Name: Dethiosulfovibrio peptidovorans DSM 11002
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17770

Type strain:

Species: Dethiosulfovibrio peptidovorans

Culture col. no.: DSM 11002, JCM 15826, SEBR 4207

Strain history: DSM 11002 <-- G. Ravot SEBR 4207.

NCBI tax ID(s): 469381 (strain), 47055 (species)

SI-ID 48997

DSM 11002, JCM 15826

Special Collections

DSMZ
JCM

Section

Dethiosulfovibrio peptidovorans DSM 11002 is an anaerobe, Gram-negative bacterium that was isolated from offshore oil-producing well.

Gram-negative
anaerobe
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	*Synergistota*
	Class	*Synergistia*
	Order	*Synergistales*
	Family	*Dethiosulfovibrionaceae*
	Genus	*Dethiosulfovibrio*
	Species	**Dethiosulfovibrio peptidovorans**
	Full Scientific Name (LPSN)	Dethiosulfovibrio peptidovorans Magot et al. 1997

Information on morphological and physiological properties Morphology

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4156]

Culture medium

DETHIOSULFOVIBRIO PEPTIDOVORANS MEDIUM (DSMZ Medium 786)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4156]			growth	42 °C
[Ref.: #67770]			growth	42 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4156]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %95.672

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	urea cycle	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	oxidative phosphorylation	56.04	51 of 91
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	55.56	5 of 9
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	tryptophan metabolism	50	19 of 38
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	pentose phosphate pathway	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	starch degradation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #4156]	Sample type/isolated from	offshore oil-producing well
[Ref.: #4156]	Geographic location (country and/or sea, region)	Emeraude oil field (well BB325)
[Ref.: #4156]	Country	Republic of the Congo
[Ref.: #4156]	Country ISO 3 Code	COG
[Ref.: #4156]	Continent	Africa

[Ref.: #67770]	Sample type/isolated from	Corroding offshore oil well in Congo
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Engineered product
#Engineered	#Industrial	#Oil reservoir

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence U52817 (>99% sequence identity) for Dethiosulfovibrio from Microbeatlas

Aquatic Samples	25
Soil Samples
Animal Samples	3
Plant Samples
Total Samples	28

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

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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.: #4156]	Desulfothiovibrio peptidovorans 16S ribosomal RNA, partial sequence	U52817	1505	GenBank ENA	469381 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Dethiosulfovibrio peptidovorans DSM 11002	GCA_000172975	contig	GenBank ENA	469381 tax ID
[Ref.: #66792]	Dethiosulfovibrio peptidovorans DSM 11002	469381.10	wgs	PATRIC	469381 tax ID	*
[Ref.: #66792]	Dethiosulfovibrio peptidovorans SEBR 4207, DSM 11002	2501533205	draft	JGI IMG/M	469381 tax ID	*

[Ref.: #4156]	GC-content	56.0 mol%
[Ref.: #67770]	GC-content	56 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Dethiosulfovibrio peptidovorans DSM 11002 PATRIC: 469381.10
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	50	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Dethiosulfovibrio peptidovorans DSM 11002 PATRIC: 469381.10
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	83.532	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	95.672	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	71.933	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	97.182	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	83.319	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	65.323	no

Availability in culture collections External links

[Ref.: #4156]

Culture collection no.

DSM 11002, JCM 15826, SEBR 4207

[Ref.: #86761]

SI-ID 48997

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207).	Labutti K, Mayilraj S, Clum A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A	Stand Genomic Sci	10.4056/sigs.1092865	2010	*
Phylogeny	Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a new anaerobic, slightly halophilic, thiosulfate-reducing bacterium from corroding offshore oil wells.	Magot M, Ravot G, Campaignolle X, Ollivier B, Patel BK, Fardeau ML, Thomas P, Crolet JL, Garcia JL	Int J Syst Bacteriol	10.1099/00207713-47-3-818	1997	*

References

#4156

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11002

#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 )

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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;

#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 )

#86761

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-ID48997.1 )

* These data were automatically processed and therefore are not curated

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