Cite this strain

Thermococcus pacificus (DSM 10394, ATCC 700653, JCM 10553)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 16871

Type strain

Strain Designation P-4

Culture col. no. DSM 10394 ATCC 700653 JCM 10553 P-4

NCBI tax ID(s) 71998

Special Collections DSMZ JCM

Links

Name and taxonomic classification

Thermococcus pacificus P-4 is an anaerobe, hyperthermophilic archaeon that was isolated from bottom deposits.

anaerobe hyperthermophilic genome sequence 16S sequence Archaea

SI-ID 44059

ATCC 700653, DSM 10394, JCM 10553

Last LPSN update 2024-12-09 10:44:58

Domain Archaea

Phylum Methanobacteriota

Class Thermococci

Order Thermococcales

Family Thermococcaceae

Genus Thermococcus

Species Thermococcus pacificus

Full scientific name Thermococcus pacificus Miroshnichenko et al. 1998

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	94

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3929	MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760)		Medium recipe at MediaDive	Name: MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3929	positive	growth	85	hyperthermophilic
67770	positive	growth	85	hyperthermophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		91.3
125438		92.604

Oxygen tolerance

@ref	Oxygen tolerance
3929	anaerobe
125439	anaerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3929	bottom deposits	Bay of Plenty	New Zealand	NZL	Australia and Oceania
67770	Geothermally heated bottom deposits of the Bay of Plenty		New Zealand	NZL	Australia and Oceania

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
3929	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
67770	53.3	thermal denaturation, midpoint method (Tm)

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Thermococcus pacificus 16S rRNA gene, strain DSM 10394 Type	AJ291811	1314	71998
20218	Thermococcus pacificus strain DSM 10394 16S ribosomal RNA gene, partial sequence	AY099182	1436	71998
20218	Thermococcus pacificus strain DSM 10394 16S-23S ribosomal RNA intergenic spacer region, complete sequence	AY099218	181	71998
20218	Thermococcus pacificus gene for 16S rRNA, partial sequence, strain:JCM 10553	AB055124	1421	71998
3929	Thermococcus pacificus 16S rRNA gene	Y16227	1335	71998

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Thermococcus pacificus P-4	GCA_002214485	complete		71998
66792	Thermococcus pacificus P-4	2758568025	complete	JGI IMG/M	71998

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Thermococcus pacificus P-4
NCBI: GCA_002214485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.30	no
125439	motility	BacteriaNetⓘ	no	66.80	no
125439	gram_stain	BacteriaNetⓘ	negative	94.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.80	no

Predictions from Diaspora project based on:
Thermococcus pacificus P-4
NCBI: GCA_002214485.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	67.39	no
125438	anaerobic	anaerobicⓘ	yes	87.13	yes
125438	aerobic	aerobicⓘ	no	87.16	yes
125438	spore-forming	spore-formingⓘ	no	92.60	no
125438	thermophilic	thermophileⓘ	yes	78.23	no
125438	flagellated	motile2+ⓘ	no	80.96	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Thermococcus gorgonarius sp. nov. and Thermococcus pacificus sp. nov.: heterotrophic extremely thermophilic archaea from New Zealand submarine hot vents.	Miroshnichenko ML, Gongadze GM, Rainey FA, Kostyukova AS, Lysenko AM, Chernyh NA, Bonch-Osmolovskaya EA	Int J Syst Bacteriol	10.1099/00207713-48-1-23	1998

Straininfo Link

@ref	Straininfo	Culture collections
85879	44059	ATCC 700653, DSM 10394, JCM 10553

Culture collection no.

Culture collection no.
DSM 10394
ATCC 700653
JCM 10553
P-4

References

#3929	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10394
#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 )
#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;
#85879	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-ID44059.1 )
#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 .

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