Name: Thermotoga petrophila RKU-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17068

Type strain:

Species: Thermotoga petrophila

Strain Designation: RKU-1

Culture col. no.: DSM 13995, JCM 10881, ATCC BAA-488

Strain history: T. Maruyama RKU-1.

NCBI tax ID(s): 93929 (species)

SI-ID 49543

DSM 13995, JCM 10881, ATCC BAA-488

Section

Thermotoga petrophila RKU-1 is an anaerobe, heterotroph, hyperthermophilic bacterium that was isolated from production fluid of an oil reservoir storage tank.

rod-shaped
anaerobe
heterotroph
hyperthermophilic
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	*Thermotoga*
	Species	**Thermotoga petrophila**
	Full Scientific Name (LPSN)	Thermotoga petrophila Takahata et al. 2001

Synonym

Thermotoga naphthophila

Information on morphological and physiological properties Morphology

[Ref.: #43376]	Cell length	2-7 µm

[Ref.: #43376]	Cell width	0.7-1 µm

[Ref.: #43376]	Cell shape	rod-shaped

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5208]

Culture medium

THERMOTOGA PETROPHILA MEDIUM (DSMZ Medium 913)

[Ref.: #5208]

Culture medium growth

[Ref.: #5208]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5208]

Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #5208]		growth	80 °C
[Ref.: #43376]		growth	47-88 °C
[Ref.: #43376]	no	growth	89 °C
[Ref.: #43376]	no	growth	46 °C
[Ref.: #43376]		optimum	80 °C
[Ref.: #67770]		growth	80 °C

[Ref.: #5208]	Temperature range	hyperthermophilic
[Ref.: #43376]	Temperature range	hyperthermophilic
[Ref.: #43376]	Temperature range	thermophilic
[Ref.: #43376]	Temperature range	hyperthermophilic
[Ref.: #67770]	Temperature range	hyperthermophilic

	Kind of pH		pH
[Ref.: #43376]		optimum	7
[Ref.: #43376]		growth	5.2-9
[Ref.: #43376]	no	growth	5
[Ref.: #43376]	no	growth	9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5208]	Oxygen tolerance	anaerobe
[Ref.: #43376]	Oxygen tolerance	obligate anaerobe

[Ref.: #43376]

Nutrition type

heterotroph

	Salt	Tested relation		Salt conc.
[Ref.: #43376]	NaCl		growth	0.1-5.5	%
[Ref.: #43376]	NaCl		optimum	1	%
[Ref.: #43376]	NaCl	no	growth	0	%
[Ref.: #43376]	NaCl	no	growth	6	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43376]	arabinose ChEBI	+	carbon source
[Ref.: #43376]	arabinose ChEBI	+	energy source
[Ref.: #43376]	cellulose ChEBI	+	carbon source
[Ref.: #43376]	cellulose ChEBI	+	energy source
[Ref.: #43376]	elemental sulfur ChEBI	+	reduction
[Ref.: #43376]	fructose ChEBI	+	carbon source
[Ref.: #43376]	fructose ChEBI	+	energy source
[Ref.: #43376]	fructose ChEBI	+/-	growth
[Ref.: #43376]	galactose ChEBI	+	carbon source
[Ref.: #43376]	galactose ChEBI	+	energy source
[Ref.: #43376]	galactose ChEBI	+/-	growth
[Ref.: #43376]	glucose ChEBI	+	carbon source
[Ref.: #43376]	glucose ChEBI	+	energy source
[Ref.: #43376]	glucose ChEBI	+	fermentation
[Ref.: #43376]	glucose ChEBI	+/-	growth
[Ref.: #43376]	lactose ChEBI	+	growth
[Ref.: #43376]	lactose ChEBI	+	carbon source
[Ref.: #43376]	lactose ChEBI	+	energy source
[Ref.: #43376]	maltose ChEBI	+	growth
[Ref.: #43376]	maltose ChEBI	+	carbon source
[Ref.: #43376]	maltose ChEBI	+	energy source
[Ref.: #43376]	mannitol ChEBI	-	growth
[Ref.: #43376]	peptone	+	carbon source
[Ref.: #43376]	peptone	+	energy source
[Ref.: #43376]	ribose ChEBI	+	growth
[Ref.: #43376]	ribose ChEBI	+	carbon source
[Ref.: #43376]	ribose ChEBI	+	energy source
[Ref.: #43376]	starch ChEBI	+	growth
[Ref.: #43376]	starch ChEBI	+	carbon source
[Ref.: #43376]	starch ChEBI	+	energy source
[Ref.: #43376]	sucrose ChEBI	+	carbon source
[Ref.: #43376]	sucrose ChEBI	+	energy source
[Ref.: #43376]	sucrose ChEBI	+/-	growth
[Ref.: #43376]	thiosulfate ChEBI	+	reduction
[Ref.: #43376]	xylose ChEBI	-	growth
[Ref.: #43376]	yeast extract	+	carbon source
[Ref.: #43376]	yeast extract	+	energy source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration
[Ref.: #43376]	chloramphenicol ChEBI	yes	100	µg/mL
[Ref.: #43376]	rifampicin ChEBI	yes	100	µg/mL
[Ref.: #43376]	streptomycin ChEBI	yes	100	µg/mL
[Ref.: #43376]	vancomycin ChEBI	yes	100	µg/mL

