Name: Pseudoclavibacter soli KP02
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7479

Type strain:

Species: Pseudoclavibacter soli

Strain Designation: KP02

Culture col. no.: DSM 23366, JCM 15058, KCTC 19255

Strain history: <- DC Yang, Kyunghee Univ.

NCBI tax ID(s): 1123013 (strain), 452623 (species)

SI-ID 403833

DSM 23366

Special Collections

Section

Pseudoclavibacter soli KP02 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from ginseng field.

Gram-positive
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Pseudoclavibacter*
	Species	**Pseudoclavibacter soli**
	Full Scientific Name (LPSN)	Pseudoclavibacter soli Kim and Jung 2009

Synonym

"Caespitibacter soli"

Information on morphological and physiological properties Morphology

[Ref.: #32523]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #32523]	Cell length	0.4 µm

[Ref.: #32523]	Cell width	0.25 µm

[Ref.: #32523]	Cell shape	rod-shaped

[Ref.: #32523]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95

[Ref.: #32523]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16809]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #16809]

Culture medium growth

[Ref.: #16809]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16809]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16809]	growth	28 °C
[Ref.: #32523]	growth	25-42 °C
[Ref.: #32523]	optimum	30 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32523]			optimum	05-08
[Ref.: #32523]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32523]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #32523]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-9, MK-8
[Ref.: #67771]	Observation	quinones: MK-8

	Enzyme	Enzyme activity	EC number
[Ref.: #32523]	acid phosphatase	+	3.1.3.2
[Ref.: #32523]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32523]	alpha-galactosidase	+	3.2.1.22
[Ref.: #32523]	catalase	+	1.11.1.6
[Ref.: #32523]	urease	+	3.5.1.5

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

[Ref.: #16809]	Sample type/isolated from	ginseng field
[Ref.: #16809]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #16809]	Country	Republic of Korea
[Ref.: #16809]	Country ISO 3 Code	KOR
[Ref.: #16809]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Ginseng field
[Ref.: #67770]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From soil
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB329630 (>99% sequence identity) for Pseudoclavibacter soli subclade from Microbeatlas

Aquatic Samples	522
Soil Samples	284
Animal Samples	2744
Plant Samples	80
Total Samples	3630

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16809]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16809]	Pseudoclavibacter soli gene for 16S ribosomal RNA, partial sequence	AB329630	1460	GenBank ENA	452623 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudoclavibacter soli DSM 23366	GCA_000423505	scaffold	GenBank ENA	1123013 tax ID
[Ref.: #66792]	Pseudoclavibacter soli DSM 23366	1123013.3	wgs	PATRIC	1123013 tax ID	*
[Ref.: #66792]	Pseudoclavibacter soli DSM 23366	2524614761	draft	JGI IMG/M	1123013 tax ID	*

[Ref.: #16809]	GC-content	64.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32523]	GC-content	64.4 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pseudoclavibacter soli DSM 23366 DSM 23366 NCBI: GCA_000423505.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoclavibacter soli DSM 23366 PATRIC: 1123013.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	87.202	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	90.315	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	80.366	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.248	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.812	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	95	yes

Availability in culture collections External links

[Ref.: #16809]

Culture collection no.

DSM 23366, JCM 15058, KCTC 19255

[Ref.: #76924]

SI-ID 403833

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoclavibacter soli sp. nov., a {beta}-glucosidase-producing bacterium.	Kim MK, Jung HY	Int J Syst Evol Microbiol	10.1099/ijs.0.65627-0	2009	*

References

#16809

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23366

#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 )

#32523

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28742 (see below)

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#69479

João 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76924

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID403833.1 )

#28742

IJSEM 835 2009 ( DOI 10.1099/ijs.0.65627-0 , PubMed 19329616 )

* These data were automatically processed and therefore are not curated

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Pseudoclavibacter soli DSM 23366 DSM 23366

Pseudoclavibacter soli DSM 23366

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