Name: Pedobacter steynii WB2.3-45
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14109

Type strain:

Species: Pedobacter steynii

Strain Designation: WB2.3-45

Culture col. no.: DSM 19110

Strain history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB2.3-45

NCBI tax ID(s): 430522 (species)

SI-ID 310981

CIP 109507, DSM 19110

Other strains from Pedobacter steynii

P. steynii CIP 109507, WB 2.3-45 (type strain)

Section

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

Gram-negative
motile
rod-shaped
mesophilic
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 steynii**
	Full Scientific Name (LPSN)	Pedobacter steynii Muurholm et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32230]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.988

[Ref.: #32230]	Cell length	2.73 µm

[Ref.: #32230]	Cell width	0.83 µm

[Ref.: #32230]	Cell shape	rod-shaped

[Ref.: #32230]	Motility	yes
[Ref.: #69480]	Motility	no Confidence in %90.201

[Ref.: #32230]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7897]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7897]

Culture medium growth

[Ref.: #7897]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7897]

Culture medium composition

expand / minimize

[Ref.: #37317]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #37317]

Culture medium growth

[Ref.: #37317]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7897]	growth	25 °C
[Ref.: #32230]	growth	10-30 °C
[Ref.: #32230]	optimum	26 °C
[Ref.: #37317]	growth	25 °C

[Ref.: #7897]	Temperature range	mesophilic
[Ref.: #32230]	Temperature range	mesophilic
[Ref.: #37317]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32230]			optimum	7.08
[Ref.: #32230]			growth	5.70-8.45

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32230]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.985

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32230]		NaCl		growth	0-4	%
[Ref.: #32230]		NaCl		optimum	2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32230]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #32230]	aspartate ChEBI	+	carbon source
[Ref.: #32230]	cellobiose ChEBI	+	carbon source
[Ref.: #32230]	dextrin ChEBI	+	carbon source
[Ref.: #32230]	esculin ChEBI	+	hydrolysis
[Ref.: #32230]	galactose ChEBI	+	carbon source
[Ref.: #32230]	gelatin ChEBI	+	carbon source
[Ref.: #32230]	glucose ChEBI	+	carbon source
[Ref.: #32230]	glutamate ChEBI	+	carbon source
[Ref.: #32230]	glycerol ChEBI	+	carbon source
[Ref.: #32230]	glycogen ChEBI	+	carbon source
[Ref.: #32230]	lactose ChEBI	+	carbon source
[Ref.: #32230]	maltose ChEBI	+	carbon source
[Ref.: #32230]	mannose ChEBI	+	carbon source
[Ref.: #32230]	melibiose ChEBI	+	carbon source
[Ref.: #32230]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #32230]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32230]	raffinose ChEBI	+	carbon source
[Ref.: #32230]	salicin ChEBI	+	carbon source
[Ref.: #32230]	serine ChEBI	+	carbon source
[Ref.: #32230]	threonine ChEBI	+	carbon source
[Ref.: #32230]	trehalose ChEBI	+	carbon source
[Ref.: #32230]	tween 80 ChEBI	+	carbon source
[Ref.: #32230]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #32230]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32230]	catalase	+	1.11.1.6
[Ref.: #32230]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32230]	gelatinase	+

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

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

[Ref.: #7897]	Sample type/isolated from	stream water
[Ref.: #7897]	Geographic location (country and/or sea, region)	Lower Saxony, Westhöfer Bach
[Ref.: #7897]	Country	Germany
[Ref.: #7897]	Country ISO 3 Code	DEU
[Ref.: #7897]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#River (Creek)

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7897]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #32230]	Pedobacter steynii partial 16S rRNA gene, type strain WB2.3-45T	AM491372	1505	GenBank	430522 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter steynii DSM 19110	GCA_900103665	scaffold	GenBank	430522 tax ID	*
[Ref.: #66792]	Pedobacter steynii strain DSM 19110	430522.10	wgs	PATRIC	430522 tax ID	*
[Ref.: #66792]	Pedobacter steynii DSM 19110	2675903693	draft	JGI IMG/M	430522 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pedobacter steynii strain DSM 19110 PATRIC: 430522.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter steynii DSM 19110 NCBI: GCA_900103665.1
[Ref.: #69480]	motile	no	84.037	yes
[Ref.: #69480]	flagellated	no	96.231	no
[Ref.: #69480]	gram-positive	no	97.224	yes
[Ref.: #69480]	anaerobic	no	99.288	no
[Ref.: #69480]	aerobic	yes	83.921	no
[Ref.: #69480]	halophile	no	96.917	no
[Ref.: #69480]	spore-forming	no	90.07	yes
[Ref.: #69480]	glucose-ferment	no	89.212	no
[Ref.: #69480]	thermophile	no	99.642	yes
[Ref.: #69480]	glucose-util	yes	88.423	yes

Availability in culture collections External links

[Ref.: #7897]

Culture collection no.

DSM 19110

[Ref.: #83276]

SI-ID 310981

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	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 )

#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 (see below)

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#83276

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-ID310981.1 )

#28472

IJSEM 2221 2007 ( DOI 10.1099/ijs.0.65166-0 , PubMed 17911287 )

* These data were automatically processed and therefore are not curated

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Pedobacter steynii strain DSM 19110

Pedobacter steynii DSM 19110

Change proposal

Change proposal