Archive BacDiveID:10.13145/bacdive512.20230509.8.1

Strain identifier

BacDive ID: 512

Type strain:

Species: Hydrogenobacter thermophilus

Strain Designation: TK-6

Strain history: T. Kodama TK-6.

NCBI tax ID(s): 608538 (strain), 940 (species)

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

General

@ref: 2720

BacDive-ID: 512

DSM-Number: 6534

keywords: genome sequence, 16S sequence, Bacteria, aerobe, chemolithotroph, thermophilic, Gram-negative, rod-shaped

description: Hydrogenobacter thermophilus TK-6 is an aerobe, chemolithotroph, thermophilic bacterium that was isolated from hot springs.

NCBI tax id

NCBI tax id	Matching level
940	species
608538	strain

strain history

@ref	history
2720	<- T. Kodama, TK-6
67770	T. Kodama TK-6.

doi: 10.13145/bacdive512.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/aquificota
domain: Bacteria
phylum: Aquificota
class: Aquificia
order: Aquificales
family: Aquificaceae
genus: Hydrogenobacter
species: Hydrogenobacter thermophilus
full scientific name: Hydrogenobacter thermophilus Kawasumi et al. 1984

@ref: 2720

domain: Bacteria

phylum: Aquificae

class: Aquificae

order: Aquificales

family: Aquificaceae

genus: Hydrogenobacter

species: Hydrogenobacter thermophilus

full scientific name: Hydrogenobacter thermophilus Kawasumi et al. 1984

strain designation: TK-6

type strain: yes

Morphology

cell morphology

@ref: 23128
gram stain: negative
cell length: 2.0-3.0 µm
cell width: 0.3-0.5 µm
cell shape: rod-shaped
motility: no

multimedia

@ref: 66793
multimedia content: EM_DSM_6534_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
2720	THERMOPHILIC HYDROGEN BACTERIA MEDIUM (DSMZ Medium 533)	yes	https://mediadive.dsmz.de/medium/533	Name: THERMOPHILIC HYDROGEN BACTERIA MEDIUM (DSMZ Medium 533) Composition: Na2HPO4 x 12 H2O 4.5 g/l KH2PO4 1.5 g/l NH4NO3 1.0 g/l NaCl 1.0 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.01 g/l FeSO4 x 7 H2O 0.01 g/l ZnSO4 x 7 H2O 1.4e-05 g/l MnSO4 x 5 H2O 2e-06 g/l MoO3 2e-06 g/l H3BO3 2e-06 g/l CoCl2 x 6 H2O 2e-06 g/l CuSO4 x 5 H2O 1e-06 g/l Distilled water
2720	MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)	yes	https://mediadive.dsmz.de/medium/81	Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
2720	positive	growth	70	thermophilic
23128	no	growth	37	mesophilic
23128	no	growth	80	hyperthermophilic
23128	positive	optimum	70-75	thermophilic
67770	positive	growth	70	thermophilic

Physiology and metabolism

oxygen tolerance

@ref: 23128
oxygen tolerance: aerobe

nutrition type

@ref: 23128
type: chemolithotroph

spore formation

@ref: 23128
spore formation: no

observation

@ref: 67770
observation: quinones: Methionaquinone (MTK)-7(VI,VII-H₄)

