Phaeovulum veldkampii (DSM 11550, ATCC 35703, CIP 103912)

Name: Phaeovulum veldkampii (DSM 11550, ATCC 35703, CIP 103912)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13821

Type strain

Strain Designation 51, BN 714

Culture col. no. DSM 11550 ATCC 35703 CIP 103912 IFO 16458 NBRC 16458 2 more

NCBI tax ID(s) 33049

Special Collections DSMZ CIP

History <- ATCC <- J. F. Imhoff; 51 <- T. A. Hansen; CIP 103912

Links

Phaeovulum veldkampii 51 is an anaerobe bacterium that was isolated from freshwater pond.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 41237

ATCC 35703,CIP 103912,DSM 11550,IFO 16458,BCRC 16405,CCRC 16405,NBRC 16458

@ref 20215

Last LPSN update 2026-02-09 11:21:15

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Phaeovulum

Species Phaeovulum veldkampii

Full scientific name Phaeovulum veldkampii (Hansen and Imhoff 1985) Suresh et al. 2020

Synonyms (2)

Rhodobacter veldkampii
Bieblia veldkampii

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	95.6
125438	negative	99

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4412	RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)		Medium recipe at MediaDive	Name: RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27) Composition: Disodium succinate 1.0 g/l KH2PO4 0.5 g/l Ammonium acetate 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgSO4 x 7 H2O 0.4 g/l Yeast extract 0.3 g/l L-Cysteine HCl 0.3 g/l CaCl2 x 2 H2O 0.05 g/l Fe(III) citrate 0.005 g/l Resazurin 0.005 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Vitamin B12 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4412	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4412	anaerobe
125439	obligate aerobe	95.9

Spore formation

@ref	Spore formation	Confidence
125439		93.6
125438		93.707

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	octane oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	gluconeogenesis	100	8 of 8
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	photosynthesis	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	Entner Doudoroff pathway	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B12 metabolism	85.29	29 of 34
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	proline metabolism	81.82	9 of 11
66794	glycogen metabolism	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	citric acid cycle	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	allantoin degradation	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	methionine metabolism	76.92	20 of 26
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	lipid metabolism	74.19	23 of 31
66794	vitamin B6 metabolism	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	degradation of sugar alcohols	68.75	11 of 16
66794	flavin biosynthesis	66.67	10 of 15
66794	cyanate degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	lysine metabolism	66.67	28 of 42
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	pentose phosphate pathway	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	non-pathway related	63.16	24 of 38
66794	cysteine metabolism	61.11	11 of 18
66794	chlorophyll metabolism	61.11	11 of 18
66794	glycine betaine biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	arginine metabolism	58.33	14 of 24
66794	d-mannose degradation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	urea cycle	53.85	7 of 13
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of pentoses	46.43	13 of 28
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	factor 420 biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	polyamine pathway	39.13	9 of 23
66794	ketogluconate metabolism	37.5	3 of 8
66794	arachidonic acid metabolism	33.33	6 of 18
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	myo-inositol biosynthesis	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of sugar acids	28	7 of 25
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	metabolism of disaccharids	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Pond (small)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
4412	freshwater pond	Netherlands	NLD	Europe

Taxonmaps

69479

Global distribution of 16S sequence D16421 (>99% sequence identity) for Bieblia veldkampii subclade from Microbeatlas

Aquatic Samples	79
Soil Samples	8
Animal Samples	12
Plant Samples	1
Total Samples	100

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4412	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	ASM436319v1 assembly for Phaeovulum veldkampii DSM 11550	scaffold	GCA_004363195	1185920.6	2795385478	1185920	63.98
66792	ASM1665343v1 assembly for Phaeovulum veldkampii DSM 11550	scaffold	GCA_016653435	1185920.8	8063230913	1185920	56.76
66792	ASM303499v1 assembly for Phaeovulum veldkampii DSM 11550	contig	GCA_003034995	1185920.4	8118700028	1185920	47.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Rhodobacter veldkampii 16S rRNA	D13477	1351		1185920
20218	Rhodobacter veldkampii gene for 16S rRNA	D16421	1389		1185920

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phaeovulum veldkampii DSM 11550
NCBI: GCA_004363195

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.90	no
125439	gram_stain	BacteriaNetⓘ	negative	95.60	no
125439	motility	BacteriaNetⓘ	yes	67.40	no
125439	spore_formation	BacteriaNetⓘ	no	93.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bieblia veldkampii DSM 11550 DSM 11550
NCBI: GCA_004363195.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	60.97	yes
125438	aerobic	aerobicⓘ	yes	63.11	no
125438	spore-forming	spore-formingⓘ	no	93.71	no
125438	thermophilic	thermophileⓘ	no	96.95	yes
125438	flagellated	motile2+ⓘ	no	58.29	no

Literature

References

#4412	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11550
#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 )
#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 .
#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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