Archive BacDiveID:10.13145/bacdive10537.20230509.8.1

Strain identifier

BacDive ID: 10537

Type strain:

Species: Thermodesulfovibrio yellowstonii

Strain Designation: YP87

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

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

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 4308

BacDive-ID: 10537

DSM-Number: 11347

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative

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

NCBI tax id

NCBI tax id	Matching level
289376	strain
28262	species

strain history

@ref: 4308
history: <- ATCC <- C. C. Gilmour, YP87

doi: 10.13145/bacdive10537.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/nitrospirota
domain: Bacteria
phylum: Nitrospirota
class: Thermodesulfovibrionia
order: Thermodesulfovibrionales
family: Thermodesulfovibrionaceae
genus: Thermodesulfovibrio
species: Thermodesulfovibrio yellowstonii
full scientific name: Thermodesulfovibrio yellowstonii Henry et al. 1994

@ref: 4308

domain: Bacteria

phylum: Nitrospirae

class: Nitrospira

order: Nitrospirales, not validated

family: Nitrospiraceae

genus: Thermodesulfovibrio

species: Thermodesulfovibrio yellowstonii

full scientific name: Thermodesulfovibrio yellowstonii Henry et al. 1994

strain designation: YP87

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.994

colony morphology

@ref: 4308
incubation period: 2-3 days

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
4308	DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)	yes	https://mediadive.dsmz.de/medium/641	Name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641) Composition: Na-DL-lactate 2.49252 g/l Na2SO4 1.99402 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l Na2CO3 0.997009 g/l MgSO4 x 7 H2O 0.997009 g/l Na2S2O3 x 5 H2O 0.997009 g/l KH2PO4 0.498504 g/l Na2S x 9 H2O 0.0997009 g/l CaCl2 x 2 H2O 0.0997009 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Pyridoxine hydrochloride 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water
4308	THERMODESULFOVIBRIO YELLOWSTONII MEDIUM (DSMZ Medium 749)	yes	https://mediadive.dsmz.de/medium/749	Name: THERMODESULFOVIBRIO YELLOWSTONII MEDIUM (DSMZ Medium 749) Composition: Na2SO4 3.95648 g/l Na-DL-lactate 2.4728 g/l NaHCO3 1.28586 g/l Yeast extract 0.49456 g/l KCl 0.49456 g/l MgCl2 x 6 H2O 0.395648 g/l NH4Cl 0.24728 g/l L-Ascorbic acid 0.197824 g/l Na2HPO4 0.197824 g/l Na-thioglycolate 0.197824 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l CoSO4 x 7 H2O 0.00178042 g/l ZnSO4 x 7 H2O 0.00178042 g/l FeSO4 x 7 H2O 0.00098912 g/l CaCl2 x 2 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l H3BO3 9.8912e-05 g/l CuSO4 x 5 H2O 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l Riboflavin 4.9456e-05 g/l Folic acid 1.97824e-05 g/l Biotin 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
4308	positive	growth	60	thermophilic
69480				thermophilic	100

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
4308	anaerobe
69480	anaerobe	99.723

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.777

Isolation, sampling and environmental information

isolation

@ref: 4308
sample type: thermal vent water
geographic location: Wyoming, Yellowstone Lake
country: USA
origin.country: USA
continent: North America

isolation source categories

Cat1: #Environmental
Cat2: #Aquatic
Cat3: #Hydrothermal vent

taxonmaps

@ref: 69479
File name: preview.99_3323.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_392;96_1731;97_2072;98_2547;99_3323&stattab=map
Last taxonomy: Thermodesulfovibrio
16S sequence: AB231858
Sequence Identity:
Total samples: 953
soil counts: 143
aquatic counts: 534
animal counts: 256
plant counts: 20

Safety information

risk assessment

@ref: 4308
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Thermodesulfovibrio yellowstonii gene for 16S rRNA, partial sequence	AB231858	1461	ena	28262
4308	Thermodesulfovibrio yellowstonii ribosomal RNA sequence	L14619	1358	ena	28262

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thermodesulfovibrio yellowstonii DSM 11347	GCA_000020985	complete	ncbi	289376
66792	Thermodesulfovibrio yellowstonii DSM 11347	289376.4	complete	patric	289376
66792	Thermodesulfovibrio yellowstonii DSM 11347	643348581	complete	img	289376

GC content

@ref	GC-content	method
4308	34	sequence analysis
4308	29.5	thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	yes	82.682	no
flagellated	no	90.466	no
gram-positive	no	99.656	no
anaerobic	yes	99.232	yes
halophile	no	85.517	no
spore-forming	no	93.826	no
thermophile	yes	100	no
glucose-util	no	57.305	no
aerobic	no	98.726	no
glucose-ferment	no	86.969	no

External links

@ref: 4308

culture collection no.: DSM 11347, ATCC 51303

straininfo link

@ref: 79813
straininfo: 49082

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh
Metabolism	16133342	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	Carbon Monoxide/metabolism, Coculture Techniques, Gram-Positive Bacteria/metabolism, Sulfates/metabolism, Sulfur-Reducing Bacteria/metabolism, Time Factors
Genetics	25635016	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

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
4308	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11347)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-11347
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
79813	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID49082.1	StrainInfo: A central database for resolving microbial strain identifiers