Pedobacter westerhofensis (DSM 19036, WB3.3-22)

Name: Pedobacter westerhofensis (DSM 19036, WB3.3-22)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14108

Type strain

Strain Designation WB3.3-22

Culture col. no. DSM 19036 WB3.3-22

NCBI tax ID(s) 425512

Special Collections DSMZ Literature strains

History <- S. Muurholm <- E. Brambilla <- O. Päuker; WB3.3-22

Links

Pedobacter westerhofensis WB3.3-22 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 310977

CIP 109479,DSM 19036

@ref 20215

Last LPSN update 2026-02-09 11:21:19

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter westerhofensis

Full scientific name Pedobacter westerhofensis Muurholm et al. 2007

BacDive ID	Other strains from **Pedobacter westerhofensis** (1)	Type strain
174325	P. westerhofensis WB3.3-22, CIP 109479 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32230	negative	2.1 µm	0.915 µm	rod-shaped
125439	negative				99.3
125438	negative				94.25

Pigmentation

32230

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7855	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
42248	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)
7855	positive	growth	25
32230	positive	growth	09-28
32230	positive	optimum	23
42248	positive	growth	15

Culture pH

@ref	Ability	Type	PH
32230	positive	optimum	6.55
32230	positive	growth	5.3-7.8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	91.5

Spore formation

@ref	Spore formation	Confidence
32230
125439		98.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32230	NaCl	positive	growth	<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	22599 ChEBI	arabinose	+	carbon source
32230	17057 ChEBI	cellobiose	+	carbon source
32230	23652 ChEBI	dextrin	+	carbon source
32230	4853 ChEBI	esculin	+	hydrolysis
32230	28757 ChEBI	fructose	+	carbon source
32230	28260 ChEBI	galactose	+	carbon source
32230	5291 ChEBI	gelatin	+	carbon source
32230	17234 ChEBI	glucose	+	carbon source
32230	17754 ChEBI	glycerol	+	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	26546 ChEBI	rhamnose	+	carbon source
32230	17822 ChEBI	serine	+	carbon source
32230	17992 ChEBI	sucrose	+	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	+

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
7855	stream water	Lower Saxony, Westhöfer Bach	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7855	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 2724679782 annotated assembly for Pedobacter westerhofensis DSM 19036	scaffold	GCA_900182595	425512.3	2724679782	425512	67.84

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
32230	Pedobacter westerhofensis partial 16S rRNA gene, type strain WB3.3-22T	AM491369	1503		425512

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter westerhofensis DSM 19036
NCBI: GCA_900182595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	no	72.50	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	91.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter westerhofensis DSM 19036
NCBI: GCA_900182595.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.25	no
125438	anaerobic	anaerobicⓘ	no	96.44	no
125438	aerobic	aerobicⓘ	yes	87.68	no
125438	spore-forming	spore-formingⓘ	no	84.03	yes
125438	thermophilic	thermophileⓘ	no	96.47	no
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine.	Covas C, Caetano T, Cruz A, Santos T, Dias L, Klein G, Abdulmawjood A, Rodriguez-Alcala LM, Pimentel LL, Gomes A, Freitas AC, Garcia-Serrano A, Fontecha J, Mendo S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001814	2017
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

#7855	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19036
#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
#42248	; 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) .
#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 westerhofensis (DSM 19036, WB3.3-22)

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

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900182595

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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