Thermotoga petrophila (DSM 13995, JCM 10881, RKU-1)

Name: Thermotoga petrophila (DSM 13995, JCM 10881, RKU-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17068

Type strain

Strain Designation RKU-1

Culture col. no. DSM 13995 JCM 10881 RKU-1 ATCC BAA-488

NCBI tax ID(s) 93929

Special Collections DSMZ JCM Literature strains

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

rod-shaped anaerobe heterotroph hyperthermophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 49543

DSM 13995,JCM 10881,ATCC BAA-488

@ref 20215

Last LPSN update 2025-12-16 09:51:00

Domain Thermotogati

Phylum Thermotogota

Class Thermotogae

Order Thermotogales

Family Thermotogaceae

Genus Thermotoga

Species Thermotoga petrophila

Full scientific name Thermotoga petrophila Takahata et al. 2001

Synonyms (1)

Thermotoga naphthophila

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape
43376	2-7 µm	0.7-1 µm	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5208	THERMOTOGA PETROPHILA MEDIUM (DSMZ Medium 913)		Medium recipe at MediaDive	Name: THERMOTOGA PETROPHILA MEDIUM (DSMZ Medium 913) Composition: MOPS 4.99501 g/l MgCl2 x 6 H2O 4.12088 g/l Yeast extract 1.998 g/l (NH4)2SO4 0.999001 g/l KH2PO4 0.499501 g/l KCl 0.487013 g/l Na2S x 9 H2O 0.2997 g/l NaBr 0.0749251 g/l MgSO4 x 7 H2O 0.02997 g/l Nitrilotriacetic acid 0.014985 g/l SrCl2 x 6 H2O 0.0112388 g/l NaCl 0.00999001 g/l Citric acid 0.00749251 g/l MnSO4 x H2O 0.00499501 g/l CoSO4 x 7 H2O 0.0017982 g/l ZnSO4 x 7 H2O 0.0017982 g/l CaCl2 x 2 H2O 0.000999001 g/l FeSO4 x 7 H2O 0.000999001 g/l Sodium resazurin 0.0004995 g/l NiCl2 x 6 H2O 0.0002997 g/l AlK(SO4)2 x 12 H2O 0.0001998 g/l H3BO3 9.99001e-05 g/l CuSO4 x 5 H2O 9.99001e-05 g/l Na2MoO4 x 2 H2O 9.99001e-05 g/l Pyridoxine hydrochloride 9.99001e-05 g/l Calcium D-(+)-pantothenate 4.995e-05 g/l p-Aminobenzoic acid 4.995e-05 g/l Nicotinic acid 4.995e-05 g/l Riboflavin 4.995e-05 g/l Thiamine HCl 4.995e-05 g/l (DL)-alpha-Lipoic acid 4.995e-05 g/l KI 3.74625e-05 g/l Folic acid 1.998e-05 g/l Biotin 1.998e-05 g/l Na2WO4 x 2 H2O 3.996e-06 g/l Na2SeO3 x 5 H2O 2.997e-06 g/l Vitamin B12 9.99001e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5208	positive	growth	80	hyperthermophilic
43376	positive	growth	47-88	hyperthermophilic
43376	negative	growth	89
43376	negative	growth	46
43376	positive	optimum	80	hyperthermophilic
67770	positive	growth	80	hyperthermophilic

Culture pH

@ref	Ability	Type	PH
43376	positive	optimum	7
43376	positive	growth	5.2-9
43376		growth	5
43376		growth	9.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
5208	anaerobe
43376	obligate anaerobe
125438	anaerobe
125439	anaerobe

Nutrition type

43376

Typeheterotroph

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43376	NaCl	positive	growth	0.1-5.5 %
43376	NaCl	positive	optimum	1 %
43376	NaCl		growth	0 %
43376	NaCl		growth	6 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43376	22599 ChEBI	arabinose	+	carbon source
43376	22599 ChEBI	arabinose	+	energy source
43376	62968 ChEBI	cellulose	+	carbon source
43376	62968 ChEBI	cellulose	+	energy source
43376	33403 ChEBI	elemental sulfur	+	reduction
43376	28757 ChEBI	fructose	+	carbon source
43376	28757 ChEBI	fructose	+	energy source
43376	28757 ChEBI	fructose	+/-	growth
43376	28260 ChEBI	galactose	+	carbon source
43376	28260 ChEBI	galactose	+	energy source
43376	28260 ChEBI	galactose	+/-	growth
43376	17234 ChEBI	glucose	+	carbon source
43376	17234 ChEBI	glucose	+	energy source
43376	17234 ChEBI	glucose	+	fermentation
43376	17234 ChEBI	glucose	+/-	growth
43376	17716 ChEBI	lactose	+	growth
43376	17716 ChEBI	lactose	+	carbon source
43376	17716 ChEBI	lactose	+	energy source
43376	17306 ChEBI	maltose	+	growth
43376	17306 ChEBI	maltose	+	carbon source
43376	17306 ChEBI	maltose	+	energy source
43376	29864 ChEBI	mannitol	-	growth
43376		peptone	+	carbon source
43376		peptone	+	energy source
43376	33942 ChEBI	ribose	+	growth
43376	33942 ChEBI	ribose	+	carbon source
43376	33942 ChEBI	ribose	+	energy source
43376	28017 ChEBI	starch	+	growth
43376	28017 ChEBI	starch	+	carbon source
43376	28017 ChEBI	starch	+	energy source
43376	17992 ChEBI	sucrose	+	carbon source
43376	17992 ChEBI	sucrose	+	energy source
43376	17992 ChEBI	sucrose	+/-	growth
43376	16094 ChEBI	thiosulfate	+	reduction
43376	18222 ChEBI	xylose	-	growth
43376		yeast extract	+	carbon source
43376		yeast extract	+	energy source

