Pseudothermotoga hypogea (DSM 11164, NBRC 106472, SEBR 7054)

Name: Pseudothermotoga hypogea (DSM 11164, NBRC 106472, SEBR 7054)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17067

Type strain

Culture col. no. DSM 11164 NBRC 106472 SEBR 7054

NCBI tax ID(s) 1123384 57487

Special Collections DSMZ

History <- M. L. Fardeau, Université de Provence, Marseille, France; SEBR 7054 <- M. L. Fardeau {1995}

Links

Pseudothermotoga hypogea DSM 11164 is an anaerobe, thermophilic prokaryote that was isolated from oil-producing well.

anaerobe thermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 49041

NBRC 106472,DSM 11164

@ref 20215

Last LPSN update 2026-02-09 11:22:07

Domain Bacteria

Phylum Thermotogota

Class Thermotogae

Order Thermotogales

Family Thermotogaceae

Genus Pseudothermotoga

Species Pseudothermotoga hypogea

Full scientific name Pseudothermotoga hypogea (Fardeau et al. 1997) Bhandari and Gupta 2017

Synonyms (2)

"Pseudothermotoga hypogea"
Thermotoga hypogea

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4223	PSEUDOTHERMOTOGA HYPOGEA MEDIUM (DSMZ Medium 794)		Medium recipe at MediaDive	Name: PSEUDOTHERMOTOGA HYPOGEA MEDIUM (DSMZ Medium 794) Composition: Na2S2O3 x 5 H2O 4.9505 g/l D-Xylose 2.9703 g/l NaHCO3 1.9802 g/l Yeast extract 1.9802 g/l Trypticase peptone 1.9802 g/l NH4Cl 0.990099 g/l Na-acetate 0.49505 g/l Na2S x 9 H2O 0.49505 g/l L-Cysteine HCl x H2O 0.49505 g/l K2HPO4 0.29703 g/l KH2PO4 0.29703 g/l MgCl2 x 6 H2O 0.19802 g/l KCl 0.0990099 g/l MgSO4 x 7 H2O 0.029703 g/l Nitrilotriacetic acid 0.0148515 g/l NaCl 0.00990099 g/l MnSO4 x H2O 0.00495049 g/l CoSO4 x 7 H2O 0.00178218 g/l ZnSO4 x 7 H2O 0.00178218 g/l FeSO4 x 7 H2O 0.000990099 g/l CaCl2 x 2 H2O 0.000990099 g/l Sodium resazurin 0.00049505 g/l NiCl2 x 6 H2O 0.00029703 g/l AlK(SO4)2 x 12 H2O 0.00019802 g/l CuSO4 x 5 H2O 9.90099e-05 g/l H3BO3 9.90099e-05 g/l Na2MoO4 x 2 H2O 9.90099e-05 g/l Na2WO4 x 2 H2O 3.9604e-06 g/l Na2SeO3 x 5 H2O 2.9703e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4223	positive	growth	70	thermophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4223	anaerobe
125438	anaerobe	94.072
125439	anaerobe	90.9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	aspartate and asparagine metabolism	100	9 of 9
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	pentose phosphate pathway	81.82	9 of 11
66794	propionate fermentation	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	butanoate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	purine metabolism	72.34	68 of 94
66794	propanol degradation	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	threonine metabolism	70	7 of 10
66794	pyrimidine metabolism	68.89	31 of 45
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	NAD metabolism	66.67	12 of 18
66794	formaldehyde oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	d-xylose degradation	63.64	7 of 11
66794	oxidative phosphorylation	62.64	57 of 91
66794	gluconeogenesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	vitamin B1 metabolism	61.54	8 of 13
66794	phenylalanine metabolism	61.54	8 of 13
66794	factor 420 biosynthesis	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	methionine metabolism	57.69	15 of 26
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	molybdenum cofactor biosynthesis	55.56	5 of 9
66794	alanine metabolism	55.17	16 of 29
66794	urea cycle	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	degradation of sugar acids	52	13 of 25
66794	citric acid cycle	50	7 of 14
66794	ethanol fermentation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	degradation of hexoses	50	9 of 18
66794	myo-inositol biosynthesis	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	cysteine metabolism	50	9 of 18
66794	ketogluconate metabolism	50	4 of 8
66794	starch degradation	50	5 of 10
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	arginine metabolism	45.83	11 of 24
66794	valine metabolism	44.44	4 of 9
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	tryptophan metabolism	42.11	16 of 38
66794	non-pathway related	42.11	16 of 38
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	flavin biosynthesis	40	6 of 15
66794	lipid metabolism	38.71	12 of 31
66794	metabolism of disaccharids	36.36	4 of 11
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	degradation of sugar alcohols	31.25	5 of 16
66794	sulfate reduction	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	coenzyme M biosynthesis	30	3 of 10
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	tyrosine metabolism	28.57	4 of 14
66794	vitamin B6 metabolism	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	cyclohexanol degradation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	leucine metabolism	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	lipid A biosynthesis	22.22	2 of 9
66794	chorismate metabolism	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Engineered product
#Engineered	#Industrial	#Oil reservoir

