Pedobacter psychrotolerans (DSM 103236, CGMCC 1.15644, V5RD)

Name: Pedobacter psychrotolerans (DSM 103236, CGMCC 1.15644, V5RD)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133008

Type strain

Strain Designation V5RD

Culture col. no. DSM 103236 CGMCC 1.15644 V5RD

NCBI tax ID(s) 1843235

Special Collections DSMZ Literature strains

History <- P. Manandhar, Chinese Acad. Sci. (CAS), Beijing; V5RD

Links

Pedobacter psychrotolerans V5RD is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and has a light-pink pigmentation.

Gram-negative rod-shaped colony-forming pigmented aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402370

DSM 103236

@ref 20215

Last LPSN update 2025-12-16 10:01:39

Domain Pseudomonadati

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter psychrotolerans

Full scientific name Pedobacter psychrotolerans Manandhar et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
24993	negative	1.6 µm	0.8 µm	rod-shaped
125439	negative				99
125438	negative				96

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
24993	light-pink	circular	3 days	R2A agar (Reasoner's 2A agar)

Pigmentation

@ref	Production	Color
24993		light-pink

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
24993	TSA (Trypticase soy agar)
24993	Reasoner's 2A agar (R2A)
24796	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
24796	positive	growth	28	mesophilic
24993	positive	growth	0.0-30.0
24993	positive	optimum	10	psychrophilic

Culture pH

@ref	Ability	Type	PH	PH range
24993	positive	optimum	9
24993	positive	growth	5.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
24993	aerobe
125439	obligate aerobe	92.6

Spore formation

@ref	Spore formation	Confidence
125439		96.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
24993	NaCl	positive	growth	1 %(w/v)
24993	NaCl	positive	maximum	3 %(w/v)
24993	NaCl	positive	growth	0.0-3.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
24993	17128 ChEBI	adipate	-	assimilation
24993	17634 ChEBI	D-glucose	-	fermentation
24993	17634 ChEBI	D-glucose	+	assimilation
24993	16899 ChEBI	D-mannitol	-	assimilation
24993	16024 ChEBI	D-mannose	+	assimilation
24993	27689 ChEBI	decanoate	-	assimilation
24993	4853 ChEBI	esculin	+	hydrolysis
24993	5291 ChEBI	gelatin	-	hydrolysis
24993	30849 ChEBI	L-arabinose	+	assimilation
24993	25115 ChEBI	malate	+	assimilation
24993	17306 ChEBI	maltose	+	assimilation
24993	506227 ChEBI	N-acetylglucosamine	+	assimilation
24993	17632 ChEBI	nitrate	-	reduction
24993	18401 ChEBI	phenylacetate	-	assimilation
24993	32032 ChEBI	potassium gluconate	-	assimilation
24993	53258 ChEBI	sodium citrate	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
24993	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
24993	acid phosphatase	+	3.1.3.2
24993	alkaline phosphatase	+	3.1.3.1
24993	alpha-chymotrypsin	+	3.4.21.1
24993	alpha-fucosidase	+	3.2.1.51
24993	alpha-galactosidase	+	3.2.1.22
24993	alpha-glucosidase	+	3.2.1.20
24993	alpha-mannosidase	-	3.2.1.24
24993	arginine dihydrolase	-	3.5.3.6
24993	beta-galactosidase	+	3.2.1.23
24993	beta-glucosidase	+	3.2.1.21
24993	beta-glucuronidase	+	3.2.1.31
24993	catalase	+	1.11.1.6
24993	cytochrome oxidase	+	1.9.3.1
24993	esterase (C 4)	+
24993	esterase Lipase (C 8)	+
24993	leucine arylamidase	+	3.4.11.1
24993	N-acetyl-beta-glucosaminidase	+	3.2.1.52
24993	naphthol-AS-BI-phosphohydrolase	+
24993	trypsin	+	3.4.21.4
24993	urease	-	3.5.1.5
24993	valine arylamidase	+

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	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
24796	soil	Qinghai-Tibetan Plateau, Damxung county (29.83° N, 90.75° E)	China	CHN	Asia	29.83	90.75 29.83/90.75
24993								R2A agar (Reasoner's 2A agar)	4-7 days	10

Taxonmaps

69479

Global distribution of 16S sequence KU535673 (>99% sequence identity) for Pedobacter psychrotolerans subclade from Microbeatlas

Aquatic Samples	414
Soil Samples	512
Animal Samples	630
Plant Samples	1085
Total Samples	2641

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24796	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM434066v1 assembly for Pedobacter psychrotolerans DSM 103236	scaffold	GCA_004340665	1843235.3	2802428854	1843235	70.91
66792	ASM1464349v1 assembly for Pedobacter psychrotolerans CGMCC 1.15644	scaffold	GCA_014643495	1843235.6	8113178836	1843235	67.74

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24796	Pedobacter psychrotolerans strain V5RD 16S ribosomal RNA gene, partial sequence	KU535673	1423		1843235

GC content

@ref	GC-content (mol%)	Method
24993	37.4	genome sequence analysis
24796	37.40	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter psychrotolerans DSM 103236
NCBI: GCA_004340665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.70	no
125439	motility	BacteriaNetⓘ	no	63.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter psychrotolerans DSM 103236
NCBI: GCA_004340665.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.00	yes
125438	anaerobic	anaerobicⓘ	no	95.45	yes
125438	aerobic	aerobicⓘ	yes	86.08	yes
125438	spore-forming	spore-formingⓘ	no	88.03	no
125438	thermophilic	thermophileⓘ	no	95.99	yes
125438	flagellated	motile2+ⓘ	no	85.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
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

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 )
#24796	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103236
#24993	P. Z. Manandhar, Gengxin,Lama, Arun,Hu, Yilun,Gao, Feng: Pedobacter psychrotolerans sp. nov., isolated from soil. IJSEM 66: 4560 - 4566 2016 ( DOI 10.1099/ijsem.0.001391 , PubMed 27498823 )
#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) .
#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 psychrotolerans (DSM 103236, CGMCC 1.15644, V5RD)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004340665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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