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
23128	17879	4-hydroxybenzoate	-	carbon source
23128	30089	acetate	-	carbon source
23128	17750	betaine	-	carbon source
23128	16947	citrate	-	carbon source
23128	16024	D-mannose	-	carbon source
23128	16551	D-trehalose	-	carbon source
23128	17170	dimethylamine	-	carbon source
23128	37054	3-hydroxybutyrate	-	carbon source
23128	24996	lactate	-	carbon source
23128	16236	ethanol	-	carbon source
23128	15740	formate	-	carbon source
23128	28757	fructose	-	carbon source
23128	29806	fumarate	-	carbon source
23128	28260	galactose	-	carbon source
23128	24265	gluconate	-	carbon source
23128	17234	glucose	-	carbon source
23128	15428	glycine	-	carbon source
23128	29805	glycolate	-	carbon source
23128	16977	L-alanine	-	carbon source
23128	16467	L-arginine	-	carbon source
23128	29991	L-aspartate	-	carbon source
23128	29985	L-glutamate	-	carbon source
23128	15971	L-histidine	-	carbon source
23128	15603	L-leucine	-	carbon source
23128	18019	L-lysine	-	carbon source
23128	17203	L-proline	-	carbon source
23128	62345	L-rhamnose	-	carbon source
23128	17115	L-serine	-	carbon source
23128	16828	L-tryptophan	-	carbon source
23128	16414	L-valine	-	carbon source
23128	18300	maleic acid	-	carbon source
23128	25115	malate	-	carbon source
23128	17306	maltose	-	carbon source
23128	29864	mannitol	-	carbon source
23128	17790	methanol	-	carbon source
23128	16830	methylamine	-	carbon source
23128	30916	2-oxoglutarate	-	carbon source
23128	17272	propionate	-	carbon source
23128	15361	pyruvate	-	carbon source
23128	16634	raffinose	-	carbon source
23128	28017	starch	-	carbon source
23128	30031	succinate	-	carbon source
23128	17992	sucrose	-	carbon source
23128	18139	trimethylamine	-	carbon source
23128	18222	xylose	-	carbon source
23128		yeast extract	-	carbon source
23128	17879	4-hydroxybenzoate	-	energy source
23128	30089	acetate	-	energy source
23128	17750	betaine	-	energy source
23128	16947	citrate	-	energy source
23128	16024	D-mannose	-	energy source
23128	16551	D-trehalose	-	energy source
23128	17170	dimethylamine	-	energy source
23128	37054	3-hydroxybutyrate	-	energy source
23128	24996	lactate	-	energy source
23128	16236	ethanol	-	energy source
23128	15740	formate	-	energy source
23128	28757	fructose	-	energy source
23128	29806	fumarate	-	energy source
23128	28260	galactose	-	energy source
23128	24265	gluconate	-	energy source
23128	17234	glucose	-	energy source
23128	15428	glycine	-	energy source
23128	29805	glycolate	-	energy source
23128	16977	L-alanine	-	energy source
23128	16467	L-arginine	-	energy source
23128	29991	L-aspartate	-	energy source
23128	29985	L-glutamate	-	energy source
23128	15971	L-histidine	-	energy source
23128	15603	L-leucine	-	energy source
23128	18019	L-lysine	-	energy source
23128	17203	L-proline	-	energy source
23128	62345	L-rhamnose	-	energy source
23128	17115	L-serine	-	energy source
23128	16828	L-tryptophan	-	energy source
23128	16414	L-valine	-	energy source
23128	18300	maleic acid	-	energy source
23128	25115	malate	-	energy source
23128	17306	maltose	-	energy source
23128	29864	mannitol	-	energy source
23128	17790	methanol	-	energy source
23128	16830	methylamine	-	energy source
23128	30916	2-oxoglutarate	-	energy source
23128	17272	propionate	-	energy source
23128	15361	pyruvate	-	energy source
23128	16634	raffinose	-	energy source
23128	28017	starch	-	energy source
23128	30031	succinate	-	energy source
23128	17992	sucrose	-	energy source
23128	18139	trimethylamine	-	energy source
23128	18222	xylose	-	energy source
23128		yeast extract	-	energy source

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
2720	hot springs	Izu, Kyushu	Japan	JPN	Asia
67770	Soil near hot-spring in Izu Peninsula		Japan	JPN	Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)

Safety information

risk assessment

@ref: 2720
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 2720
description: H.thermophilus TK-6 (IAM-12695) 16S ribosomal RNA
accession: Z30214
length: 1513
database: ena
NCBI tax ID: 608538

