Name: Pedobacter panaciterrae KCTC 12594
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 134222

Type strain:

Species: Pedobacter panaciterrae

Culture col. no.: KCTC 12594, LMG 23400, Gsoil 042

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 363849 (species)

SI-ID 289682

LMG 23400, KCTC 12594

Special Collections

Section

Pedobacter panaciterrae KCTC 12594 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.

Gram-negative
rod-shaped
facultative anaerobe
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 panaciterrae**
	Full Scientific Name (LPSN)	Pedobacter panaciterrae Yoon et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31944]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98

[Ref.: #31944]	Cell length	2 µm

[Ref.: #31944]	Cell width	0.75 µm

[Ref.: #31944]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31944]	Motility	no
[Ref.: #67771]	Motility	no

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #31944]	growth	04-30 °C
[Ref.: #31944]	optimum	25 °C
[Ref.: #67771]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #31944]			optimum	6.75
[Ref.: #31944]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31944]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31944]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31944]		NaCl		growth	<1	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31944]	arabinose ChEBI	+	carbon source
[Ref.: #31944]	cellobiose ChEBI	+	carbon source
[Ref.: #31944]	glucose ChEBI	+	carbon source
[Ref.: #31944]	glycerol ChEBI	+	carbon source
[Ref.: #31944]	lactose ChEBI	+	carbon source
[Ref.: #31944]	maltose ChEBI	+	carbon source
[Ref.: #31944]	mannose ChEBI	+	carbon source
[Ref.: #31944]	melibiose ChEBI	+	carbon source
[Ref.: #31944]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31944]	raffinose ChEBI	+	carbon source
[Ref.: #31944]	salicin ChEBI	+	carbon source
[Ref.: #31944]	sucrose ChEBI	+	carbon source
[Ref.: #31944]	trehalose ChEBI	+	carbon source
[Ref.: #31944]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31944]		catalase	+	1.11.1.6
[Ref.: #31944]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #31944]	Sample type/isolated from	soil

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

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB245368 (>99% sequence identity) for Pedobacter from Microbeatlas

Aquatic Samples	50
Soil Samples	523
Animal Samples	111
Plant Samples	96
Total Samples	780

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.: #31944]	Pedobacter panaciterrae gene for 16S rRNA, partial sequence, strain: Gsoil 042	AB245368	1463	GenBank ENA	363849 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter panaciterrae LMG 23400	GCA_013204795	contig	GenBank ENA	363849 tax ID	*
[Ref.: #66792]	Pedobacter panaciterrae strain LMG 23400	363849.11	wgs	PATRIC	363849 tax ID	*

[Ref.: #31944]

GC-content

44.2 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter panaciterrae strain LMG 23400 PATRIC: 363849.11
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.978	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	85.8	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.754	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.49	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	85.507	no

Availability in culture collections External links

[Ref.: #31944]

Culture collection no.

KCTC 12594, LMG 23400, Gsoil 042

[Ref.: #91816]

SI-ID 289682

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana.	Qi SS, Cnockaert M, Carlier A, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijsem.0.004667	2021	*
Phylogeny	Pedobacterlycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.).	Cho H, Ahn JH, Weon HY, Joa JH, Kwon SW, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001532	2016	*
Phylogeny	Pedobacter humi sp. nov., isolated from a playground soil.	Trinh H, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001032	2016	*
Phylogeny	Pedobacter nutrimenti sp. nov., isolated from chilled food.	Derichs J, Kampfer P, Lipski A	Int J Syst Evol Microbiol	10.1099/ijs.0.058677-0	2014	*
Phylogeny	Pedobacter panaciterrae sp. nov., isolated from soil in South Korea.	Yoon MH, Ten LN, Im WT, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64693-0	2007	*

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 )

#31944

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 #28200 (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) .

#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) .

#91816

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-ID289682.1 )

#28200

IJSEM 381 2007 ( DOI 10.1099/ijs.0.64693-0 , PubMed 17267983 )

* These data were automatically processed and therefore are not curated

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Pedobacter panaciterrae strain LMG 23400

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