Methanothermobacter tenebrarum (DSM 23052, JCM 16532, NBRC 106236)

Name: Methanothermobacter tenebrarum (DSM 23052, JCM 16532, NBRC 106236)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23082

Type strain

Strain Designation RMAS

Culture col. no. DSM 23052 JCM 16532 NBRC 106236 RMAS

NCBI tax ID(s) 680118

Special Collections DSMZ JCM Literature strains

Links

Methanothermobacter tenebrarum RMAS is an anaerobe, thermophilic, Gram-positive prokaryote that was isolated from gas-associated formation water from a well of natural gas field.

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

Name and taxonomic classification

SI-ID 398257

NBRC 106236,JCM 16532,DSM 23052

@ref 20215

Last LPSN update 2025-12-16 09:52:34

Domain Methanobacteriati

Phylum Methanobacteriota

Class Methanobacteria

Order Methanobacteriales

Family Methanobacteriaceae

Genus Methanothermobacter

Species Methanothermobacter tenebrarum

Full scientific name Methanothermobacter tenebrarum Nakamura et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30672	positive	7 µm	0.5 µm	rod-shaped

Colony morphology

19215

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19215	METHANOBACTERIUM MEDIUM (DSMZ Medium 119)		Medium recipe at MediaDive	Name: METHANOBACTERIUM MEDIUM (DSMZ Medium 119) Composition: NaHCO3 3.98804 g/l Na-formate 1.99402 g/l Na-acetate 0.997009 g/l Na2S x 9 H2O 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l KH2PO4 0.498504 g/l NH4Cl 0.398804 g/l NaCl 0.398804 g/l MgSO4 x 7 H2O 0.398804 g/l Yeast extract 0.199402 g/l CaCl2 x 2 H2O 0.0498504 g/l HCl 0.00249252 g/l FeSO4 x 7 H2O 0.00199402 g/l FeCl2 x 4 H2O 0.00149551 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 ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Isobutyric acid DL-2-Methylbutyric acid Valeric acid Isovaleric acid H2SO4 Sludge Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
19215	positive	growth	70	thermophilic
30672	positive	growth	45-80	hyperthermophilic
30672	positive	optimum	70	thermophilic
67770	positive	growth	65	thermophilic

Culture pH

@ref	Ability	Type	PH	PH range
30672	positive	optimum	7.3
30672	positive	growth	5.8-8.7	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
19215	anaerobe
30672	anaerobe
125439	anaerobe	95.4

Spore formation

@ref	Spore formation	Confidence
125439		95.9
125438		91.645

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30672	NaCl	positive	growth	0-2 %

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Geologic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19215	gas-associated formation water from a well of natural gas field	Niigata	Japan	JPN	Asia
67770	Gas-associated formation water of a gas-producing well in a natural gas field		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB523785 (>99% sequence identity) for Methanothermobacter tenebrarum subclade from Microbeatlas

Aquatic Samples	42
Soil Samples	3
Animal Samples
Plant Samples	1
Total Samples	46

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19215	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
66792	ASM2316746v1 assembly for Methanothermobacter tenebrarum RMAS	complete	GCA_023167465	680118.6	8046181379	680118	87.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19215	Methanothermobacter tenebrarum gene for 16S rRNA, partial sequence	AB523785	1414		680118

GC content

@ref	GC-content (mol%)	Method
19215	41.5	high performance liquid chromatography (HPLC)
30672	41.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanothermobacter tenebrarum RMAS
NCBI: GCA_023167465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	no	84.20	no
125439	gram_stain	BacteriaNetⓘ	positive	67.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	95.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanothermobacter tenebrarum RMAS
NCBI: GCA_023167465.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	55.36	yes
125438	anaerobic	anaerobicⓘ	yes	89.24	yes
125438	aerobic	aerobicⓘ	no	91.49	yes
125438	spore-forming	spore-formingⓘ	no	91.65	no
125438	thermophilic	thermophileⓘ	yes	65.06	yes
125438	flagellated	motile2+ⓘ	no	85.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field.	Nakamura K, Takahashi A, Mori C, Tamaki H, Mochimaru H, Nakamura K, Takamizawa K, Kamagata Y	Int J Syst Evol Microbiol	10.1099/ijs.0.041681-0	2012

References

#19215	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23052
#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 )
#30672	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 #27003 (see below)
#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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Methanothermobacter tenebrarum (DSM 23052, JCM 16532, NBRC 106236)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_023167465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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