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Hydrogenobacter thermophilus TK-6	GCA_000164905	complete	ncbi	608538
66792	Hydrogenobacter thermophilus TK-6	GCA_000010785	complete	ncbi	608538
66792	Hydrogenobacter thermophilus TK-6	608538.3	complete	patric	608538
66792	Hydrogenobacter thermophilus TK-6, DSM 6534	650377953	complete	img	608538
66792	Hydrogenobacter thermophilus TK-6, DSM 6534	646311936	complete	img	608538

GC content

@ref: 67770
GC-content: 43.7
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	no	71.208	no
flagellated	no	98.142	no
gram-positive	no	99.121	yes
anaerobic	no	51.228	yes
aerobic	no	95.579	no
halophile	no	93.663	no
spore-forming	no	95.212	yes
thermophile	yes	99.999	no
glucose-util	no	53.311	yes
glucose-ferment	no	88.043	no

External links

@ref: 2720

culture collection no.: DSM 6534, IAM 12695, JCM 7687, NBRC 102181

straininfo link

@ref: 70191
straininfo: 323294

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	2536668	Amino acid sequence of cytochrome c-552 from a thermophilic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus.	Sanbongi Y, Ishii M, Igarashi Y, Kodama T	J Bacteriol	10.1128/jb.171.1.65-69.1989	1989	Amino Acid Sequence, Bacteria/metabolism, Chromatography, High Pressure Liquid, Cytochrome c Group/isolation & purification, Molecular Sequence Data, Peptide Fragments/isolation & purification, Protein Conformation, Species Specificity	Enzymology
Enzymology	2703459	Purification and characterization of ATP:citrate lyase from Hydrogenobacter thermophilus TK-6.	Ishii M, Igarashi Y, Kodama T	J Bacteriol	10.1128/jb.171.4.1788-1792.1989	1989	Bacteria/enzymology, Cations, Divalent/pharmacology, Citrate (si)-Synthase/metabolism, Hot Temperature, Hydrogen-Ion Concentration, Kinetics, Molecular Weight, Multienzyme Complexes/isolation & purification, Nucleotides/pharmacology, Oxo-Acid-Lyases/*isolation & purification	Stress
Enzymology	3584059	2-Methylthio-1,4-naphthoquinone, a unique sulfur-containing quinone from a thermophilic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus.	Ishii M, Kawasumi T, Igarashi Y, Kodama T, Minoda Y	J Bacteriol	10.1128/jb.169.6.2380-2384.1987	1987	Bacteria/analysis, Mass Spectrometry, Naphthoquinones/isolation & purification, Spectrophotometry, Infrared	Phylogeny
Phylogeny	7981093	Phylogenetic position of the genus Hydrogenobacter.	Pitulle C, Yang Y, Marchiani M, Moore ER, Siefert JL, Aragno M, Jurtshuk P Jr, Fox GE	Int J Syst Bacteriol	10.1099/00207713-44-4-620	1994	Bacteria/*classification, Base Sequence, DNA, Bacterial/analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/chemistry	Genetics
Enzymology	8655524	Purification and characterization of 2-oxoglutarate:ferredoxin oxidoreductase from a thermophilic, obligately chemolithoautotrophic bacterium, Hydrogenobacter thermophilus TK-6.	Yoon KS, Ishii M, Igarashi Y, Kodama T	J Bacteriol	10.1128/jb.178.11.3365-3368.1996	1996	Amino Acid Sequence, Bacteria, Aerobic/enzymology/growth & development, Ferredoxins/metabolism, Ketoglutaric Acids/metabolism, Molecular Sequence Data, Oxidation-Reduction, Oxidoreductases/chemistry/isolation & purification/metabolism, Substrate Specificity	Metabolism
Enzymology	8987606	Purification and characterization of ferredoxin from Hydrogenobacter thermophilus strain TK-6.	Ishii M, Ueda Y, Yoon KS, Igarashi Y, Kodama T	Biosci Biotechnol Biochem	10.1271/bbb.60.1513	1996	Amino Acid Sequence, Bacteria, Aerobic/chemistry, Chromatography, Gel, Ferredoxins/chemistry/isolation & purification, Molecular Sequence Data, Molecular Weight, Spectrophotometry/methods, Spectrophotometry, Ultraviolet	Genetics
