Name: Pedobacter westerhofensis WB3.3-22
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14108

Type strain:

Species: Pedobacter westerhofensis

Strain Designation: WB3.3-22

Culture col. no.: DSM 19036

Strain history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB3.3-22

NCBI tax ID(s): 425512 (species)

SI-ID 310977

CIP 109479, DSM 19036

Other strains from Pedobacter westerhofensis

P. westerhofensis WB3.3-22, CIP 109479 (type strain)

Section

Pedobacter westerhofensis WB3.3-22 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 westerhofensis**
	Full Scientific Name (LPSN)	Pedobacter westerhofensis Muurholm et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32230]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #32230]	Cell length	2.1 µm

[Ref.: #32230]	Cell width	0.915 µm

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

[Ref.: #32230]	Motility	yes

[Ref.: #32230]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7855]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7855]

Culture medium growth

[Ref.: #7855]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7855]

Culture medium composition

expand / minimize

[Ref.: #42248]

Culture medium

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

[Ref.: #42248]

Culture medium growth

[Ref.: #42248]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7855]	growth	25 °C
[Ref.: #32230]	growth	09-28 °C
[Ref.: #32230]	optimum	23 °C
[Ref.: #42248]	growth	15 °C

[Ref.: #7855]	Temperature range	mesophilic
[Ref.: #32230]	Temperature range	psychrophilic
[Ref.: #42248]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #32230]			optimum	6.55
[Ref.: #32230]			growth	5.3-7.8

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	<4	%
[Ref.: #32230]		NaCl		optimum	2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32230]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #32230]	arabinose ChEBI	+	carbon source
[Ref.: #32230]	cellobiose ChEBI	+	carbon source
[Ref.: #32230]	dextrin ChEBI	+	carbon source
[Ref.: #32230]	esculin ChEBI	+	hydrolysis
[Ref.: #32230]	fructose ChEBI	+	carbon source
[Ref.: #32230]	galactose ChEBI	+	carbon source
[Ref.: #32230]	gelatin ChEBI	+	carbon source
[Ref.: #32230]	glucose ChEBI	+	carbon source
[Ref.: #32230]	glycerol 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]	rhamnose ChEBI	+	carbon source
[Ref.: #32230]	serine ChEBI	+	carbon source
[Ref.: #32230]	sucrose 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	+

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

[Ref.: #7855]	Sample type/isolated from	stream water
[Ref.: #7855]	Geographic location (country and/or sea, region)	Lower Saxony, Westhöfer Bach
[Ref.: #7855]	Country	Germany
[Ref.: #7855]	Country ISO 3 Code	DEU
[Ref.: #7855]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#River (Creek)

What are isolation sources categories?

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

[Ref.: #7855]

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 westerhofensis partial 16S rRNA gene, type strain WB3.3-22T	AM491369	1503	GenBank	425512 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter westerhofensis DSM 19036	GCA_900182595	scaffold	GenBank	425512 tax ID	*
[Ref.: #66792]	Pedobacter westerhofensis strain DSM 19036	425512.3	wgs	PATRIC	425512 tax ID	*
[Ref.: #66792]	Pedobacter westerhofensis DSM 19036	2724679782	draft	JGI IMG/M	425512 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 westerhofensis DSM 19036 NCBI: GCA_900182595.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter westerhofensis DSM 19036 NCBI: GCA_900182595.1
[Ref.: #69480]	motile	no	86.032	no
[Ref.: #69480]	flagellated	no	97.556	no
[Ref.: #69480]	gram-positive	no	97.011	yes
[Ref.: #69480]	anaerobic	no	99.23	no
[Ref.: #69480]	aerobic	yes	86.004	no
[Ref.: #69480]	halophile	no	95.822	no
[Ref.: #69480]	spore-forming	no	93.314	yes
[Ref.: #69480]	thermophile	no	99.559	yes
[Ref.: #69480]	glucose-util	yes	91.459	yes
[Ref.: #69480]	glucose-ferment	no	87.235	no

Availability in culture collections External links

[Ref.: #7855]

Culture collection no.

DSM 19036

[Ref.: #83275]

SI-ID 310977

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 )

#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)

#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) .

#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 )

#83275

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-ID310977.1 )

#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 westerhofensis DSM 19036

Pedobacter westerhofensis DSM 19036

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