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
4223	oil-producing well	Cameroon	CMR	Africa

Taxonmaps

69479

Global distribution of 16S sequence U89768 (>99% sequence identity) for Pseudothermotoga from Microbeatlas

Aquatic Samples	5
Soil Samples
Animal Samples
Plant Samples
Total Samples	5

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4223	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	ASM81614v1 assembly for Pseudothermotoga hypogea DSM 11164 = NBRC 106472	complete	GCA_000816145	1123384.7		1123384	98.03
66792	ASM50410v1 assembly for Pseudothermotoga hypogea DSM 11164 = NBRC 106472	complete	GCA_000504105	1219084.8	2558309119	1123384	97.45
66792	ASM71181v1 assembly for Pseudothermotoga hypogea DSM 11164 = NBRC 106472	scaffold	GCA_000711815	1123384.3	2565956526	1123384	76.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4223	Thermotoga hypogea 16S ribosomal RNA gene, partial sequence	U89768	1521		57487

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudothermotoga hypogea DSM 11164 = NBRC 106472
NCBI: GCA_000504105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	90.90	no
125439	gram_stain	BacteriaNetⓘ	variable	82.80	no
125439	motility	BacteriaNetⓘ	yes	51.20	no
125439	spore_formation	BacteriaNetⓘ	no	59.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudothermotoga hypogea DSM 11164 = NBRC 106472 NBRC 106472
NCBI: GCA_000504105.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	69.49	no
125438	anaerobic	anaerobicⓘ	yes	94.07	yes
125438	aerobic	aerobicⓘ	no	95.63	no
125438	spore-forming	spore-formingⓘ	no	78.41	no
125438	thermophilic	thermophileⓘ	yes	82.20	yes
125438	flagellated	motile2+ⓘ	yes	56.39	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Molecular Characterization of the Iron-Containing Alcohol Dehydrogenase from the Extremely Thermophilic Bacterium Pseudothermotoga hypogea.	Hao L, Ayinla Z, Ma K.	Microorganisms	10.3390/microorganisms12020311	2024
	List of new names and new combinations previously effectively, but not validly, published.	Oren A, Garrity GM.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002278	2017
Enzymology	Characterization of the GH13 and GH57 glycogen branching enzymes from Petrotoga mobilis SJ95 and potential role in glycogen biosynthesis.	Zhang X, Leemhuis H, van der Maarel MJEC.	PLoS One	10.1371/journal.pone.0219844	2019
Genetics	The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses.	Thiel V, Hugler M, Ward DM, Bryant DA.	Front Microbiol	10.3389/fmicb.2017.00943	2017
	The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing.	Thiel V, Wood JM, Olsen MT, Tank M, Klatt CG, Ward DM, Bryant DA.	Front Microbiol	10.3389/fmicb.2016.00919	2016
Phylogeny	Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs.	Mori K, Yamazoe A, Hosoyama A, Ohji S, Fujita N, Ishibashi JI, Kimura H, Suzuki KI	Int J Syst Evol Microbiol	10.1099/ijs.0.060137-0	2014
Phylogeny	Thermotoga hypogea sp. nov., a xylanolytic, thermophilic bacterium from an oil-producing well.	Fardeau ML, Ollivier B, Patel BK, Magot M, Thomas P, Rimbault A, Rocchiccioli F, Garcia JL	Int J Syst Bacteriol	10.1099/00207713-47-4-1013	1997

References

#4223	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11164
#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 )
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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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Pseudothermotoga hypogea (DSM 11164, NBRC 106472, SEBR 7054)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000816145

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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