Enzymology	9094223	Purification and characterization of pyruvate:ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6.	Yoon KS, Ishii M, Kodama T, Igarashi Y	Arch Microbiol	10.1007/s002030050443	1997	Amino Acid Sequence, Bacteria, Aerobic/enzymology/genetics, Electron Transport, Enzyme Stability, Hydrogen-Ion Concentration, Ketone Oxidoreductases/chemistry/genetics/isolation & purification, Kinetics, Molecular Sequence Data, Molecular Weight, Protein Conformation, Pyruvate Synthase, Substrate Specificity, Temperature	Genetics
Enzymology	10803945	Purification and characterization of membrane-bound hydrogenase from Hydrogenobacter thermophilus strain TK-6, an obligately autotrophic, thermophilic, hydrogen-oxidizing bacterium.	Ishii M, Takishita S, Iwasaki T, Peerapornpisal Y, Yoshino J, Kodama T, Igarashi Y	Biosci Biotechnol Biochem	10.1271/bbb.64.492	2000	Amino Acid Sequence, Amino Acids/analysis, Bacteria, Aerobic/enzymology, Electron Spin Resonance Spectroscopy, Electrons, Heating, Hydrogen/metabolism, Hydrogenase/isolation & purification, Membrane Proteins/*isolation & purification, Metals, Molecular Sequence Data, Molecular Weight, Oxidation-Reduction, Sequence Analysis	Phylogeny
Metabolism	11271424	Nitrate respiratory metabolism in an obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6.	Suzuki M, Cui ZJ, Ishii M, Igarashi Y	Arch Microbiol	10.1007/s002030000230	2001	Adenosine Triphosphate/metabolism, Anaerobiosis, Bacteria, Aerobic/growth & development/metabolism, Blotting, Western, Cytochromes, Electron Transport Complex IV/analysis, Heme/analysis, Multienzyme Complexes/metabolism, Nitrates/metabolism, Nitrite Reductases/analysis, Oxo-Acid-Lyases/metabolism	Enzymology
Enzymology	11401501	The genes for anabolic 2-oxoglutarate: ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6.	Yun NR, Arai H, Ishii M, Igarashi Y	Biochem Biophys Res Commun	10.1006/bbrc.2001.4542	2001	Amino Acid Sequence, Bacteria, Aerobic/enzymology/genetics, Base Sequence, Binding Sites/genetics, Chromosome Mapping, Cloning, Molecular, DNA Primers/genetics, Escherichia coli/genetics, Gene Expression, Genes, Bacterial, Ketoglutaric Acids/metabolism, Ketone Oxidoreductases/chemistry/genetics/metabolism, Molecular Sequence Data, Recombinant Proteins/chemistry/genetics/metabolism, Substrate Specificity	Metabolism
Enzymology	11591674	Chemical structure of a novel aminophospholipid from Hydrogenobacter thermophilus strain TK-6.	Yoshino J, Sugiyama Y, Sakuda S, Kodama T, Nagasawa H, Ishii M, Igarashi Y	J Bacteriol	10.1128/JB.183.21.6302-6304.2001	2001	Amino Sugars/chemistry/isolation & purification, Archaea/chemistry, Gram-Negative Chemolithotrophic Bacteria/chemistry, Phosphatidic Acids/*chemistry/isolation & purification, Phospholipids/chemistry	Phylogeny
Phylogeny	11679343	Signature lipids and stable carbon isotope analyses of Octopus Spring hyperthermophilic communities compared with those of Aquificales representatives.	Jahnke LL, Eder W, Huber R, Hope JM, Hinrichs KU, Hayes JM, Des Marais DJ, Cady SL, Summons RE	Appl Environ Microbiol	10.1128/AEM.67.11.5179-5189.2001	2001	Bacteria/chemistry/classification/genetics, Biofilms, Carbon Isotopes/analysis, DNA, Bacterial/genetics, Ecosystem, Fresh Water/microbiology, Genes, rRNA, Lipids/*analysis, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature	Genetics
