Name: Pseudothermotoga hypogea DSM 11164
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17067

Type strain:

Species: Pseudothermotoga hypogea

Culture col. no.: DSM 11164, NBRC 106472, SEBR 7054

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

NCBI tax ID(s): 1123384 (strain), 57487 (species)

SI-ID 49041

DSM 11164

Section

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

Gram-negative
anaerobe
thermophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Thermotogota*
	Class	*Thermotogae*
	Order	*Thermotogales*
	Family	*Thermotogaceae*
	Genus	*Pseudothermotoga*
	Species	**Pseudothermotoga hypogea**
	Full Scientific Name (LPSN)	Pseudothermotoga hypogea (Fardeau et al. 1997) Bhandari and Gupta 2017

	Synonym	"Pseudothermotoga* hypogea"*
	Synonym	Thermotoga hypogea

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.92

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4223]

Culture medium

THERMOTOGA HYPOGEA MEDIUM (DSMZ Medium 794)

[Ref.: #4223]

Culture medium growth

[Ref.: #4223]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4223]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4223]			growth	70 °C

[Ref.: #4223]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.615

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4223]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #69481]	Ability of spore formation	no Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.919

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #4223]	Sample type/isolated from	oil-producing well
[Ref.: #4223]	Country	Cameroon
[Ref.: #4223]	Country ISO 3 Code	CMR
[Ref.: #4223]	Continent	Africa
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Engineered product
#Engineered	#Industrial	#Oil reservoir

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #4223]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #4223]	Thermotoga hypogea 16S ribosomal RNA gene, partial sequence	U89768	1521	ENA	57487 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudothermotoga hypogea DSM 11164	2565956526	draft	JGI IMG/M	1123384 tax ID	*
[Ref.: #66792]	Pseudothermotoga hypogea DSM 11164 = NBRC 106472	GCA_000816145	complete	GenBank	1123384 tax ID	*
[Ref.: #66792]	Pseudothermotoga hypogea DSM 11164 = NBRC 106472	GCA_000711815	scaffold	GenBank	1123384 tax ID	*
[Ref.: #66792]	Pseudothermotoga hypogea DSM 11164 = NBRC 106472	1123384.7	complete	PATRIC	1123384 tax ID	*
[Ref.: #66792]	Thermotoga hypogea DSM 11164	1123384.3	wgs	PATRIC	1123384 tax ID	*
[Ref.: #66792]	Thermotoga hypogea NBRC 106472	1219084.8	complete	PATRIC	1123384 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pseudothermotoga hypogea DSM 11164 = NBRC 106472 NBRC 106472 NCBI: GCA_000504105.1
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudothermotoga hypogea DSM 11164 = NBRC 106472 NBRC 106472 NCBI: GCA_000504105.1
[Ref.: #69480]	motile	yes	82.44	no
[Ref.: #69480]	flagellated	no	94.239	no
[Ref.: #69480]	gram-positive	no	95.875	no
[Ref.: #69480]	anaerobic	yes	99.342	yes
[Ref.: #69480]	halophile	no	91.053	no
[Ref.: #69480]	spore-forming	no	88.976	no
[Ref.: #69480]	thermophile	yes	100	yes
[Ref.: #69480]	glucose-util	yes	88.533	no
[Ref.: #69480]	aerobic	no	97.616	yes
[Ref.: #69480]	glucose-ferment	no	58.563	no

Availability in culture collections External links

[Ref.: #4223]

Culture collection no.

DSM 11164, NBRC 106472, SEBR 7054

[Ref.: #86067]

SI-ID 49041

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86067

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID49041.1 )

* These data were automatically processed and therefore are not curated

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Pseudothermotoga hypogea DSM 11164 = NBRC 106472 NBRC 106472

Pseudothermotoga hypogea DSM 11164 = NBRC 106472 NBRC 106472

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