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.
43376	17698	chloramphenicol	100 µg/mL
43376	28077	rifampicin	100 µg/mL
43376	17076	streptomycin	100 µg/mL
43376	28001	vancomycin	100 µg/mL

Metabolite production

@ref	Chebi-ID	Metabolite
43376	30089 ChEBI	acetate
43376	16526 ChEBI	carbon dioxide
43376	18276 ChEBI	dihydrogen
43376	24996 ChEBI	DL-lactate

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Oil reservoir
#Environmental	#Aquatic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5208	production fluid of an oil reservoir storage tank	Niigata, Kubiki oil reservoir	Japan	JPN	Asia
67770	Oil reservoir near the coast of the Sea of Japan	Niigata	Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5208	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	ASM1678v1 assembly for Thermotoga petrophila RKU-1	complete	GCA_000016785	390874.12	640427150	390874	99.47

Genome browser: GCA_000016785

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5208	Thermotoga petrophila RKU-1 gene for 16S rRNA, partial sequence	AB027016	1482		390874

GC content

@ref	GC-content (mol%)	Method
5208	46.6	high performance liquid chromatography (HPLC)
67770	46.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thermotoga petrophila RKU-1
PATRIC: 390874.12

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	63.40	no
125439	motility	BacteriaNetⓘ	no	61.70	no
125439	gram_stain	BacteriaNetⓘ	variable	66.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thermotoga petrophila RKU-1 RKU-1
NCBI: GCA_000016785.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	62.48	no
125438	anaerobic	anaerobicⓘ	yes	90.84	yes
125438	aerobic	aerobicⓘ	no	93.48	yes
125438	spore-forming	spore-formingⓘ	no	71.10	no
125438	thermophilic	thermophileⓘ	yes	79.71	yes
125438	flagellated	motile2+ⓘ	yes	59.37	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Characterization of a novel thermostable and xylose-tolerant GH 39 beta-xylosidase from Dictyoglomus thermophilum.	Li Q, Wu T, Qi Z, Zhao L, Pei J, Tang F.	BMC Biotechnol	10.1186/s12896-018-0440-3	2018
Metabolism	Immobilization of GH78 alpha-L-Rhamnosidase from Thermotoga petrophilea with High-Temperature-Resistant Magnetic Particles Fe₃O₄-SiO₂-NH₂-Cellu-ZIF8 and Its Application in the Production of Prunin Form Naringin.	Xu J, Shi X, Zhang X, Wang Z, Xiao W, Zhao L.	J Microbiol Biotechnol	10.4014/jmb.2004.04055	2021
	Highly Efficient Biotransformation of Notoginsenoside R1 into Ginsenoside Rg1 by Dictyoglomus thermophilum beta-xylosidase Xln-DT.	Li Q, Wang L, Fang X, Zhao L.	J Microbiol Biotechnol	10.4014/jmb.2111.11020	2022
	Purification and Characterization of a Novel alpha-L-Rhamnosidase from Papiliotrema laurentii ZJU-L07 and Its Application in Production of Icariin from Epimedin C.	Lou H, Liu X, Liu S, Chen Q.	J Fungi (Basel)	10.3390/jof8060644	2022
	beta-Glucosidase and Its Application in Bioconversion of Ginsenosides in Panax ginseng.	Tran TNA, Son JS, Awais M, Ko JH, Yang DC, Jung SK.	Bioengineering (Basel)	10.3390/bioengineering10040484	2023
	Antitumor, antioxidant and anti-inflammatory activities of kaempferol and its corresponding glycosides and the enzymatic preparation of kaempferol.	Wang J, Fang X, Ge L, Cao F, Zhao L, Wang Z, Xiao W.	PLoS One	10.1371/journal.pone.0197563	2018
Metabolism	Ligands of thermophilic ABC transporters encoded in a newly sequenced genomic region of Thermotoga maritima MSB8 screened by differential scanning fluorimetry.	Boucher N, Noll KM.	Appl Environ Microbiol	10.1128/aem.05418-11	2011
	beta-Xylosidases: Structural Diversity, Catalytic Mechanism, and Inhibition by Monosaccharides.	Rohman A, Dijkstra BW, Puspaningsih NNT.	Int J Mol Sci	10.3390/ijms20225524	2019
	Global Association between Thermophilicity and Vancomycin Susceptibility in Bacteria.	Roy C, Alam M, Mandal S, Haldar PK, Bhattacharya S, Mukherjee T, Roy R, Rameez MJ, Misra AK, Chakraborty R, Nanda AK, Mukhopadhyay SK, Ghosh W.	Front Microbiol	10.3389/fmicb.2016.00412	2016
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
	[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
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
	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
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

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 .
#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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Thermotoga petrophila (DSM 13995, JCM 10881, RKU-1)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000016785

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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