Polynucleobacter victoriensis (DSM 21486, JCM 32005, MWH-VicM1)

Name: Polynucleobacter victoriensis (DSM 21486, JCM 32005, MWH-VicM1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2072

Type strain

Strain Designation MWH-VicM1

Culture col. no. DSM 21486 JCM 32005 MWH-VicM1

NCBI tax ID(s) 2049319

Special Collections DSMZ JCM Literature strains

History <- M. W. Hahn, Austrian Academy of Sci., Inst. Limnology; MWH-VicM1 (Polynucleobacter cosmopolitanus) E. Lang; DSMZ, Germany; DSM 21486 <-- M. W. Hahn; Univ. Innsbruck, Austria; MWH-VicM1.

Links

Polynucleobacter victoriensis MWH-VicM1 is a facultative anaerobe, chemoorganotroph, rod-shaped bacterium that forms circular colonies and was isolated from water.

rod-shaped colony-forming facultative anaerobe chemoorganotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398185

JCM 32005,DSM 21486

@ref 20215

Last LPSN update 2026-02-09 11:18:14

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Polynucleobacter

Species Polynucleobacter victoriensis

Full scientific name Polynucleobacter victoriensis Hahn et al. 2017

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Gram stain	Confidence
44087	0.4-1.1 µm	0.3-0.5 µm	rod-shaped
125439				negative	99.8

Colony morphology

@ref	Colony shape	Medium used
44087	circular	NSY

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
44087	NSY
15737	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

Culture temp

@ref	Growth	Type	Temperature (°C)
15737	positive	growth	28
44087	positive	growth	6-38
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44087	facultative anaerobe
125439	obligate aerobe	98.1

Nutrition type

44087

Typechemoorganotroph

Spore formation

@ref	Spore formation	Confidence
125439		99.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
44087	NaCl	positive	growth	0-0.5 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44087	39150 ChEBI	4-oxopentanoate	-	assimilation
44087	30089 ChEBI	acetate	+	assimilation
44087	17750 ChEBI	betaine	-	assimilation
44087	16947 ChEBI	citrate	-	assimilation
44087	15824 ChEBI	D-fructose	-	assimilation
44087	28847 ChEBI	D-fucose	-	assimilation
44087	12936 ChEBI	D-galactose	+/-	assimilation
44087	18024 ChEBI	D-galacturonic acid	+/-	assimilation
44087	17634 ChEBI	D-glucose	-	assimilation
44087	62318 ChEBI	D-lyxose	-	assimilation
44087	16024 ChEBI	D-mannose	-	assimilation
44087	17924 ChEBI	D-sorbitol	-	assimilation
44087	29806 ChEBI	fumarate	+	assimilation
44087	29805 ChEBI	glycolate	-	assimilation
44087	36655 ChEBI	glyoxylate	-	assimilation
44087	16977 ChEBI	L-alanine	+	assimilation
44087	17196 ChEBI	L-asparagine	-	assimilation
44087	29991 ChEBI	L-aspartate	-	assimilation
44087	17561 ChEBI	L-cysteine	+	assimilation
44087	29985 ChEBI	L-glutamate	-	assimilation
44087	17115 ChEBI	L-serine	-	assimilation
44087	25115 ChEBI	malate	+	assimilation
44087	15792 ChEBI	malonate	+	assimilation
44087	30623 ChEBI	oxalate	-	assimilation
44087	16452 ChEBI	oxaloacetate	+	assimilation
44087	17272 ChEBI	propionate	+	assimilation
44087	15361 ChEBI	pyruvate	+	assimilation
44087	30031 ChEBI	succinate	+	assimilation

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	methylglyoxal degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	heme metabolism	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	phenylalanine metabolism	76.92	10 of 13
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	threonine metabolism	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	lipid A biosynthesis	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	purine metabolism	64.89	61 of 94
66794	flavin biosynthesis	60	9 of 15
66794	glycolysis	58.82	10 of 17
66794	alanine metabolism	58.62	17 of 29
66794	non-pathway related	57.89	22 of 38
66794	pyrimidine metabolism	57.78	26 of 45
66794	d-mannose degradation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	vitamin B6 metabolism	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	sulfate reduction	53.85	7 of 13
66794	oxidative phosphorylation	52.75	48 of 91
66794	histidine metabolism	51.72	15 of 29
66794	pantothenate biosynthesis	50	3 of 6
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	suberin monomers biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	methionine metabolism	50	13 of 26
66794	tyrosine metabolism	50	7 of 14
66794	isoprenoid biosynthesis	50	13 of 26
66794	lysine metabolism	47.62	20 of 42
66794	vitamin B1 metabolism	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	pentose phosphate pathway	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	tryptophan metabolism	44.74	17 of 38
66794	glutathione metabolism	42.86	6 of 14
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	ketogluconate metabolism	37.5	3 of 8
66794	formaldehyde oxidation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	urea cycle	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	Entner Doudoroff pathway	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	propanol degradation	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	glycogen biosynthesis	25	1 of 4
66794	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	vitamin E metabolism	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	degradation of hexoses	22.22	4 of 18
66794	degradation of pentoses	21.43	6 of 28

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Climate	#Hot	#Tropical
#Environmental	#Aquatic	#Lake (large)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15737	water	Lake Victoria	Uganda	UGA	Africa
44087	tropical lake	Lake Vicoria, Kampala	Uganda	UGA	Africa
67770	Large tropical Lake Victoria located in East Africa

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15737	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
67770	IMG-taxon 2710264786 annotated assembly for Polynucleobacter victoriensis MWH-VicM1	contig	GCA_900187875	1938815.3	2710264786	2049319	69.15

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15737	Polynucleobacter victoriensis partial 16S rRNA gene and ITS1, strain MWH-VicM1	AJ550651	2016		2049319

GC content

@ref	GC-content (mol%)	Method
44087	43.1	genome sequence analysis
15737	43.1	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Polynucleobacter victoriensis MWH-VicM1
NCBI: GCA_900187875

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	yes	82.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov.	Hahn MW, Schmidt J, Asiyo GS, Kyrpides NC, Woyke T, Whitman WB	Int J Syst Evol Microbiol	10.1099/ijsem.0.002421	2017

References

#15737	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21486
#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 )
#44087	Martin W. Hahn, Johanna Schmidt, Grace Ssanyu Asiyo, Nikos C. Kyrpides, Tanja Woyke and William B. Whitman: Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov.. IJSEM 67: 5087 - 5093 2017 ( DOI 10.1099/ijsem.0.002421 , PubMed 29068276 )
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Polynucleobacter victoriensis (DSM 21486, JCM 32005, MWH-VicM1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900187875

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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