Pedobacter panaciterrae (KCTC 12594, LMG 23400, Gsoil 042)

Name: Pedobacter panaciterrae (KCTC 12594, LMG 23400, Gsoil 042)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134222

Type strain

Culture col. no. KCTC 12594 LMG 23400 Gsoil 042

NCBI tax ID(s) 363849

Special Collections KCTC Literature strains

History KCTC <- ST Lee, KAIST

Links

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

Gram-negative rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 289682

LMG 23400,KCTC 12594

@ref 20215

Last LPSN update 2026-05-29 08:38:16

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter panaciterrae

Full scientific name Pedobacter panaciterrae Yoon et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31944	negative	2 µm	0.75 µm	rod-shaped
67771				rod-shaped
67771	negative
125439	negative				97.596
125438	negative				98

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
31944	positive	growth	04-30
31944	positive	optimum	25
67771	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
31944	positive	optimum	6.75
31944	positive	growth	5.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31944	facultative anaerobe
67771	aerobe
125439	obligate aerobe	94.78

Spore formation

@ref	Spore formation	Confidence
31944
67771
125439		98.548

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31944	NaCl	positive	growth	<1 %

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31944	22599 ChEBI	arabinose	+	carbon source
31944	17057 ChEBI	cellobiose	+	carbon source
31944	17234 ChEBI	glucose	+	carbon source
31944	17754 ChEBI	glycerol	+	carbon source
31944	17716 ChEBI	lactose	+	carbon source
31944	17306 ChEBI	maltose	+	carbon source
31944	37684 ChEBI	mannose	+	carbon source
31944	28053 ChEBI	melibiose	+	carbon source
31944	506227 ChEBI	N-acetylglucosamine	+	carbon source
31944	16634 ChEBI	raffinose	+	carbon source
31944	17814 ChEBI	salicin	+	carbon source
31944	17992 ChEBI	sucrose	+	carbon source
31944	27082 ChEBI	trehalose	+	carbon source
31944	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31944	catalase	+	1.11.1.6
31944	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
31944	soil
67771	From soil of the ginseng field	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1320479v1 assembly for Pedobacter panaciterrae LMG 23400	contig	GCA_013204795	363849.11	2996072888	363849	73.59

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31944	Pedobacter panaciterrae gene for 16S rRNA, partial sequence, strain: Gsoil 042	AB245368	1463		363849

GC content

31944

GC-content (mol%)44.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1320479v1 assembly for Pedobacter panaciterrae LMG 23400
NCBI: GCA_013204795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.78	no
125439	motility	BacteriaNetⓘ	no	75.53	no
125439	gram_stain	BacteriaNetⓘ	negative	97.60	no
125439	spore_formation	BacteriaNetⓘ	no	98.55	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter panaciterrae strain LMG 23400
PATRIC: 363849.11

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	95.98	yes
125438	spore-forming	spore-formingⓘ	no	85.80	yes
125438	aerobic	aerobicⓘ	yes	87.75	no
125438	thermophilic	thermophileⓘ	no	98.49	yes
125438	flagellated	motile2+ⓘ	no	85.51	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Exploration of Social Spreading Reveals That This Behavior Is Prevalent among Pedobacter and Pseudomonas fluorescens Isolates and That There Are Variations in the Induction of the Phenotype.	McCully LM, Graslie J, McGraw AR, Bitzer AS, Sigurbjornsdottir AM, Vilhelmsson O, Silby MW.	Appl Environ Microbiol	10.1128/aem.01344-21	2021
	Immobilized Enzymes for ABO-Independent Blood Cell Transfusions.	Moller C, Pohlschroder F, Wesche J, Schmiade P, Baselau M, Wende K, Stloukalova B, Bottcher D, Greinacher A, Bornscheuer UT, Terholsen H, Aurich K.	Chembiochem	10.1002/cbic.202500542	2025
	Identification and Protein Engineering of Galactosidases for the Conversion of Blood Type B to Blood Type O.	Moller C, Terholsen H, Schmoker O, Le TLA, Wesche J, Schmiade P, Eppendorfer E, Rimkus N, Girbardt B, Bottcher D, Palm GJ, Hoppen J, Lammers M, Greinacher A, Aurich K, Bornscheuer UT.	Chembiochem	10.1002/cbic.202500072	2025
	Membrane lipid adaptation of soil Bacteroidetes isolates to temperature and pH.	Hellequin E, Collin S, Seder-Colomina M, Vequaud P, Anquetil C, Kish A, Huguet A.	Front Microbiol	10.3389/fmicb.2023.1032032	2023
Metabolism	Characterization of Endofungal Bacteria and Their Role in the Ectomycorrhizal Fungus Helvella bachu.	Wei C, Liu M, Meng G, Wang M, Zhou X, Xu J, Hu J, Zhang L, Dong C.	J Fungi (Basel)	10.3390/jof10120889	2024
	Legumes of the Sardinia Island: Knowledge on Symbiotic and Endophytic Bacteria and Interactive Software Tool for Plant Species Determination.	Muresu R, Porceddu A, Concheri G, Stevanato P, Squartini A.	Plants (Basel)	10.3390/plants11111521	2022
Biotechnology	Increased Biomass Production by Mesophilic Food-Associated Bacteria through Lowering the Growth Temperature from 30°C to 10°C.	Seel W, Derichs J, Lipski A.	Appl Environ Microbiol	10.1128/aem.00211-16	2016
Enzymology	Diversity of Cultivable Microbes From Soil of the Fildes Peninsula, Antarctica, and Their Potential Application.	Cong B, Yin X, Deng A, Shen J, Tian Y, Wang S, Yang H.	Front Microbiol	10.3389/fmicb.2020.570836	2020
	The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization.	Chavarro-Carrero EA, Snelders NC, Torres DE, Kraege A, Lopez-Moral A, Petti GC, Punt W, Wieneke J, Garcia-Velasco R, Lopez-Herrera CJ, Seidl MF, Thomma BPHJ.	PLoS Pathog	10.1371/journal.ppat.1011866	2024
Pathogenicity	A qnr-plasmid allows aminoglycosides to induce SOS in Escherichia coli.	Babosan A, Skurnik D, Muggeo A, Pier GB, Baharoglu Z, Jove T, Ploy MC, Griveau S, Bedioui F, Vergnolle S, Moussalih S, de Champs C, Mazel D, Guillard T.	Elife	10.7554/elife.69511	2022
	Pedobacter alpinus sp. nov., isolated from a plateau lake.	Li AH, Liu HC, Zhou YG.	Int J Syst Evol Microbiol	10.1099/ijsem.0.000498	2015
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 )
#28200	IJSEM 381 2007 ( DOI 10.1099/ijs.0.64693-0 , PubMed 17267983 )
#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
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Pedobacter panaciterrae (KCTC 12594, LMG 23400, Gsoil 042)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_013204795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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