Name: Pedobacter metabolipauper WB2.3-71
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14107

Type strain:

Species: Pedobacter metabolipauper

Strain Designation: WB2.3-71

Culture col. no.: DSM 19035

Strain history: <- S. Muurholm <- E. Brambilla <- O. Päuker; WB2.3-71

NCBI tax ID(s): 425513 (species)

Section

Pedobacter metabolipauper WB2.3-71 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	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter metabolipauper**
	Full Scientific Name (PNU)	Pedobacter metabolipauper Muurholm et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32230]	Gram stain	negative
[Ref.: #32230]	Cell length	2.2 µm
[Ref.: #32230]	Cell width	0.83 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.: #7854]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7854]

Culture medium growth

[Ref.: #7854]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #7854]

Culture medium composition

expand / minimize

[Ref.: #33301]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #33301]

Culture medium growth

[Ref.: #33301]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7854]	growth	25 °C
[Ref.: #32230]	growth	08-31 °C
[Ref.: #32230]	optimum	25 °C
[Ref.: #33301]	growth	15 °C

[Ref.: #7854]	Temperature range	mesophilic
[Ref.: #32230]	Temperature range	mesophilic
[Ref.: #33301]	Temperature range	psychrophilic

	pH	Kind of pH		pH	pH range
[Ref.: #32230]			optimum	6.95
[Ref.: #32230]			growth	5.9-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32230]

Ability of spore formation

	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]	cellobiose ChEBI	+	carbon source
[Ref.: #32230]	esculin ChEBI	+	hydrolysis
[Ref.: #32230]	glucose 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]	sucrose ChEBI	+	carbon source
[Ref.: #32230]	trehalose ChEBI	+	carbon source
[Ref.: #32230]	tween 80 ChEBI	+	carbon source

	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

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[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]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	carotenoid biosynthesis	63.64	14 of 22
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	oxidative phosphorylation	51.65	47 of 91
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #7854]	Sample type/isolated from	stream water
[Ref.: #7854]	Geographic location (country and/or sea, region)	Lower Saxony, Westhöfer Bach
[Ref.: #7854]	Country	Germany
[Ref.: #7854]	Country ISO 3 Code	DEU
[Ref.: #7854]	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.: #7854]

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 metabolipauper partial 16S rRNA gene, type strain WB2.3-71T	AM491370	1505	GenBank	425513 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter metabolipauper DSM 19035	GCA_004362715	scaffold	GenBank	425513 tax ID	*
[Ref.: #66792]	Pedobacter metabolipauper strain DSM 19035	425513.4	wgs	PATRIC	425513 tax ID	*
[Ref.: #66792]	Pedobacter metabolipauper DSM 19035	2636416080	draft	JGI IMG/M	425513 tax ID	*
[Ref.: #66792]	Clostridia bacterium RGIG8983	GCA_017938185	contig	PATRIC	2044939 tax ID	*

Availability in culture collections External links

[Ref.: #7854]

Culture collection no.

DSM 19035

[Ref.: #20218]

Associated Passport(s) in StrainInfo

740311

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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 bambusae sp. nov., isolated from soil of a bamboo plantation.	Won KH, Kook M, Yi TH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0352-8	2014	*

References

#7854

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19035

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#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)

#33301 ; 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 )

#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) .

#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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