Name: Thermodesulfovibrio yellowstonii YP87
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 10537

Type strain:

Species: Thermodesulfovibrio yellowstonii

Strain Designation: YP87

Culture col. no.: DSM 11347, ATCC 51303

Strain history: <- ATCC <- C. C. Gilmour, YP87

NCBI tax ID(s): 289376 (strain), 28262 (species)

SI-ID 49082

DSM 11347, ATCC 51303

Section

Thermodesulfovibrio yellowstonii YP87 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from thermal vent water.

Gram-negative
anaerobe
thermophilic
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	*Nitrospirota*
	Class	*Thermodesulfovibrionia*
	Order	*Thermodesulfovibrionales*
	Family	*Thermodesulfovibrionaceae*
	Genus	*Thermodesulfovibrio*
	Species	**Thermodesulfovibrio yellowstonii**
	Full Scientific Name (LPSN)	Thermodesulfovibrio yellowstonii Henry et al. 1994

Information on morphological and physiological properties Morphology

[Ref.: #69480]

Gram stain

negative Confidence in %99.994

[Ref.: #4308]

Incubation period

2-3 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4308]

Culture medium

DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)

[Ref.: #4308]

Culture medium growth

[Ref.: #4308]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4308]

Culture medium composition

expand / minimize

[Ref.: #4308]

Culture medium

THERMODESULFOVIBRIO YELLOWSTONII MEDIUM (DSMZ Medium 749)

[Ref.: #4308]

Culture medium growth

[Ref.: #4308]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4308]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4308]			growth	60 °C

[Ref.: #4308]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %100

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4308]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.723

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.777

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	palmitate biosynthesis	86.36	19 of 22
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	41.76	38 of 91
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	lipid metabolism	35.48	11 of 31
[Ref.: #66794]	cysteine metabolism	33.33	6 of 18
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		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.: #4308]	Sample type/isolated from	thermal vent water
[Ref.: #4308]	Geographic location (country and/or sea, region)	Wyoming, Yellowstone Lake
[Ref.: #4308]	Country	USA
[Ref.: #4308]	Country ISO 3 Code	USA
[Ref.: #4308]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Hydrothermal vent

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB231858 (>99% sequence identity) for Thermodesulfovibrio from Microbeatlas

Aquatic Samples	534
Soil Samples	143
Animal Samples	256
Plant Samples	20
Total Samples	953

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

[Ref.: #4308]

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.: #4308]	Thermodesulfovibrio yellowstonii ribosomal RNA sequence	L14619	1358	ENA	28262 tax ID
[Ref.: #20218]	Thermodesulfovibrio yellowstonii gene for 16S rRNA, partial sequence	AB231858	1461	ENA	28262 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Thermodesulfovibrio yellowstonii DSM 11347	GCA_000020985	complete	GenBank	289376 tax ID	*
[Ref.: #66792]	Thermodesulfovibrio yellowstonii DSM 11347	289376.4	complete	PATRIC	289376 tax ID	*
[Ref.: #66792]	Thermodesulfovibrio yellowstonii DSM 11347	643348581	complete	JGI IMG/M	289376 tax ID	*

[Ref.: #4308]	GC-content	34 mol%	sequence analysis
[Ref.: #4308]	GC-content	29.5 mol%	thermal denaturation, midpoint method (Tm)

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: Thermodesulfovibrio yellowstonii DSM 11347 DSM 11347 NCBI: GCA_000020985.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thermodesulfovibrio yellowstonii DSM 11347 DSM 11347 NCBI: GCA_000020985.1
[Ref.: #69480]	motile	yes	82.682	no
[Ref.: #69480]	flagellated	no	90.466	no
[Ref.: #69480]	gram-positive	no	99.656	no
[Ref.: #69480]	anaerobic	yes	99.232	yes
[Ref.: #69480]	halophile	no	85.517	no
[Ref.: #69480]	spore-forming	no	93.826	no
[Ref.: #69480]	thermophile	yes	100	no
[Ref.: #69480]	glucose-util	no	57.305	no
[Ref.: #69480]	aerobic	no	98.726	no
[Ref.: #69480]	glucose-ferment	no	86.969	no

Availability in culture collections External links

[Ref.: #4308]

Culture collection no.

DSM 11347, ATCC 51303

[Ref.: #79813]

SI-ID 49082

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae).	Bhatnagar S, Badger JH, Madupu R, Khouri HM, O'Connor EM, Robb FT, Ward NL, Eisen JA	Genome Announc	10.1128/genomeA.01489-14	2015	*
Metabolism	Carbon monoxide conversion by thermophilic sulfate-reducing bacteria in pure culture and in co-culture with Carboxydothermus hydrogenoformans.	Parshina SN, Kijlstra S, Henstra AM, Sipma J, Plugge CM, Stams AJ	Appl Microbiol Biotechnol	10.1007/s00253-004-1878-x	2005	*

References

#4308

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11347

#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 )

#79813

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-ID49082.1 )

* These data were automatically processed and therefore are not curated

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Thermodesulfovibrio yellowstonii DSM 11347 DSM 11347

Thermodesulfovibrio yellowstonii DSM 11347 DSM 11347

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