Enzymology	11890705	A novel five-subunit-type 2-oxoglutalate:ferredoxin oxidoreductases from Hydrogenobacter thermophilus TK-6.	Yun NR, Yamamoto M, Arai H, Ishii M, Igarashi Y	Biochem Biophys Res Commun	10.1006/bbrc.2002.6651	2002	Bacteria, Aerobic/enzymology, Bacterial Proteins/chemistry/genetics/metabolism, Base Sequence, Escherichia coli/genetics, Genes, Bacterial, Ketone Oxidoreductases/chemistry/genetics/metabolism, Molecular Sequence Data, Multigene Family, Protein Subunits, Substrate Specificity, Transcription Initiation Site, Transformation, Genetic	Metabolism
Enzymology	14652015	Characterization of two different 2-oxoglutarate:ferredoxin oxidoreductases from Hydrogenobacter thermophilus TK-6.	Yamamoto M, Arai H, Ishii M, Igarashi Y	Biochem Biophys Res Commun	10.1016/j.bbrc.2003.11.078	2003	Bacteria/chemistry/enzymology, Bacteria, Aerobic/chemistry/enzymology, Bacteria, Anaerobic/chemistry/metabolism, Citric Acid Cycle/physiology, Enzyme Activation, Enzyme Stability, Gene Expression Regulation, Bacterial/physiology, Gene Expression Regulation, Enzymologic/physiology, Hydrogen-Ion Concentration, Ketone Oxidoreductases/chemistry/classification/genetics/metabolism, Molecular Weight, Recombinant Proteins/chemistry/metabolism, Species Specificity, Temperature	Metabolism
Enzymology	14731279	A novel biotin protein required for reductive carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6.	Aoshima M, Ishii M, Igarashi Y	Mol Microbiol	10.1046/j.1365-2958.2003.03863.x	2004	Amino Acid Sequence, Bacteria/enzymology, Bacterial Proteins/genetics/isolation & purification/metabolism, Biotin/metabolism, Carbon/metabolism, Isocitrate Dehydrogenase/isolation & purification/metabolism, Ketoglutaric Acids/metabolism, Molecular Sequence Data, Sequence Alignment	Metabolism
Metabolism	15101981	A novel enzyme, citryl-CoA synthetase, catalysing the first step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6.	Aoshima M, Ishii M, Igarashi Y	Mol Microbiol	10.1111/j.1365-2958.2004.04009.x	2004	ATP Citrate (pro-S)-Lyase/metabolism, Acyl Coenzyme A/metabolism, Amino Acid Sequence, Animals, Bacteria/enzymology/genetics, Citric Acid/metabolism, Coenzyme A Ligases/chemistry/genetics/isolation & purification/metabolism, Evolution, Molecular, Molecular Sequence Data, Protein Subunits/genetics/isolation & purification/metabolism, Sequence Alignment	Enzymology
Metabolism	15101982	A novel enzyme, citryl-CoA lyase, catalysing the second step of the citrate cleavage reaction in Hydrogenobacter thermophilus TK-6.	Aoshima M, Ishii M, Igarashi Y	Mol Microbiol	10.1111/j.1365-2958.2004.04010.x	2004	Acyl Coenzyme A/metabolism, Amino Acid Sequence, Bacteria/enzymology/genetics/metabolism, Bacterial Proteins/genetics/isolation & purification/metabolism, Citric Acid/metabolism, Molecular Sequence Data, Oxo-Acid-Lyases/genetics/isolation & purification/*metabolism, Recombinant Proteins/genetics/isolation & purification/metabolism, Sequence Alignment	Enzymology
Genetics	15973049	Two tandemly arranged ferredoxin genes in the Hydrogenobacter thermophilus genome: comparative characterization of the recombinant [4Fe-4S] ferredoxins.	Ikeda T, Yamamoto M, Arai H, Ohmori D, Ishii M, Igarashi Y	Biosci Biotechnol Biochem	10.1271/bbb.69.1172	2005	Amino Acid Sequence, Bacteria/genetics/metabolism, Chromosome Mapping, Chromosomes, Bacterial, Ferredoxins/biosynthesis/chemistry/genetics, Gene Expression, Genome, Bacterial, Recombinant Proteins/biosynthesis/chemistry, Sequence Alignment, Sequence Homology, Amino Acid	Metabolism
