Pedobacter agri (DSM 19486, KCTC 12511, JCM 15120)

Name: Pedobacter agri (DSM 19486, KCTC 12511, JCM 15120)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14113

Type strain

Strain Designation PB92

Variant Isotype of BacDive ID 132884

Culture col. no. DSM 19486 KCTC 12511 JCM 15120 PB92

NCBI tax ID(s) 454586

Special Collections DSMZ JCM KCTC Literature strains

Links

Pedobacter agri PB92 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from soil.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 412334

KCTC 12511,DSM 19486

@ref 20215

Last LPSN update 2025-12-16 09:50:16

Domain Pseudomonadati

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter agri

Full scientific name Pedobacter agri Roh et al. 2008

BacDive ID	Other strains from **Pedobacter agri** (1)	Type strain
132884	P. agri PB92, DSM 17718, KCTC 12511

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32616	negative	3 µm	0.7 µm	rod-shaped
67771				rod-shaped
67771	negative
125438	negative				95.5
125439	negative				99.5

Pigmentation

32616

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8114	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8114	positive	growth	28	mesophilic
32616	positive	growth	10-30
32616	positive	optimum	25	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
32616	positive	optimum	7
32616	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32616	aerobe
67771	aerobe
125439	obligate aerobe	98.8

Spore formation

@ref	Spore formation	Confidence
32616
125439		97.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32616	NaCl	positive	growth	0-2.5 %
32616	NaCl	positive	optimum	0-2.5 %

Observation

32616

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32616	58143 ChEBI	5-dehydro-D-gluconate	+	carbon source
32616	22599 ChEBI	arabinose	+	carbon source
32616	17057 ChEBI	cellobiose	+	carbon source
32616	4853 ChEBI	esculin	+	hydrolysis
32616	28260 ChEBI	galactose	+	carbon source
32616	17234 ChEBI	glucose	+	carbon source
32616	28087 ChEBI	glycogen	+	carbon source
32616	17716 ChEBI	lactose	+	carbon source
32616	17306 ChEBI	maltose	+	carbon source
32616	37684 ChEBI	mannose	+	carbon source
32616	28053 ChEBI	melibiose	+	carbon source
32616	506227 ChEBI	N-acetylglucosamine	+	carbon source
32616	16634 ChEBI	raffinose	+	carbon source
32616	26546 ChEBI	rhamnose	+	carbon source
32616	15963 ChEBI	ribitol	+	carbon source
32616	17814 ChEBI	salicin	+	carbon source
32616	17992 ChEBI	sucrose	+	carbon source
32616	27082 ChEBI	trehalose	+	carbon source
32616	18222 ChEBI	xylose	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
8114	soil	Daejeon	Republic of Korea	KOR	Asia
67770	Soil	Daejeon	Republic of Korea	KOR	Asia
67771	From soil	Daejeon	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8114	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM2627536v1 assembly for Pedobacter agri DSM 19486	contig	GCA_026275365	454586.4	8118558559	454586	73.62
67770	PB92_1.0 assembly for Pedobacter agri PB92	contig	GCA_000258495	1149865.7	2548876984	1149865

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8114	Pedobacter agri PB92 16S ribosomal RNA gene, partial sequence	EF660751	1460		1149865

GC content

@ref	GC-content (mol%)	Method
8114	41.4
67770	41.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter agri PB92
NCBI: GCA_000258495

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.90	no
125439	motility	BacteriaNetⓘ	no	80.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter agri PB92
PATRIC: 1149865.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.50	yes
125438	anaerobic	anaerobicⓘ	no	97.94	yes
125438	spore-forming	spore-formingⓘ	no	89.31	yes
125438	aerobic	aerobicⓘ	yes	87.05	yes
125438	thermophilic	thermophileⓘ	no	97.49	yes
125438	flagellated	motile2+ⓘ	no	85.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter changchengzhani sp. nov., isolated from soil of Antarctica.	He RH, Liu ZW, Yu Y, Li HR, Du ZJ	Antonie Van Leeuwenhoek	10.1007/s10482-019-01305-4	2019
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 agri sp. nov., from soil.	Roh SW, Quan ZX, Nam YD, Chang HW, Kim KH, Kim MK, Im WT, Jin L, Kim SH, Lee ST, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.65783-0	2008

References

#8114	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19486
#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 )
#28828	IJSEM 1640 2008 ( DOI 10.1099/ijs.0.65783-0 , PubMed 18599709 )
#32616	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 #28828
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 agri (DSM 19486, KCTC 12511, JCM 15120)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_026275365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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