Name: Pseudodesulfovibrio profundus 500-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 4129

Type strain:

Species: Pseudodesulfovibrio profundus

Strain Designation: 500-1

Culture col. no.: DSM 11384, MCCC 1A01905

Strain history: <- R. J. Parkes, University of Bristol, Department of Geology, United Kingdom; 500-1 <- S. J. Bale {1989}

NCBI tax ID(s): 57320 (species)

SI-ID 49091

DSM 11384

Special Collections

DSMZ

Section

When using BacDive for research please cite our paper

Pseudodesulfovibrio profundus 500-1 is an anaerobe, mesophilic bacterium that was isolated from marine sediment, 500 m below sea floor.

anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Deltaproteobacteria*
	Order	*Desulfovibrionales*
	Family	*Desulfovibrionaceae*
	Genus	*Pseudodesulfovibrio*
	Species	**Pseudodesulfovibrio profundus**
	Full Scientific Name (LPSN)	Pseudodesulfovibrio profundus (Bale et al. 1997) Cao et al. 2016

Synonym

Desulfovibrio profundus

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	negative Confidence in %98.7
[Ref.: #125438]	Gram stain	negative Confidence in %96.463

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4336]

Culture medium

DESULFOBACTER SP. MEDIUM (LACTATE) (DSMZ Medium 195c)

[Ref.: #4336]

Culture medium growth

[Ref.: #4336]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4336]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4336]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4336]

Oxygen tolerance

anaerobe

[Ref.: #125439]	Ability of spore formation	no Confidence in %98.1
[Ref.: #125438]	Ability of spore formation	no Confidence in %90.473

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	chorismate metabolism	100	9 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	nitrate assimilation	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	methionine metabolism	80.77	21 of 26
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[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.: #4336]	Sample type/isolated from	marine sediment, 500 m below sea floor
[Ref.: #4336]	Geographic location (country and/or sea, region)	Japan Sea, ocean drilling program site 798B
[Ref.: #4336]	Country	Japan
[Ref.: #4336]	Country ISO 3 Code	JPN
[Ref.: #4336]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence U90726 (>99% sequence identity) for Pseudodesulfovibrio profundus subclade from Microbeatlas

Aquatic Samples	239
Soil Samples	10
Animal Samples	29
Plant Samples
Total Samples	278

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

[Ref.: #4336]

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.: #4336]	Desulfovibrio profundus partial 16S rRNA gene, type strain DSM11384T	FR733706	1545	GenBank ENA	57320 tax ID
[Ref.: #20218]	Desulfovibrio profundus DSM 11384 16S ribosomal RNA gene, partial sequence	AF418172	1547	GenBank ENA	57320 tax ID	*
[Ref.: #20218]	Desulfovibrio profundus 16S ribosomal RNA gene, partial sequence	U90726	1366	GenBank ENA	57320 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudodesulfovibrio profundus 500-1	GCA_900217235	complete	GenBank ENA	57320 tax ID	*
[Ref.: #66792]	Pseudodesulfovibrio profundus 500-1	2775506867	complete	JGI IMG/M	57320 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudodesulfovibrio profundus 500-1 NCBI: GCA_900217235.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.463	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	72.846	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	82.282	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.473	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	90.91	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	81.448	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudodesulfovibrio profundus 500-1 IMG: 2775506867
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	73.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	54.9

Availability in culture collections External links

[Ref.: #4336]

Culture collection no.

DSM 11384, MCCC 1A01905

[Ref.: #73632]

SI-ID 49091

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome Sequence of Piezophilic Bacterium Desulfovibrio profundus Strain 500-1, Isolated from a Deep Sediment Layer in the Japan Sea.	Fouteau S, Guerin T, Magdelenat G, Roumagnac M, Bartoli M, Ollivier B, Dolla A, Barbe V, Pradel N	Genome Announc	10.1128/genomeA.01181-17	2017	*
Phylogeny	Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio.	Cao J, Gayet N, Zeng X, Shao Z, Jebbar M, Alain K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001286	2016	*
Phylogeny	Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea.	Bale SJ, Goodman K, Rochelle PA, Marchesi JR, Fry JC, Weightman AJ, Parkes RJ	Int J Syst Bacteriol	10.1099/00207713-47-2-515	1997	*

References

#4336

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11384

#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 .

#73632

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-ID49091.1 )

#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 .

* These data were automatically processed and therefore are not curated

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