Thermodesulfovibrio thiophilus (DSM 17215, JCM 13216, TDV)

Name: Thermodesulfovibrio thiophilus (DSM 17215, JCM 13216, TDV)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10541

Type strain

Strain Designation TDV

Culture col. no. DSM 17215 JCM 13216 TDV

NCBI tax ID(s) 1123376 340095

Special Collections DSMZ JCM Literature strains

History <- Y. Sekiguchi; TDV Y. Sekiguchi TDV.

Links

Thermodesulfovibrio thiophilus TDV is an anaerobe, thermophilic, Gram-negative prokaryote that was isolated from thermophilic sewage sludge decomposing organic solid wastes.

Gram-negative rod-shaped anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397855

JCM 13216,DSM 17215

@ref 20215

Last LPSN update 2026-02-09 11:20:17

Domain Bacteria

Phylum Nitrospirota

Class Thermodesulfovibrionia

Order Thermodesulfovibrionales

Family Thermodesulfovibrionaceae

Genus Thermodesulfovibrio

Species Thermodesulfovibrio thiophilus

Full scientific name Thermodesulfovibrio thiophilus Sekiguchi et al. 2008

BacDive ID	Other strains from **Thermodesulfovibrio thiophilus** (1)	Type strain
130473	T. thiophilus TSL-P1, DSM 17286, JCM 13215

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31197	negative	02-03 µm	0.3-0.4 µm	rod-shaped
125438	negative				97
125439	negative				97.8

Pigmentation

31197

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6819	DESULFOVIBRIO (MV) MEDIUM (DSMZ Medium 641)		Medium recipe at MediaDive	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6819	positive	growth	55	thermophilic
31197	positive	growth	45-60	thermophilic
31197	positive	optimum	55	thermophilic
67770	positive	growth	55	thermophilic

Culture pH

@ref	Ability	Type	PH	PH range
31197	positive	optimum	7-7.5
31197	positive	growth	6-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6819	anaerobe
31197	anaerobe

Spore formation

31197

Spore formationno

Observation

31197

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31197	30089 ChEBI	acetate	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Sewage sludge
#Engineered	#Waste	#Solid waste
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6819	thermophilic sewage sludge decomposing organic solid wastes	Japan	JPN	Asia
67770	Thermophilic sewage sludge decomposing organic solid wastes

Taxonmaps

69479

Global distribution of 16S sequence AB231857 (>99% sequence identity) for Thermodesulfovibrio thiophilus subclade from Microbeatlas

Aquatic Samples	481
Soil Samples	285
Animal Samples	202
Plant Samples	27
Total Samples	995

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6819	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	ASM42386v1 assembly for Thermodesulfovibrio thiophilus DSM 17215	scaffold	GCA_000423865	1123376.3	2523533630	1123376	74.18

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6819	Thermodesulfovibrio thiophilus gene for 16S rRNA, partial sequence	AB231857	1490		340095

GC content

@ref	GC-content (mol%)	Method
6819	34.0	high performance liquid chromatography (HPLC)
31197	34
67770	34	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: Thermodesulfovibrio thiophilus DSM 17215
NCBI: GCA_000423865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	85.50	no
125439	gram_stain	BacteriaNetⓘ	negative	97.80	no
125439	motility	BacteriaNetⓘ	no	60.30	no
125439	spore_formation	BacteriaNetⓘ	no	83.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thermodesulfovibrio thiophilus DSM 17215
PATRIC: 1123376.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.00	yes
125438	anaerobic	anaerobicⓘ	yes	87.46	yes
125438	spore-forming	spore-formingⓘ	no	89.32	yes
125438	aerobic	aerobicⓘ	no	89.64	yes
125438	thermophilic	thermophileⓘ	yes	68.54	no
125438	flagellated	motile2+ⓘ	yes	66.29	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle.	Detman A, Mielecki D, Plesniak L, Bucha M, Janiga M, Matyasik I, Chojnacka A, Jedrysek MO, Blaszczyk MK, Sikora A.	Biotechnol Biofuels	10.1186/s13068-018-1106-z	2018
Metabolism	Life based on phosphite: a genome-guided analysis of Desulfotignum phosphitoxidans.	Poehlein A, Daniel R, Schink B, Simeonova DD.	BMC Genomics	10.1186/1471-2164-14-753	2013
Enzymology	Halalkalicoccus subterraneus sp. nov., an extremely halophilic archaeon isolated from a subterranean halite deposit.	Chen S, Xu Y, Sun S, Chen F, Liu J.	Antonie Van Leeuwenhoek	10.1007/s10482-019-01241-3	2019
Phylogeny	Thermodesulfovibrio aggregans sp. nov. and Thermodesulfovibrio thiophilus sp. nov., anaerobic, thermophilic, sulfate-reducing bacteria isolated from thermophilic methanogenic sludge, and emended description of the genus Thermodesulfovibrio.	Sekiguchi Y, Muramatsu M, Imachi H, Narihiro T, Ohashi A, Harada H, Hanada S, Kamagata Y	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/000893-0	2008

References

#6819	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17215
#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 )
#27524	IJSEM 2541 2008 ( DOI 10.1099/ijs.0.2008/000893-0 , PubMed 18984690 )
#31197	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 #27524
#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 .
#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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Thermodesulfovibrio thiophilus (DSM 17215, JCM 13216, TDV)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000423865

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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