Name: Clavibacter capsici PF008
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133135

Type strain:

Species: Clavibacter capsici

Strain Designation: PF008

Culture col. no.: KACC 18448, LMG 29047

NCBI tax ID(s): 1874630 (species)

Special Collections

Literature strains

Section

When using BacDive for research please cite our paper

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

Gram-positive
aerobe
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Clavibacter*
	Species	**Clavibacter capsici**
	Full Scientific Name (LPSN)	Clavibacter capsici (Oh et al. 2016) Li et al. 2018

	Synonym	Clavibacter capsici
	Synonym	Clavibacter michiganensis subsp. capsici

Information on morphological and physiological properties Morphology

[Ref.: #24897]	Gram stain	positive
[Ref.: #125439]	Gram stain	positive Confidence in %97.4

[Ref.: #125438]	Motility	no Confidence in %93

[Ref.: #24897]	Colony color	orange
[Ref.: #24897]	Incubation period	3 days
[Ref.: #24897]	Cultivation medium used	King’s B medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24897]

Culture medium

King’s B medium

[Ref.: #24897]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #24897]		negative	growth	>34.0 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24897]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %90.8

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24897]		NaCl	maximum	6	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #24897]	amygdalin ChEBI	+	carbon source
[Ref.: #24897]	arbutin ChEBI	+	carbon source
[Ref.: #24897]	cellobiose ChEBI	+	carbon source
[Ref.: #24897]	D-fructose ChEBI	+	carbon source
[Ref.: #24897]	D-galactose ChEBI	+	carbon source
[Ref.: #24897]	D-glucose ChEBI	+	carbon source
[Ref.: #24897]	D-mannitol ChEBI	+	carbon source
[Ref.: #24897]	D-mannose ChEBI	+	carbon source
[Ref.: #24897]	D-trehalose ChEBI	+	carbon source
[Ref.: #24897]	D-xylose ChEBI	+	carbon source
[Ref.: #24897]	esculin ferric citrate	+	carbon source
[Ref.: #24897]	gentiobiose ChEBI	+	carbon source
[Ref.: #24897]	glycerol ChEBI	+	carbon source
[Ref.: #24897]	L-arabinose ChEBI	+	carbon source
[Ref.: #24897]	lactose ChEBI	+	carbon source
[Ref.: #24897]	maltose ChEBI	+	carbon source
[Ref.: #24897]	melibiose ChEBI	+	carbon source
[Ref.: #24897]	methyl alpha-D-mannoside ChEBI	+	carbon source
[Ref.: #24897]	methyl beta-D-xylopyranoside ChEBI	+	carbon source
[Ref.: #24897]	myo-inositol ChEBI	+	carbon source
[Ref.: #24897]	potassium gluconate ChEBI	+	carbon source
[Ref.: #24897]	raffinose ChEBI	+	carbon source
[Ref.: #24897]	salicin ChEBI	+	carbon source
[Ref.: #24897]	sucrose ChEBI	+	carbon source
[Ref.: #24897]	turanose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #24897]	acid phosphatase	+	3.1.3.2
[Ref.: #24897]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24897]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #24897]	alpha-galactosidase	+	3.2.1.22
[Ref.: #24897]	alpha-glucosidase	+	3.2.1.20
[Ref.: #24897]	beta-galactosidase	+	3.2.1.23
[Ref.: #24897]	beta-glucosidase	+	3.2.1.21
[Ref.: #24897]	esterase (C 4)	+
[Ref.: #24897]	esterase lipase (C 8)	+
[Ref.: #24897]	leucine arylamidase	+	3.4.11.1
[Ref.: #24897]	trypsin	+	3.4.21.4
	Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #24897]	Sample type/isolated from	pepper showing bacterial canker disease
[Ref.: #24897]	Geographic location (country and/or sea, region)	Anyang
[Ref.: #24897]	Country	Republic of Korea
[Ref.: #24897]	Country ISO 3 Code	KOR
[Ref.: #24897]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Clavibacter michiganensis strain PF008	28447.7	complete	PATRIC	28447 tax ID	*

[Ref.: #24897]

GC-content

73.2 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Clavibacter michiganensis strain PF008 PATRIC: 28447.7
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	89.408	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.682	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	78.967	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	84.992	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	93.833	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	93	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clavibacter michiganensis strain PF008 PATRIC: 28447.7
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	72.4
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	60.3
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	97.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	90.8

Availability in culture collections External links

[Ref.: #24897]

Culture collection no.

KACC 18448, LMG 29047

Literature:

	Title	Authors	Journal	DOI	Year
	Plasmid composition and the chpG gene determine the virulence level of Clavibacter capsici natural isolates in pepper.	Hwang IS, Lee HM, Oh EJ, Lee S, Heu S, Oh CS	Mol Plant Pathol	10.1111/mpp.12932	2020	*

References

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#24897

E.-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-Sik: Clavibacter michiganensis subsp. capsici subsp. nov., causing bacterial canker disease in pepper. IJSEM 66: 4065 - 4070 2016 ( DOI 10.1099/ijsem.0.001311 , PubMed 27412674 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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Clavibacter michiganensis strain PF008

Clavibacter michiganensis strain PF008

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