Name: Rhodovulum sulfidophilum W4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13742

Type strain:

Species: Rhodovulum sulfidophilum

Strain Designation: W4

Culture col. no.: DSM 1374, ATCC 35886, LMG 5202

Strain history: <- T.A. Hansen, W4

NCBI tax ID(s): 1188256 (strain), 35806 (species)

SI-ID 4840

LMG 5201, DSM 1374, ATCC 35886, BCRC 16417, CCRC 16417

Other strains from Rhodovulum sulfidophilum

R. sulfidophilum W12, DSM 2351

Section

Rhodovulum sulfidophilum W4 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from mud from intertidal flats.

Gram-negative
anaerobe
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Rhodovulum*
	Species	**Rhodovulum sulfidophilum**
	Full Scientific Name (LPSN)	Rhodovulum sulfidophilum (Hansen and Veldkamp 1973) Hiraishi and Ueda 1994

	Synonym	Rhodopseudomonas sulfidophila
	Synonym	Rhodobacter sulfidophilus

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.999

Information on culture and growth conditions Culture and growth conditions

[Ref.: #754]

Culture medium

RHODOSPIRILLACEAE MEDIUM (modified) (DSMZ Medium 27)

[Ref.: #754]

Culture medium growth

[Ref.: #754]

Culture medium link

Medium recipe at MediaDive

[Ref.: #754]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #754]			growth	25 °C

[Ref.: #754]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #754]

Oxygen tolerance

anaerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.81

[Ref.: #754]	Name of produced compound	ubiquinone-10
[Ref.: #754]	Name of produced compound	hydrogen

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	glycogen biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	propionate fermentation	100	10 of 10
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	alanine metabolism	89.66	26 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	84.04	79 of 94
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	creatinine degradation	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	oxidative phosphorylation	74.73	68 of 91
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	chlorophyll metabolism	72.22	13 of 18
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	mevalonate metabolism	57.14	4 of 7
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		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.: #754]	Sample type/isolated from	mud from intertidal flats
[Ref.: #754]	Country	Netherlands
[Ref.: #754]	Country ISO 3 Code	NLD
[Ref.: #754]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Terrestrial	#Tidal flat

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence D16423 (>99% sequence identity) for Rhodovulum sulfidophilum from Microbeatlas

Aquatic Samples	4467
Soil Samples	533
Animal Samples	971
Plant Samples	101
Total Samples	6072

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

[Ref.: #754]

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.: #20218]	Rhodovulum sulfidophilum strain ATCC 35886 16S ribosomal RNA gene, partial sequence	DQ342323	1389	ENA	1188256 tax ID	*
[Ref.: #20218]	Rhodovulum sulfidophilum gene for 16S ribosomal RNA, partial sequence and upstream region, strain: DSM 1374	AB513346	726	ENA	1188256 tax ID	*
[Ref.: #20218]	Rhodovulum sulfidophilum gene for 16S rRNA, strain: DSM1374	D16423	1389	ENA	1188256 tax ID	*
[Ref.: #20218]	Rhodovulum sulfidophilum 16S rRNA	D13475	1378	ENA	35806 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodovulum sulfidophilum DSM 1374	2667527571	complete	JGI IMG/M	1188256 tax ID	*
[Ref.: #66792]	Rhodovulum sulfidophilum DSM 1374	GCA_000520135	chromosome	GenBank	1188256 tax ID	*
[Ref.: #66792]	Rhodovulum sulfidophilum DSM 1374	1188256.8	complete	PATRIC	1188256 tax ID	*
[Ref.: #66792]	Rhodovulum sulfidophilum DSM 1374	1188256.18	plasmid	PATRIC	1188256 tax ID	*
[Ref.: #66792]	Rhodovulum sulfidophilum DSM 1374	1188256.19	plasmid	PATRIC	1188256 tax ID	*
[Ref.: #66792]	Rhodovulum sulfidophilum DSM 1374	1188256.3	complete	PATRIC	1188256 tax ID	*

[Ref.: #754]

GC-content

70.0 mol%

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: Rhodovulum sulfidophilum DSM 1374 DSM 1374 NCBI: GCA_001633165.1
[Ref.: #69481]	spore-forming	no	69	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodovulum sulfidophilum DSM 1374 DSM 1374 NCBI: GCA_001633165.1
[Ref.: #69480]	flagellated	no	73.144	no
[Ref.: #69480]	gram-positive	no	99.108	no
[Ref.: #69480]	anaerobic	yes	74.655	no
[Ref.: #69480]	halophile	yes	54.582	no
[Ref.: #69480]	spore-forming	no	94.709	no
[Ref.: #69480]	glucose-util	yes	86.105	no
[Ref.: #69480]	motile	yes	75.142	no
[Ref.: #69480]	aerobic	no	90.154	yes
[Ref.: #69480]	thermophile	no	95.717	yes
[Ref.: #69480]	glucose-ferment	no	85.545	no

Availability in culture collections External links

[Ref.: #754]

Culture collection no.

DSM 1374, ATCC 35886, LMG 5202

[Ref.: #82924]

SI-ID 4840

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodovulum visakhapatnamense sp. nov.	Srinivas TNR, Anil Kumar P, Sasikala C, Ramana CV, Imhoff JF	Int J Syst Evol Microbiol	10.1099/ijs.0.65076-0	2007	*
	Distribution of Phototrophic Purple Nonsulfur Bacteria in Massive Blooms in Coastal and Wastewater Ditch Environments.	Hiraishi A, Nagao N, Yonekawa C, Umekage S, Kikuchi Y, Eki T, Hirose Y	Microorganisms	10.3390/microorganisms8020150	2020	*

References

#754	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1374

#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 .

#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 )

#82924

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-ID4840.1 )

* These data were automatically processed and therefore are not curated

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Rhodovulum sulfidophilum DSM 1374 DSM 1374

Rhodovulum sulfidophilum DSM 1374 DSM 1374

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