	Metabolite	Production
[Ref.: #43376]	acetate ChEBI	yes
[Ref.: #43376]	carbon dioxide ChEBI	yes
[Ref.: #43376]	dihydrogen ChEBI	yes
[Ref.: #43376]	DL-lactate ChEBI	yes

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

[Ref.: #5208]	Sample type/isolated from	production fluid of an oil reservoir storage tank
[Ref.: #5208]	Geographic location (country and/or sea, region)	Niigata, Kubiki oil reservoir
[Ref.: #5208]	Country	Japan
[Ref.: #5208]	Country ISO 3 Code	JPN
[Ref.: #5208]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Oil reservoir near the coast of the Sea of Japan
[Ref.: #67770]	Geographic location (country and/or sea, region)	Niigata
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Oil reservoir
#Environmental	#Aquatic	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB027016 (>99% sequence identity) for Thermotoga from Microbeatlas

Aquatic Samples	246
Soil Samples	93
Animal Samples	428
Plant Samples	10
Total Samples	777

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

[Ref.: #5208]

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.: #5208]	Thermotoga sp. RKU-1 gene for 16S rRNA, partial sequence	AB027016	1482	ENA	390874 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Thermotoga petrophila RKU-1	GCA_000016785	complete	GenBank	390874 tax ID	*
[Ref.: #66792]	Thermotoga petrophila RKU-1	390874.12	complete	PATRIC	390874 tax ID	*
[Ref.: #66792]	Thermotoga petrophila RKU-1	640427150	complete	JGI IMG/M	390874 tax ID	*

[Ref.: #5208]	GC-content	46.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	46.8 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thermotoga petrophila RKU-1 RKU-1 NCBI: GCA_000016785.1
[Ref.: #69480]	motile	yes	85.716	no
[Ref.: #69480]	flagellated	no	88.667	no
[Ref.: #69480]	gram-positive	no	92.834	no
[Ref.: #69480]	anaerobic	yes	99.014	yes
[Ref.: #69480]	halophile	no	87.451	yes
[Ref.: #69480]	spore-forming	no	91.323	no
[Ref.: #69480]	glucose-util	yes	88.486	yes
[Ref.: #69480]	aerobic	no	97.772	yes
[Ref.: #69480]	thermophile	yes	100	no
[Ref.: #69480]	glucose-ferment	yes	53.831	no

Availability in culture collections External links

[Ref.: #5208]

Culture collection no.

DSM 13995, JCM 10881, ATCC BAA-488

[Ref.: #86068]

