Pyrococcus horikoshii (DSM 12428, JCM 9974, NBRC 100139)

Name: Pyrococcus horikoshii (DSM 12428, JCM 9974, NBRC 100139)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16857

Type strain

Strain Designation OT-3

Culture col. no. DSM 12428 JCM 9974 NBRC 100139 OT-3

NCBI tax ID(s) 53953

Special Collections DSMZ JCM

History DSMZ <- JCM <- C. Kato, Japan Marine Science and Technology Center, Yokosuka, Japan <- F. T. Robb, University of Maryland Biotechnology Institute, Baltimore MD, USA; OT-3 {1992} JCM <-- C. Kato <-- F. Robb OT-3.

Links

Pyrococcus horikoshii OT-3 is an anaerobe archaeon that was isolated from marine hydrothermal vent at 1395 m depth.

anaerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 44181

ATCC 700860,JCM 9974,DSM 12428,NBRC 100139

@ref 20215

Last LPSN update 2026-05-29 08:28:52

Domain Archaea

Phylum Methanobacteriota

Class Thermococci

Order Thermococcales

Family Thermococcaceae

Genus Pyrococcus

Species Pyrococcus horikoshii

Full scientific name Pyrococcus horikoshii González et al. 1999

BacDive ID	Other strains from **Pyrococcus horikoshii** (1)	Type strain
16858	P. horikoshii JA-1, DSM 13347, JCM 9975

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4716	PYROCOCCUS MEDIUM (DSMZ Medium 377)		Medium recipe at MediaDive	Name: PYROCOCCUS MEDIUM (DSMZ Medium 377) Composition: Sulfur 30.0 g/l Peptone 5.0 g/l MgCl2 x 6 H2O 2.75 g/l Yeast extract 1.0 g/l KH2PO4 0.5 g/l Na2S x 9 H2O 0.5 g/l KCl 0.33 g/l NaBr 0.05 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l (NH4)2SO4 0.01 g/l SrCl2 x 6 H2O 0.007 g/l Citric acid 0.005 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l CuSO4 x 5 H2O 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l KI 5e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
4716	positive	growth	95
67770	positive	growth	95

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4716	anaerobe
125439	anaerobe	99.728

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
4716	marine hydrothermal vent at 1395 m depth	Pacific Ocean, Okinawa Trough	Japan	JPN	Asia	27.55	126.933 27.55/126.933
67770	Hydrothermal vent at the Okinawa Trough

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4716	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
67770	ASM1110v1 assembly for Pyrococcus horikoshii OT3	complete	GCA_000011105	70601.8	2923400019	70601	98.28

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Pyrococcus horikoshii strain DSM 12428 16S ribosomal RNA gene, partial sequence	AY099169	1454		53953
20218	Pyrococcus horikoshii strain DSM 12428 16S-23S ribosomal RNA intergenic spacer region, complete sequence	AY099205	190		53953

GC content

@ref	GC-content (mol%)	Method
4716	41	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1110v1 assembly for Pyrococcus horikoshii OT3
NCBI: GCA_000011105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.73	no
125439	gram_stain	BacteriaNetⓘ	positive	58.19	no
125439	motility	BacteriaNetⓘ	yes	45.14	no
125439	spore_formation	BacteriaNetⓘ	no	66.94	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Comprehensive mutagenesis to identify amino acid residues contributing to the difference in thermostability between two originally thermostable ancestral proteins.	Akanuma S, Yamaguchi M, Yamagishi A.	PLoS One	10.1371/journal.pone.0258821	2021
	Extremophilic 50S Ribosomal RNA-Binding Protein L35Ae as a Basis for Engineering of an Alternative Protein Scaffold.	Lomonosova AV, Ovchinnikova EV, Kazakov AS, Denesyuk AI, Sofin AD, Mikhailov RV, Ulitin AB, Mirzabekov TA, Permyakov EA, Permyakov SE.	PLoS One	10.1371/journal.pone.0134906	2015
Enzymology	Purification and crystallization of the entire recombinant subunit E of the energy producer A(1)A(o) ATP synthase.	Balakrishna AM, Hunke C, Gruber G.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309110001016	2010
Enzymology	Characterization of quinolinate synthases from Escherichia coli, Mycobacterium tuberculosis, and Pyrococcus horikoshii indicates that [4Fe-4S] clusters are common cofactors throughout this class of enzymes.	Saunders AH, Griffiths AE, Lee KH, Cicchillo RM, Tu L, Stromberg JA, Krebs C, Booker SJ.	Biochemistry	10.1021/bi801268f	2008
Metabolism	Polysaccharide-degrading thermophiles generated by heterologous gene expression in Geobacillus kaustophilus HTA426.	Suzuki H, Yoshida K, Ohshima T.	Appl Environ Microbiol	10.1128/aem.01506-13	2013
	A Novel PLP-Dependent Alanine/Serine Racemase From the Hyperthermophilic Archaeon Pyrococcus horikoshii OT-3.	Kawakami R, Ohshida T, Sakuraba H, Ohshima T	Front Microbiol	10.3389/fmicb.2018.01481	2018
Metabolism	Crystal structure of a novel type of ornithine delta-aminotransferase from the hyperthermophilic archaeon Pyrococcus horikoshii.	Kawakami R, Ohshida T, Hayashi J, Yoneda K, Furumoto T, Ohshima T, Sakuraba H	Int J Biol Macromol	10.1016/j.ijbiomac.2022.03.114	2022
Metabolism	First characterization of an archaeal amino acid racemase with broad substrate specificity from the hyperthermophile Pyrococcus horikoshii OT-3.	Kawakami R, Sakuraba H, Ohmori T, Ohshima T	J Biosci Bioeng	10.1016/j.jbiosc.2017.02.004	2017
Metabolism	Identification of a novel amino acid racemase from a hyperthermophilic archaeon Pyrococcus horikoshii OT-3 induced by D-amino acids.	Kawakami R, Ohmori T, Sakuraba H, Ohshima T	Amino Acids	10.1007/s00726-015-2001-6	2015
Enzymology	Comparative analysis of the catalytic components in the archaeal dye-linked L-proline dehydrogenase complexes.	Kawakami R, Noguchi C, Higashi M, Sakuraba H, Ohshima T	Appl Microbiol Biotechnol	10.1007/s00253-012-4201-2	2012
Enzymology	A second novel dye-linked L-proline dehydrogenase complex is present in the hyperthermophilic archaeon Pyrococcus horikoshii OT-3.	Kawakami R, Sakuraba H, Tsuge H, Goda S, Katunuma N, Ohshima T	FEBS J	10.1111/j.1742-4658.2005.04810.x	2005
Enzymology	Oxidative stress response in an anaerobic hyperthermophilic archaeon: presence of a functional peroxiredoxin in Pyrococcus horikoshii.	Kawakami R, Sakuraba H, Kamohara S, Goda S, Kawarabayasi Y, Ohshima T	J Biochem	10.1093/jb/mvh157	2004
Enzymology	L-aspartate oxidase is present in the anaerobic hyperthermophilic archaeon Pyrococcus horikoshii OT-3: characteristics and role in the de novo biosynthesis of nicotinamide adenine dinucleotide proposed by genome sequencing.	Sakuraba H, Satomura T, Kawakami R, Yamamoto S, Kawarabayasi Y, Kikuchi H, Ohshima T	Extremophiles	10.1007/s00792-001-0254-3	2002

References

#4716	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12428
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Pyrococcus horikoshii (DSM 12428, JCM 9974, NBRC 100139)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000011105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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