Name: Pedobacter ginsenosidimutans THG-45
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134016

Type strain:

Species: Pedobacter ginsenosidimutans

Strain Designation: THG-45

Culture col. no.: KACC 14530, JCM 16721

Strain history: W.-T. Im THG 45.

NCBI tax ID(s): 687842 (species)

Section

Pedobacter ginsenosidimutans THG-45 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

Gram-negative
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	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter ginsenosidimutans**
	Full Scientific Name (LPSN)	Pedobacter ginsenosidimutans Yang et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31064]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.981

[Ref.: #31064]	Cell length	1.25 µm

[Ref.: #31064]	Cell width	0.45 µm

[Ref.: #31064]	Cell shape	rod-shaped

[Ref.: #31064]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.468

[Ref.: #31064]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #31064]	growth	35-45 °C
[Ref.: #31064]	optimum	27.5 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #31064]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31064]			optimum	7.25
[Ref.: #31064]			growth	5.5-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31064]

Oxygen tolerance

aerobe

[Ref.: #31064]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.989

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31064]		NaCl		growth	0-2	%
[Ref.: #31064]		NaCl		optimum	0.5	%

[Ref.: #31064]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31064]	arabinose ChEBI	+	carbon source
[Ref.: #31064]	glucose ChEBI	+	carbon source
[Ref.: #31064]	malate ChEBI	+	carbon source
[Ref.: #31064]	maltose ChEBI	+	carbon source
[Ref.: #31064]	mannose ChEBI	+	carbon source
[Ref.: #31064]	melibiose ChEBI	+	carbon source
[Ref.: #31064]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31064]	rhamnose ChEBI	+	carbon source
[Ref.: #31064]	salicin ChEBI	+	carbon source
[Ref.: #31064]	sucrose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #31064]	acid phosphatase	+	3.1.3.2
[Ref.: #31064]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31064]	catalase	+	1.11.1.6
[Ref.: #31064]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #31064]	Sample type/isolated from	soil

[Ref.: #67770]	Sample type/isolated from	Soil of a ginseng field of Pocheon Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GU138374 (>99% sequence identity) for Pedobacter ginsenosidimutans from Microbeatlas

Aquatic Samples	103
Soil Samples	466
Animal Samples	88
Plant Samples	440
Total Samples	1097

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.: #31064]	Pedobacter ginsenosidimutans strain THG-45 16S ribosomal RNA gene, partial sequence	GU138374	1443	GenBank	687842 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pedobacter ginsenosidimutans KACC 14530	GCA_001442625	contig	GenBank	687842 tax ID
[Ref.: #66792]	Pedobacter ginsenosidimutans strain KACC 14530	687842.4	wgs	PATRIC	687842 tax ID	*
[Ref.: #66792]	Pedobacter ginsenosidimutans KACC 14530	2724679004	draft	JGI IMG/M	687842 tax ID	*

[Ref.: #31064]

GC-content

39 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pedobacter ginsenosidimutans strain KACC 14530 PATRIC: 687842.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter ginsenosidimutans strain KACC 14530 PATRIC: 687842.4
[Ref.: #69480]	gram-positive	no	97.196	yes
[Ref.: #69480]	anaerobic	no	99.582	yes
[Ref.: #69480]	halophile	no	96.626	yes
[Ref.: #69480]	spore-forming	no	93.516	yes
[Ref.: #69480]	glucose-util	yes	91.55	no
[Ref.: #69480]	flagellated	no	97.183	yes
[Ref.: #69480]	thermophile	no	99.055	yes
[Ref.: #69480]	motile	no	90.797	yes
[Ref.: #69480]	aerobic	yes	89.228	yes
[Ref.: #69480]	glucose-ferment	no	90.682	no

Availability in culture collections External links

[Ref.: #31064]

Culture collection no.

KACC 14530, JCM 16721

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter kyonggii sp. nov., a psychrotolerant bacterium isolated from forest soil.	Chaudhary DK, Lee SD, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002428	2017	*
Phylogeny	Pedobacterpsychrotolerans sp. nov., isolated from soil.	Manandhar P, Zhang G, Lama A, Hu Y, Gao F	Int J Syst Evol Microbiol	10.1099/ijsem.0.001391	2016	*
Phylogeny	Pedobacter ginsenosidimutans sp. nov., with ginsenoside-converting activity.	Yang JE, Son HM, Lee JM, Shin HS, Park SY, Lee DG, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.051102-0	2013	*

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 )

#31064

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 #27393 (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;

#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 )

#27393

IJSEM 4396 2013 ( DOI 10.1099/ijs.0.051102-0 , PubMed 23832973 )

* These data were automatically processed and therefore are not curated

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Pedobacter ginsenosidimutans strain KACC 14530

Pedobacter ginsenosidimutans strain KACC 14530

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