SI-ID 49543

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Biotechnology	Efficient production of inositol from glucose via a tri-enzymatic cascade pathway.	Wang J, Cheng H, Zhao Z, Zhang Y	Bioresour Technol	10.1016/j.biortech.2022.127125	2022	*
Phylogeny	A novel Thermotoga strain TFO isolated from a Californian petroleum reservoir phylogenetically related to Thermotoga petrophila and T. naphthophila, two thermophilic anaerobic isolates from a Japanese reservoir: Taxonomic and genomic considerations.	Summers ZM, Belahbib H, Pradel N, Bartoli M, Mishra P, Tamburini C, Dolla A, Ollivier B, Armougom F	Syst Appl Microbiol	10.1016/j.syapm.2020.126132	2020	*
Enzymology	Enhanced production, overexpression and characterization of a hyperthermophilic multimodular GH family 2 betaglucuronidase (TpGUS) cloned from Thermotoga petrophila RKU-1(T) in a mesophilic host.	Haq IU, Akram F	Int J Biol Macromol	10.1016/j.ijbiomac.2018.11.189	2018	*
Metabolism	Thermostable Recombinant Polypeptides as the Source of L-Amino Acids for Culture Media.	Grishin DV, Zhdanov DD, Gladilina YA, Podobed OV, Pokrovsky VS, Pokrovskaya MV, Aleksandrova SS, Sokolov NN	Bull Exp Biol Med	10.1007/s10517-018-4194-7	2018	*
Metabolism	[Comparison of three different thermophilic beta-glucosidases for baicalin transformation].	Wu T, Zhang SS, Pei JJ, Xiao W, Wang ZZ, Zhao LG	Zhongguo Zhong Yao Za Zhi	10.19540/j.cnki.cjcmm.20180201.002	2018	*
Enzymology	Thermodynamic and saccharification analysis of cloned GH12 endo-1,4-beta-glucanase from Thermotoga petrophila in a mesophilic host.	Ul Haq I, Muneer B, Hussain Z, Khan MA, Afzal S, Majeed S, Akram F, Akmal S	Protein Pept Lett	10.2174/0929866522666150630105035	2015	*
Metabolism	Overexpression and characterization of a Ca(2+) activated thermostable beta-glucosidase with high ginsenoside Rb1 to ginsenoside 20(S)-Rg3 bioconversion productivity.	Xie J, Zhao D, Zhao L, Pei J, Xiao W, Ding G, Wang Z	J Ind Microbiol Biotechnol	10.1007/s10295-015-1608-7	2015	*
Enzymology	Cloning, characterization and molecular docking of a highly thermostable beta-1,4-glucosidase from Thermotoga petrophila.	Haq IU, Khan MA, Muneer B, Hussain Z, Afzal S, Majeed S, Rashid N, Javed MM, Ahmad I	Biotechnol Lett	10.1007/s10529-012-0953-0	2012	*
Enzymology	Structure of a novel thermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila RKU-1.	Souza TA, Santos CR, Souza AR, Oldiges DP, Ruller R, Prade RA, Squina FM, Murakami MT	Protein Sci	10.1002/pro.693	2011	*
Enzymology	Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1.	Santos CR, Meza AN, Hoffmam ZB, Silva JC, Alvarez TM, Ruller R, Giesel GM, Verli H, Squina FM, Prade RA, Murakami MT	Biochem Biophys Res Commun	10.1016/j.bbrc.2010.11.010	2010	*
Enzymology	Functional and biophysical characterization of a hyperthermostable GH51 alpha-L-arabinofuranosidase from Thermotoga petrophila.	dos Santos CR, Squina FM, Navarro AM, Oldiges DP, Paes Leme AF, Ruller R, Mort AJ, Prade R, Murakami MT	Biotechnol Lett	10.1007/s10529-010-0409-3	2010	*
Enzymology	Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of the catalytic domain of a hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1.	Santos CR, Squina FM, Navarro AM, Ruller R, Prade R, Murakami MT	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309110029131	2010	*
Phylogeny	Thermotoga petrophila sp. nov. and Thermotoga naphthophila sp. nov., two hyperthermophilic bacteria from the Kubiki oil reservoir in Niigata, Japan.	Takahata Y, Nishijima M, Hoaki T, Maruyama T	Int J Syst Evol Microbiol	10.1099/00207713-51-5-1901	2001	*
	[Construction and characterization of a recombinant mutant homolog of the CheW protein from Thermotoga petrophila RKU-1].	Grishin DV, Zhdanov DD, Gladilina JA, Pokrovsky VS, Podobed OV, Pokrovskaya MV, Aleksandrova SS, Milyushkina AL, Vigovskiy MA, Sokolov NN	Biomed Khim	10.18097/PBMC20186401053	2018	*
	Computer-Aided Design of alpha-L-Rhamnosidase to Increase the Synthesis Efficiency of Icariside I.	Huang JJ, Hu HX, Lu YJ, Bao YD, Zhou JL, Huang M	Front Bioeng Biotechnol	10.3389/fbioe.2022.926829	2022	*

References

#5208

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13995

#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 )

#43376

Yoh Takahata, Miyuki Nishijima, Toshihiro Hoaki, Tadashi Maruyama: Thermotoga petrophila sp. nov. and Thermotoga naphthophila sp. nov., two hyperthermophilic bacteria from the Kubiki oil reservoir in Niigata, Japan.. IJSEM 51: 1901 - 1909 2001 ( DOI 10.1099/00207713-51-5-1901 , PubMed 11594624 )

#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 .

#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) .

#86068

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-ID49543.1 )

* These data were automatically processed and therefore are not curated

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Thermotoga petrophila RKU-1 RKU-1

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