Genetics	16343420	Anabolic five subunit-type pyruvate:ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6.	Ikeda T, Ochiai T, Morita S, Nishiyama A, Yamada E, Arai H, Ishii M, Igarashi Y	Biochem Biophys Res Commun	10.1016/j.bbrc.2005.11.155	2005	Amino Acid Sequence, Anabolic Agents/analysis/chemistry, Bacterial Proteins/analysis/chemistry, Enzyme Activation, Molecular Sequence Data, Molecular Weight, Protein Subunits, Pyruvate Synthase/analysis/chemistry	Enzymology
Enzymology	16781467	Purification, characterization, and gene cloning of thermophilic cytochrome cd1 nitrite reductase from Hydrogenobacter thermophilus TK-6.	Suzuki M, Hirai T, Arai H, Ishii M, Igarashi Y	J Biosci Bioeng	10.1263/jbb.101.391	2006	Amino Acid Sequence, Bacteria/enzymology, Cloning, Molecular, Cytochromes/chemistry/genetics/isolation & purification/metabolism, Enzyme Activation, Enzyme Stability, Molecular Sequence Data, Molecular Weight, Nitrite Reductases/chemistry/genetics/isolation & purification/metabolism, Protein Engineering/methods, Sequence Homology, Amino Acid, Temperature	Phylogeny
Metabolism	16861801	Gene structure and expression profile of cytochrome bc nitric oxide reductase from Hydrogenobacter thermophilus TK-6.	Suzuki M, Arai H, Ishii M, Igarashi Y	Biosci Biotechnol Biochem	10.1271/bbb.60018	2006	Bacteria/enzymology/genetics, Bacterial Proteins/genetics/metabolism, Cytochromes b/genetics/metabolism, Cytochromes c/genetics/metabolism, Genes, Bacterial, Nitrates/pharmacology, Nitric Oxide Donors/pharmacology, Nitrites/pharmacology, Nitroprusside/pharmacology, Oxidoreductases/genetics/*metabolism, Phylogeny, Promoter Regions, Genetic	Enzymology
Metabolism	16978355	Role of two 2-oxoglutarate:ferredoxin oxidoreductases in Hydrogenobacter thermophilus under aerobic and anaerobic conditions.	Yamamoto M, Arai H, Ishii M, Igarashi Y	FEMS Microbiol Lett	10.1111/j.1574-6968.2006.00415.x	2006	Aerobiosis, Anaerobiosis, Ferredoxins/metabolism, Gene Expression Regulation, Bacterial/physiology, Gene Expression Regulation, Enzymologic/physiology, Ketoglutaric Acids/metabolism, Ketone Oxidoreductases/genetics/metabolism/physiology, Oxidation-Reduction, Oxygen/metabolism	Enzymology
Metabolism	17076668	A novel oxalosuccinate-forming enzyme involved in the reductive carboxylation of 2-oxoglutarate in Hydrogenobacter thermophilus TK-6.	Aoshima M, Igarashi Y	Mol Microbiol	10.1111/j.1365-2958.2006.05399.x	2006	Adenosine Triphosphate/metabolism, Bacteria/metabolism, Bacterial Proteins/genetics/metabolism, Cloning, Molecular, Enzymes/genetics/metabolism, Gene Expression Regulation, Bacterial, Isocitrate Dehydrogenase/metabolism, Isocitrates/metabolism, Ketoglutaric Acids/metabolism, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Pyruvate Carboxylase/metabolism, Sequence Analysis	Enzymology
Enzymology	17116577	Purification and properties of glutamine synthetase from Hydrogenobacter thermophilus TK-6.	Kameya M, Arai H, Ishii M, Igarashi Y	J Biosci Bioeng	10.1263/jbb.102.311	2006	Bacterial Proteins/chemistry/isolation & purification, Enzyme Activation, Enzyme Stability, Glutamate-Ammonia Ligase/chemistry/isolation & purification	Phylogeny
