Name: Psychrobacter pacificensis DSM 23406
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 8205

Type strain:

Species: Psychrobacter pacificensis

Culture col. no.: DSM 23406, NBRC 103191, NIBH P2K6, CIP 110991, NIBH P2K16

Strain history: CIP <- 2015, DSMZ <- A. Maruyama, AIST <- IFO <- A. Maruyama, Res. Inst. Genome-based BIofactory, Sapporo, Japan: strain NIBH P2K16

NCBI tax ID(s): 112002 (species)

SI-ID 62368

IFO 16270, NBRC 103191

Section

Psychrobacter pacificensis DSM 23406 is a mesophilic bacterium that was isolated from Seawater from a depth of 6000 m.

mesophilic
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Pseudomonadales*
	Family	*Moraxellaceae*
	Genus	*Psychrobacter*
	Species	**Psychrobacter pacificensis**
	Full Scientific Name (LPSN)	Psychrobacter pacificensis Maruyama et al. 2000

Information on morphological and physiological properties Morphology

[Ref.: #121502]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.976

[Ref.: #121502]	Cell shape	rod-shaped

[Ref.: #121502]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %96.203

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16848]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #16848]

Culture medium growth

[Ref.: #16848]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16848]

Culture medium composition

expand / minimize

[Ref.: #36201]

Culture medium

Marine agar (MA)

[Ref.: #36201]

Culture medium growth

[Ref.: #36201]

Culture medium composition

expand / minimize

[Ref.: #121502]

Culture medium

CIP Medium 13

[Ref.: #121502]

Culture medium growth

[Ref.: #121502]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #16848]			growth	28 °C
[Ref.: #36201]			growth	30 °C

[Ref.: #16848]	Temperature range	mesophilic
[Ref.: #36201]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

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

[Ref.: #16848]	Sample type/isolated from	Seawater from a depth of 6000 m
[Ref.: #16848]	Country	Japan
[Ref.: #16848]	Country ISO 3 Code	JPN
[Ref.: #16848]	Continent	Asia

[Ref.: #121502]	Sample type/isolated from	Environment, Seawater from a depth of 6000 m
[Ref.: #121502]	Country	Japan
[Ref.: #121502]	Country ISO 3 Code	JPN
[Ref.: #121502]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Core sample

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681982 (>99% sequence identity) for Psychrobacter pacificensis subclade from Microbeatlas

Aquatic Samples	2631
Soil Samples	90
Animal Samples	395
Plant Samples	6
Total Samples	3122

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

[Ref.: #16848]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121502]	Biosafety level	1	Risk group (French classification)

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.: #20218]	Psychrobacter pacificensis DNA for 16S rRNA, partial sequence, strain:NIBH P2K6(T)(=IFO 16279(T))	AB016057	1526	ENA	112002 tax ID	*
[Ref.: #20218]	Psychrobacter pacificensis gene for 16S rRNA, partial sequence, strain: NBRC 103191	AB681982	1464	ENA	112002 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Psychrobacter pacificensis DSM 23406	GCA_900101915	scaffold	GenBank	112002 tax ID	*
[Ref.: #66792]	Psychrobacter pacificensis strain DSM 23406	112002.5	wgs	PATRIC	112002 tax ID	*
[Ref.: #66792]	Psychrobacter pacificensis DSM 23406	2599185216	draft	JGI IMG/M	112002 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Psychrobacter pacificensis DSM 23406 NCBI: GCA_900101915.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Psychrobacter pacificensis DSM 23406 NCBI: GCA_900101915.1
[Ref.: #69480]	motile	no	88.034	no
[Ref.: #69480]	flagellated	no	88.354	no
[Ref.: #69480]	gram-positive	no	98.15	no
[Ref.: #69480]	anaerobic	no	98.629	no
[Ref.: #69480]	aerobic	yes	84.368	no
[Ref.: #69480]	halophile	yes	84.071	no
[Ref.: #69480]	spore-forming	no	96.887	no
[Ref.: #69480]	glucose-ferment	no	93.042	no
[Ref.: #69480]	thermophile	no	99.254	yes
[Ref.: #69480]	glucose-util	yes	50.723	no

Availability in culture collections External links

[Ref.: #16848]

Culture collection no.

DSM 23406, NBRC 103191, NIBH P2K6, CIP 110991, NIBH P2K16

[Ref.: #77608]

SI-ID 62368

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Psychrobacter pocilloporae sp. nov., isolated from a coral, Pocillopora eydouxi.	Zachariah S, Kumari P, Das SK	Int J Syst Evol Microbiol	10.1099/ijsem.0.001476	2016	*
Phylogeny	Psychrobacter oceani sp. nov., isolated from marine sediment.	Matsuyama H, Minami H, Sakaki T, Kasahara H, Watanabe A, Onoda T, Hirota K, Yumoto I	Int J Syst Evol Microbiol	10.1099/ijs.0.000118	2015	*
Phylogeny	Psychrobacter aestuarii sp. nov., isolated from a tidal flat sediment.	Baik KS, Park SC, Lim CH, Lee KH, Jeon DY, Kim CM, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.016782-0	2009	*
Phylogeny	Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov.	Maruyama A, Honda D, Yamamoto H, Kitamura K, Higashihara T	Int J Syst Evol Microbiol	10.1099/00207713-50-2-835	2000	*

References

#16848

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23406

#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 )

#36201 ; Curators of the CIP;

#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) .

#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) .

#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 )

#77608

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-ID62368.1 )

#121502 Collection of Institut Pasteur ; Curators of the CIP; CIP 110991
* These data were automatically processed and therefore are not curated

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