Pedobacter steynii (DSM 19110, WB2.3-45)

Name: Pedobacter steynii (DSM 19110, WB2.3-45)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14109

Type strain

Strain Designation WB2.3-45

Culture col. no. DSM 19110 WB2.3-45

NCBI tax ID(s) 430522

Special Collections DSMZ Literature strains

History DSMZ <- S. Muurholm <- E. Brambilla <- O. Päuker; WB2.3-45

Links

Pedobacter steynii WB2.3-45 is a Gram-negative, motile, rod-shaped bacterium that was isolated from stream water.

Gram-negative motile rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 310981

LMG 31390,CIP 109507,DSM 19110

@ref 20215

Last LPSN update 2026-05-29 08:28:12

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter steynii

Full scientific name Pedobacter steynii Muurholm et al. 2007

BacDive ID	Other strains from **Pedobacter steynii** (1)	Type strain
174175	P. steynii CIP 109507, WB 2.3-45 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
32230	negative	2.73 µm	0.83 µm	rod-shaped
125438	negative					97

Pigmentation

32230

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7897	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
37317	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati			Distilled water make up to (1000.000 ml);R2A agar (18.200 g)

Culture temp

@ref	Growth	Type	Temperature (°C)
7897	positive	growth	25
32230	positive	growth	10-30
32230	positive	optimum	26
37317	positive	growth	25

Culture pH

@ref	Ability	Type	PH
32230	positive	optimum	7.08
32230	positive	growth	5.70-8.45

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
32230
125439		98.515

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32230	NaCl	positive	growth	0-4 %
32230	NaCl	positive	optimum	2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32230	40585 ChEBI	alpha-cyclodextrin	+	carbon source
32230	35391 ChEBI	aspartate	+	carbon source
32230	17057 ChEBI	cellobiose	+	carbon source
32230	23652 ChEBI	dextrin	+	carbon source
32230	4853 ChEBI	esculin	+	hydrolysis
32230	28260 ChEBI	galactose	+	carbon source
32230	5291 ChEBI	gelatin	+	carbon source
32230	17234 ChEBI	glucose	+	carbon source
32230	29987 ChEBI	glutamate	+	carbon source
32230	17754 ChEBI	glycerol	+	carbon source
32230	28087 ChEBI	glycogen	+	carbon source
32230	17716 ChEBI	lactose	+	carbon source
32230	17306 ChEBI	maltose	+	carbon source
32230	37684 ChEBI	mannose	+	carbon source
32230	28053 ChEBI	melibiose	+	carbon source
32230	37657 ChEBI	methyl D-glucoside	+	carbon source
32230	506227 ChEBI	N-acetylglucosamine	+	carbon source
32230	16634 ChEBI	raffinose	+	carbon source
32230	17814 ChEBI	salicin	+	carbon source
32230	17822 ChEBI	serine	+	carbon source
32230	26986 ChEBI	threonine	+	carbon source
32230	27082 ChEBI	trehalose	+	carbon source
32230	53426 ChEBI	tween 80	+	carbon source
32230	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32230	alkaline phosphatase	+	3.1.3.1
32230	catalase	+	1.11.1.6
32230	cytochrome oxidase	+	1.9.3.1
32230	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	kanosamine biosynthesis II	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	pentose phosphate pathway	100	11 of 11
66794	ribulose monophosphate pathway	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	NAD metabolism	94.44	17 of 18
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	starch degradation	80	8 of 10
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	pyrimidine metabolism	75.56	34 of 45
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	ketogluconate metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	vitamin B1 metabolism	69.23	9 of 13
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	degradation of sugar acids	68	17 of 25
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	histidine metabolism	65.52	19 of 29
66794	methionine metabolism	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	citric acid cycle	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	urea cycle	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	non-pathway related	60.53	23 of 38
66794	gallate degradation	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	lysine metabolism	57.14	24 of 42
66794	nitrate assimilation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	sulfate reduction	53.85	7 of 13
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	oxidative phosphorylation	50.55	46 of 91
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	arginine metabolism	50	12 of 24
66794	butanoate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	vitamin E metabolism	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	carotenoid biosynthesis	45.45	10 of 22
66794	metabolism of disaccharids	45.45	5 of 11
66794	ascorbate metabolism	40.91	9 of 22
66794	D-cycloserine biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	O-antigen biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	phenol degradation	35	7 of 20
66794	polyamine pathway	34.78	8 of 23
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7897	stream water	Lower Saxony, Westhöfer Bach	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AM491372 (>99% sequence identity) for Pedobacter from Microbeatlas

Aquatic Samples	488
Soil Samples	673
Animal Samples	754
Plant Samples	348
Total Samples	2263

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7897	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
66792	IMG-taxon 2675903693 annotated assembly for Pedobacter steynii DSM 19110	scaffold	GCA_900103665	430522.10	2675903693	430522	68.25

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
32230	Pedobacter steynii partial 16S rRNA gene, type strain WB2.3-45T	AM491372	1505		430522

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2675903693 annotated assembly for Pedobacter steynii DSM 19110
NCBI: GCA_900103665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	75.52	no
125439	motility	BacteriaNetⓘ	no	70.98	no
125439	gram_stain	BacteriaNetⓘ	negative	84.66	no
125439	spore_formation	BacteriaNetⓘ	no	98.52	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter steynii DSM 19110
NCBI: GCA_900103665.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	yes
125438	anaerobic	anaerobicⓘ	no	97.28	no
125438	aerobic	aerobicⓘ	yes	80.30	no
125438	spore-forming	spore-formingⓘ	no	81.72	yes
125438	thermophilic	thermophileⓘ	no	96.33	yes
125438	flagellated	motile2+ⓘ	no	86.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4.	Chang S, Zhang G, Chen X, Long H, Wang Y, Chen T, Liu G.	Stand Genomic Sci	10.1186/s40793-017-0249-z	2017
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	Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field.	Ngo HT, Son HM, Park SY, Kim KY, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0154-z	2014
Phylogeny	Pedobacter duraquae sp. nov., Pedobacter westerhofensis sp. nov., Pedobacter metabolipauper sp. nov., Pedobacter hartonius sp. nov. and Pedobacter steynii sp. nov., isolated from a hard-water rivulet.	Muurholm S, Cousin S, Pauker O, Brambilla E, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.65166-0	2007

References

#7897	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19110
#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 )
#28472	IJSEM 2221 2007 ( DOI 10.1099/ijs.0.65166-0 , PubMed 17911287 )
#32230	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 #28472
#37317	; Curators of the CIP;
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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 steynii (DSM 19110, WB2.3-45)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900103665

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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