Enzymology	17237175	A novel ferredoxin-dependent glutamate synthase from the hydrogen-oxidizing chemoautotrophic bacterium Hydrogenobacter thermophilus TK-6.	Kameya M, Ikeda T, Nakamura M, Arai H, Ishii M, Igarashi Y	J Bacteriol	10.1128/JB.01360-06	2007	Bacteria/classification/enzymology/genetics, Bacterial Proteins/metabolism, DNA Primers, Electron Spin Resonance Spectroscopy, Ferredoxins/metabolism, Glutamate Synthase/genetics/isolation & purification/*metabolism, Hydrogen/metabolism, Kinetics, Molecular Sequence Data, Phylogeny, Recombinant Proteins/isolation & purification/metabolism, Spectrophotometry	Phylogeny
Enzymology	18215633	Sequencing and reverse transcription-polymerase chain reaction (RT-PCR) analysis of four hydrogenase gene clusters from an obligately autotrophic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6.	Ueda Y, Yamamoto M, Urasaki T, Arai H, Ishii M, Igarashi Y	J Biosci Bioeng	10.1263/jbb.104.470	2007	Aquifoliaceae/enzymology/genetics, Hydrogen/metabolism, Hydrogenase/genetics, Multigene Family/genetics, Oxidation-Reduction, Reverse Transcriptase Polymerase Chain Reaction/methods, Sequence Analysis, DNA/*methods	Transcriptome
Genetics	18757546	A soluble NADH-dependent fumarate reductase in the reductive tricarboxylic acid cycle of Hydrogenobacter thermophilus TK-6.	Miura A, Kameya M, Arai H, Ishii M, Igarashi Y	J Bacteriol	10.1128/JB.00747-08	2008	Bacteria/enzymology/genetics/metabolism, Bacterial Proteins/genetics/metabolism, Citric Acid Cycle/physiology, Genome, Bacterial, Molecular Sequence Data, Oxidation-Reduction, Oxidoreductases Acting on CH-CH Group Donors/classification/genetics/metabolism, Phylogeny, Solubility	Enzymology
Enzymology	19552713	Ferredoxin-NADP reductase from the thermophilic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6.	Ikeda T, Nakamura M, Arai H, Ishii M, Igarashi Y	FEMS Microbiol Lett	10.1111/j.1574-6968.2009.01667.x	2009	Amino Acid Sequence, Bacteria/chemistry/enzymology/genetics/metabolism, Bacterial Proteins/chemistry/genetics/isolation & purification/metabolism, Ferredoxin-NADP Reductase/chemistry/genetics/isolation & purification/metabolism, Flavin Mononucleotide/metabolism, Hot Temperature, Hydrogen/metabolism, Molecular Sequence Data, Sequence Alignment	Metabolism
Enzymology	19894084	Carboxylation reaction catalyzed by 2-oxoglutarate:ferredoxin oxidoreductases from Hydrogenobacter thermophilus.	Yamamoto M, Ikeda T, Arai H, Ishii M, Igarashi Y	Extremophiles	10.1007/s00792-009-0289-4	2009	Acyl Coenzyme A/chemistry/metabolism, Bacteria/enzymology/genetics, Bacterial Proteins/chemistry/genetics/metabolism, Citric Acid Cycle/physiology, Genome, Bacterial/physiology, Ketone Oxidoreductases/chemistry/genetics/metabolism, Kinetics	Metabolism
Metabolism	20015072	Enzymatic and electron paramagnetic resonance studies of anabolic pyruvate synthesis by pyruvate: ferredoxin oxidoreductase from Hydrogenobacter thermophilus.	Ikeda T, Yamamoto M, Arai H, Ohmori D, Ishii M, Igarashi Y	FEBS J	10.1111/j.1742-4658.2009.07506.x	2009	Acetyl Coenzyme A/metabolism, Bacteria/enzymology/genetics, Bacterial Proteins/genetics/metabolism, Carbon Dioxide/metabolism, Citric Acid Cycle, Electron Spin Resonance Spectroscopy, Energy Metabolism, Ketone Oxidoreductases/genetics/metabolism, Kinetics, L-Lactate Dehydrogenase/genetics/metabolism, Pyruvate Synthase/genetics/metabolism, Pyruvic Acid/metabolism, Recombinant Proteins/genetics/metabolism	Enzymology
