Desulfovirgula thermocuniculi (DSM 16036, JCM 13928, RL80JIV)

Name: Desulfovirgula thermocuniculi (DSM 16036, JCM 13928, RL80JIV)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16849

Type strain

Strain Designation RL80JIV

Culture col. no. DSM 16036 JCM 13928 RL80JIV

NCBI tax ID(s) 1121468 348842

Special Collections DSMZ JCM Literature strains

History <- A. H. Kaksonen, Tampere Univ. Technol., Finland; RL80JIV <- A. H. Kaksonen {2002} DSM 16036 <-- A. Kaksonen RL80JIV.

Links

Desulfovirgula thermocuniculi RL80JIV is an anaerobe, spore-forming, Gram-positive bacterium that was isolated from Toyoha mine.

spore-forming Gram-positive motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 297156

DSM 16036,JCM 13928

@ref 20215

Last LPSN update 2026-02-09 11:22:04

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Thermoanaerobacterales

Family Thermoanaerobacteraceae

Genus Desulfovirgula

Species Desulfovirgula thermocuniculi

Full scientific name Desulfovirgula thermocuniculi Kaksonen et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
31922	positive	rod-shaped

Multimedia

@ref:	66793
multimedia content:	EM_DSM_16036_1.jpg
multimedia.multimedia content:	EM_DSM_16036_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_16036_2.jpg
multimedia.multimedia content:	EM_DSM_16036_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_16036_3.jpg
multimedia.multimedia content:	EM_DSM_16036_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_16036_4.jpg
multimedia.multimedia content:	EM_DSM_16036_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6170	DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)		Medium recipe at MediaDive	Name: DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641; with strain-specific modifications) Composition: Na-pyruvate 2.49252 g/l Na2SO4 1.99402 g/l Na2S2O3 x 5 H2O 0.997009 g/l MgSO4 x 7 H2O 0.997009 g/l NH4Cl 0.997009 g/l Yeast extract 0.997009 g/l Na2CO3 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 Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Nicotinic 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 Folic acid 1.99402e-05 g/l Biotin 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

Culture temp

@ref	Growth	Type	Temperature (°C)
6170	positive	growth	70
31922	positive	growth	61-80
31922	positive	optimum	69-72
67770	positive	growth	70

Culture pH

@ref	Ability	Type	PH
31922	positive	optimum	6.8-7.3
31922	positive	growth	6.4-7.9

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6170	anaerobe
125438	anaerobe	93.715
125439	anaerobe	98.9

Spore formation

31922

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31922	NaCl	positive	growth	0-0.5 %

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31922	24996 ChEBI	lactate	+	carbon source
31922	15361 ChEBI	pyruvate	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6170	Toyoha mine	Hokkaido	Japan	JPN	Asia
67770	Geothermally active underground mine	Hokkaido	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6170	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM42934v1 assembly for Desulfovirgula thermocuniculi DSM 16036	scaffold	GCA_000429345	1121468.4	2524023160	1121468	50.02

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6170	Desulfovirgula thermocuniculi strain RL80JIV 16S ribosomal RNA gene, partial sequence	DQ208689	1436		348842

GC content

@ref	GC-content (mol%)	Method
31922	60.1
67770	60.1	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfovirgula thermocuniculi DSM 16036
NCBI: GCA_000429345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	61.80	no
125439	motility	BacteriaNetⓘ	yes	55.20	no
125439	gram_stain	BacteriaNetⓘ	negative	70.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfovirgula thermocuniculi DSM 16036
PATRIC: 1121468.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	64.72	yes
125438	anaerobic	anaerobicⓘ	yes	93.72	yes
125438	spore-forming	spore-formingⓘ	yes	78.84	yes
125438	aerobic	aerobicⓘ	no	96.24	no
125438	thermophilic	thermophileⓘ	yes	67.80	no
125438	flagellated	motile2+ⓘ	yes	65.49	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment.	Omae K, Yoneda Y, Fukuyama Y, Yoshida T, Sako Y.	Appl Environ Microbiol	10.1128/aem.00832-17	2017
Phylogeny	Desulfovirgula thermocuniculi gen. nov., sp. nov., a thermophilic sulfate-reducer isolated from a geothermal underground mine in Japan.	Kaksonen AH, Spring S, Schumann P, Kroppenstedt RM, Puhakka JA	Int J Syst Evol Microbiol	10.1099/ijs.0.64655-0	2007

References

#6170	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16036
#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 )
#28179	IJSEM 98 2007 ( DOI 10.1099/ijs.0.64655-0 , PubMed 17220449 )
#31922	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28179
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Desulfovirgula thermocuniculi (DSM 16036, JCM 13928, RL80JIV)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000429345

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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