Name: Thermococcus pacificus P-4
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16871

Type strain:

Species: Thermococcus pacificus

Strain Designation: P-4

Culture col. no.: DSM 10394, ATCC 700653, JCM 10553

Strain history: DSM 10394 <-- E. A. Bonch-Osmolovskaya P-4.

NCBI tax ID(s): 71998 (species)

SI-ID 44059

ATCC 700653, DSM 10394, JCM 10553

Special Collections

DSMZ
JCM

Section

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

Gram-negative
anaerobe
16S sequence
Archaea
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Archaea"
	Phylum	*Methanobacteriota*
	Class	*Thermococci*
	Order	*Thermococcales*
	Family	*Thermococcaceae*
	Genus	*Thermococcus*
	Species	**Thermococcus pacificus**
	Full Scientific Name (LPSN)	Thermococcus pacificus Miroshnichenko et al. 1998

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3929]

Culture medium

MARINE THERMOCOCCUS MEDIUM (DSMZ Medium 760)

[Ref.: #3929]

Culture medium growth

[Ref.: #3929]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3929]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3929]			growth	85 °C
[Ref.: #67770]			growth	85 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3929]

Oxygen tolerance

anaerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %92.604
[Ref.: #69481]	Ability of spore formation	no Confidence in %98

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

[Ref.: #3929]	Sample type/isolated from	bottom deposits
[Ref.: #3929]	Geographic location (country and/or sea, region)	Bay of Plenty
[Ref.: #3929]	Country	New Zealand
[Ref.: #3929]	Country ISO 3 Code	NZL
[Ref.: #3929]	Continent	Australia and Oceania

[Ref.: #67770]	Sample type/isolated from	Geothermally heated bottom deposits of the Bay of Plenty
[Ref.: #67770]	Country	New Zealand
[Ref.: #67770]	Country ISO 3 Code	NZL
[Ref.: #67770]	Continent	Australia and Oceania
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

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

[Ref.: #3929]

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.: #3929]	Thermococcus pacificus 16S rRNA gene	Y16227	1335	GenBank ENA	71998 tax ID
[Ref.: #20218]	Thermococcus pacificus 16S rRNA gene, strain DSM 10394 Type	AJ291811	1314	GenBank ENA	71998 tax ID	*
[Ref.: #20218]	Thermococcus pacificus strain DSM 10394 16S ribosomal RNA gene, partial sequence	AY099182	1436	GenBank ENA	71998 tax ID	*
[Ref.: #20218]	Thermococcus pacificus strain DSM 10394 16S-23S ribosomal RNA intergenic spacer region, complete sequence	AY099218	181	GenBank ENA	71998 tax ID	*
[Ref.: #20218]	Thermococcus pacificus gene for 16S rRNA, partial sequence, strain:JCM 10553	AB055124	1421	GenBank ENA	71998 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Thermococcus pacificus P-4	GCA_002214485	complete	GenBank ENA	71998 tax ID	*
[Ref.: #66792]	Thermococcus pacificus P-4	2758568025	complete	JGI IMG/M	71998 tax ID	*

[Ref.: #67770]

GC-content

53.3 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Thermococcus pacificus P-4 NCBI: GCA_002214485.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	98	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thermococcus pacificus P-4 NCBI: GCA_002214485.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	67.385	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	87.13	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	87.162	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.604	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	78.232	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	80.958	no

Availability in culture collections External links

[Ref.: #3929]

Culture collection no.

DSM 10394, ATCC 700653, JCM 10553

[Ref.: #85879]

SI-ID 44059

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	*

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;

#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 )

#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 )

* These data were automatically processed and therefore are not curated

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