Thermodesulfovibrio aggregans (DSM 17283, JCM 13213, TGE-P1)

Name: Thermodesulfovibrio aggregans (DSM 17283, JCM 13213, TGE-P1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10540

Type strain

Strain Designation TGE-P1

Culture col. no. DSM 17283 JCM 13213 TGE-P1

NCBI tax ID(s) 1295128 86166

Special Collections DSMZ JCM Literature strains

History DSMZ <- Y. Sekiguchi; TGE-P1 JCM <-- Y. Sekiguchi TGE-P1.

Links

Thermodesulfovibrio aggregans TGE-P1 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from sludge granules of thermophilic UASB reactor treating organic wastewater.

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

Name and taxonomic classification

SI-ID 399740

JCM 13213,DSM 17283

@ref 20215

Last LPSN update 2026-05-29 08:27:21

Domain Bacteria

Phylum Nitrospirota

Class Thermodesulfovibrionia

Order Thermodesulfovibrionales

Family Thermodesulfovibrionaceae

Genus Thermodesulfovibrio

Species Thermodesulfovibrio aggregans

Full scientific name Thermodesulfovibrio aggregans Sekiguchi et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31197	negative	03-07 µm	0.3-0.4 µm	rod-shaped
125438	negative					97.833

Pigmentation

31197

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6871	DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63)		Medium recipe at MediaDive	Name: DESULFOVIBRIO (POSTGATE) MEDIUM (DSMZ Medium 63) Composition: MgSO4 x 7 H2O 2.0 g/l Na-DL-lactate 2.0 g/l NH4Cl 1.0 g/l Yeast extract 1.0 g/l Na2SO4 1.0 g/l FeSO4 x 7 H2O 0.5 g/l K2HPO4 0.5 g/l CaCl2 x 2 H2O 0.1 g/l Na-thioglycolate 0.1 g/l Ascorbic acid 0.1 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6871	positive	growth	60
31197	positive	growth	45-70
31197	positive	optimum	60
67770	positive	growth	55

Culture pH

@ref	Ability	Type	PH	PH range
31197	positive	optimum	6.5-7
31197	positive	growth	6-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6871	anaerobe
31197	anaerobe

Spore formation

@ref	Spore formation	Confidence
31197
125439		92.802

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	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Wastewater
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6871	sludge granules of thermophilic UASB reactor treating organic wastewater	Japan	JPN	Asia
67770	Thermophilic methanogenic sludge granules treating organic wastewater

Taxonmaps

69479

Global distribution of 16S sequence AB021302 (>99% sequence identity) for Thermodesulfovibrio aggregans subclade from Microbeatlas

Aquatic Samples	32
Soil Samples	3
Animal Samples	10
Plant Samples	0
Total Samples	45

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6871	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	ASM151453v1 assembly for Thermodesulfovibrio aggregans TGE-P1	scaffold	GCA_001514535	86166.4		86166	69.6
66792	ASM131208v1 assembly for Thermodesulfovibrio aggregans JCM 13213	contig	GCA_001312085	1295128.3	2728369708	1295128	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6871	Thermodesulfovibrio aggregans gene for 16S rRNA	AB021302	1485		86166

GC content

@ref	GC-content (mol%)	Method
6871	35.2	high performance liquid chromatography (HPLC)
31197	34

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM151453v1 assembly for Thermodesulfovibrio aggregans TGE-P1
NCBI: GCA_001514535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	61.29	no
125439	gram_stain	BacteriaNetⓘ	negative	73.70	no
125439	motility	BacteriaNetⓘ	no	72.27	no
125439	spore_formation	BacteriaNetⓘ	no	92.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thermodesulfovibrio aggregans JCM 13213
PATRIC: 1295128.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.83	no
125438	anaerobic	anaerobicⓘ	yes	85.75	yes
125438	spore-forming	spore-formingⓘ	no	89.20	no
125438	aerobic	aerobicⓘ	no	92.04	yes
125438	thermophilic	thermophileⓘ	yes	74.01	yes
125438	flagellated	motile2+ⓘ	yes	59.45	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface.	Frank YA, Kadnikov VV, Lukina AP, Banks D, Beletsky AV, Mardanov AV, Sen'kina EI, Avakyan MR, Karnachuk OV, Ravin NV.	Front Microbiol	10.3389/fmicb.2016.02000	2016
Genetics	Draft Genome Sequence of Thermodesulfovibrio aggregans TGE-P1T, an Obligately Anaerobic, Thermophilic, Sulfate-Reducing Bacterium in the Phylum Nitrospirae.	Matsuura N, Ohashi A, Tourlousse DM, Sekiguchi Y	Genome Announc	10.1128/genomeA.00089-16	2016
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

#6871	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17283
#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
#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) .
#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 aggregans (DSM 17283, JCM 13213, TGE-P1)

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_001514535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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