Enzymology	20214682	Purification of three aminotransferases from Hydrogenobacter thermophilus TK-6--novel types of alanine or glycine aminotransferase: enzymes and catalysis.	Kameya M, Arai H, Ishii M, Igarashi Y	FEBS J	10.1111/j.1742-4658.2010.07604.x	2010	Alanine Transaminase/genetics/isolation & purification/metabolism, Amino Acid Sequence, Catalysis, Conserved Sequence, Eukaryota/enzymology, Glycine Transaminase/genetics/isolation & purification/metabolism, Isoenzymes/genetics/isolation & purification/metabolism, Kinetics, Models, Biological, Molecular Sequence Data, Phylogeny, Substrate Specificity/genetics, Transaminases/genetics/isolation & purification/metabolism	Phylogeny
Genetics	20348262	Complete genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6.	Arai H, Kanbe H, Ishii M, Igarashi Y	J Bacteriol	10.1128/JB.00158-10	2010	Aquifoliaceae/genetics, Genome, Bacterial/genetics, Molecular Sequence Data
Genetics	21677850	Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6).	Zeytun A, Sikorski J, Nolan M, Lapidus A, Lucas S, Han J, Tice H, Cheng JF, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Ngatchou-Djao OD, Land M, Hauser L, Jeffries CD, Han C, Detter JC, Ubler S, Rohde M, Tindall BJ, Goker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC	Stand Genomic Sci	10.4056/sigs.1463589	2011
Enzymology	22869120	Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6.	Chiba Y, Horita S, Ohtsuka J, Arai H, Nagata K, Igarashi Y, Tanokura M, Ishii M	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309112025213	2012	Bacteria/enzymology, Crystallization, Crystallography, X-Ray, Phosphoric Monoester Hydrolases/chemistry
Metabolism	23479726	Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis.	Chiba Y, Horita S, Ohtsuka J, Arai H, Nagata K, Igarashi Y, Tanokura M, Ishii M	J Biol Chem	10.1074/jbc.M112.449561	2013	Bacteria/enzymology/growth & development, Bacterial Proteins/chemistry/metabolism, Crystallography, X-Ray, Phosphoric Monoester Hydrolases/chemistry/metabolism, Phosphoserine/chemistry/metabolism, Protein Structure, Tertiary	Enzymology
Phylogeny	30473565	Nitrogenase Activity in Thermophilic Chemolithoautotrophic Bacteria in the Phylum Aquificae Isolated under Nitrogen-Fixing Conditions from Nakabusa Hot Springs.	Nishihara A, Matsuura K, Tank M, McGlynn SE, Thiel V, Haruta S	Microbes Environ	10.1264/jsme2.ME18041	2018	Bacteria/classification/enzymology, Bacterial Proteins/genetics/metabolism, DNA, Bacterial/genetics, Hot Springs/microbiology, Japan, Nitrogen Fixation, Nitrogen-Fixing Bacteria/classification/genetics/metabolism, Oxidation-Reduction, Oxidoreductases/genetics/*metabolism, Oxygen, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Amino Acid	Metabolism

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
2720	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6534)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-6534
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
23128	Toshiyuki Kawasumi, Yasuo Igarashi, Tohru Kodama, Yasuji Minoda		10.1099/00207713-34-1-5	Hydrogenobacter thermophilus gen. nov., sp. nov., an Extremely Thermophilic, Aerobic, Hydrogen-Oxidizing Bacterium	IJSEM 34: 5-10 1984
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)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
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
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
70191	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID323294.1	StrainInfo: A central database for resolving microbial strain identifiers