: Clavibacter capsici (Oh et al. 2016) Li et al. 2018

  • synonyms

    @refsynonym
    20215Clavibacter michiganensis subsp. capsici
    20215Clavibacter capsici

@ref: 24897

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Microbacteriaceae

genus: Clavibacter

species: Clavibacter capsici

strain designation: PF008

type strain: yes

Morphology

cell morphology

  • @ref: 24897
  • gram stain: positive

colony morphology

  • @ref: 24897
  • colony color: orange
  • incubation period: 3 days
  • medium used: King’s B medium

Culture and growth conditions

culture medium

  • @ref: 24897
  • name: King’s B medium
  • growth: yes

culture temp

  • @ref: 24897
  • growth: no
  • type: growth
  • temperature: >34.0
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 24897
  • oxygen tolerance: aerobe

halophily

  • @ref: 24897
  • salt: NaCl
  • tested relation: maximum
  • concentration: 6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2489727613amygdalin+carbon source
2489718305arbutin+carbon source
2489717057cellobiose+carbon source
2489715824D-fructose+carbon source
2489712936D-galactose+carbon source
2489717634D-glucose+carbon source
2489717716lactose+carbon source
2489717306maltose+carbon source
2489716899D-mannitol+carbon source
2489716024D-mannose+carbon source
2489728053melibiose+carbon source
2489716634raffinose+carbon source
2489717992sucrose+carbon source
2489716551D-trehalose+carbon source
2489732528turanose+carbon source
2489765327D-xylose+carbon source
24897esculin ferric citrate+carbon source
2489728066gentiobiose+carbon source
2489717754glycerol+carbon source
2489717268myo-inositol+carbon source
2489730849L-arabinose+carbon source
2489743943methyl alpha-D-mannoside+carbon source
2489774863methyl beta-D-xylopyranoside+carbon source
2489732032potassium gluconate+carbon source
2489717814salicin+carbon source

enzymes

@refvalueactivityec
24897acid phosphatase+3.1.3.2
24897alkaline phosphatase+3.1.3.1
24897alpha-chymotrypsin+3.4.21.1
24897alpha-galactosidase+3.2.1.22
24897alpha-glucosidase+3.2.1.20
24897beta-galactosidase+3.2.1.23
24897beta-glucosidase+3.2.1.21
24897esterase (C 4)+
24897esterase lipase (C 8)+
24897leucine arylamidase+3.4.11.1
24897trypsin+3.4.21.4

Isolation, sampling and environmental information

isolation

  • @ref: 24897
  • sample type: pepper showing bacterial canker disease
  • geographic location: Anyang
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Microbial#Bacteria
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Fruit (Seed)

Sequence information

Genome sequences

  • @ref: 66792
  • description: Clavibacter michiganensis strain PF008
  • accession: 28447.7
  • assembly level: complete
  • database: patric
  • NCBI tax ID: 28447

GC content

  • @ref: 24897
  • GC-content: 73.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.442no
gram-positiveyes94.158yes
anaerobicno99.397no
halophileno84.462no
spore-formingno93.824no
glucose-utilyes87.23no
flagellatedno98.007no
aerobicyes92.493yes
thermophileno98.982yes
glucose-fermentno90.697no

External links

@ref: 24897

culture collection no.: KACC 18448, LMG 29047

literature

  • Pubmed-ID: 32196887
  • title: Plasmid composition and the chpG gene determine the virulence level of Clavibacter capsici natural isolates in pepper.
  • authors: Hwang IS, Lee HM, Oh EJ, Lee S, Heu S, Oh CS
  • journal: Mol Plant Pathol
  • DOI: 10.1111/mpp.12932
  • year: 2020
  • mesh: Capsicum/*microbiology, Clavibacter/genetics/*pathogenicity, Genetic Loci, Plant Diseases/*microbiology, Plant Leaves/microbiology, Plasmids/*genetics, Virulence/genetics, Virulence Factors/*genetics

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24897E.-J. B. Oh, Chungyun,Lee, Han-Beoyl,Hwang, In Sun,Lee, Hyok-In,Yea, Mi Chi,Yim, Kyu-Ock,Lee, Seungdon,Heu, Sunggi,Cha, Jae-Soon,Oh, Chang-SikClavibacter michiganensis subsp. capsici subsp. nov., causing bacterial canker disease in pepper10.1099/ijsem.0.001311IJSEM 66: 4065-4070 201627412674
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes