Archive BacDiveID:10.13145/bacdive8194.20221219.7.1

Strain identifier

BacDive ID: 8194

Type strain:

Species: Psychrobacter cibarius

Strain Designation: JG-219

Strain history: <- J.H. Yoon

NCBI tax ID(s): 282669 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 6369

BacDive-ID: 8194

DSM-Number: 16327

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Psychrobacter cibarius JG-219 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from jeotgal, a traditional Korean fermented seafood.

NCBI tax id

NCBI tax id: 282669
Matching level: species

strain history

doi: 10.13145/bacdive8194.20221219.7.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Pseudomonadales
family: Moraxellaceae
genus: Psychrobacter
species: Psychrobacter cibarius
full scientific name: Psychrobacter cibarius Jung et al. 2005

@ref: 6369

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Moraxellaceae

genus: Psychrobacter

species: Psychrobacter cibarius

full scientific name: Psychrobacter cibarius Jung et al. 2005

strain designation: JG-219

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell shape	motility	confidence
31359	negative	rod-shaped	no
67771	negative
69480	positive			94.481

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
6369	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	yes	https://mediadive.dsmz.de/medium/514	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) 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
41750	Marine agar (MA)	yes		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)

culture temp

@ref	growth	type	temperature	range
6369	positive	growth	30	mesophilic
31359	positive	growth	04-32
31359	positive	optimum	27.5	mesophilic
41750	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

culture pH

@ref	ability	type	pH
31359	positive	growth	05-08
31359	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
31359	aerobe
67771	aerobe

spore formation

@ref: 69480
spore formation: no
confidence: 98.663

halophily

@ref	salt	growth	tested relation	concentration	halophily level	confidence
31359	NaCl	positive	growth	<11 %
31359	NaCl	positive	optimum	3.5 %
69480					non-halophilic	90.838

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
31359	30089	acetate	+	carbon source
31359	16449	alanine	+	carbon source
31359	25115	malate	+	carbon source
31359	15361	pyruvate	+	carbon source
31359	17822	serine	+	carbon source
31359	30031	succinate	+	carbon source
31359	53426	tween 80	+	carbon source
31359	17632	nitrate	+	reduction

enzymes

@ref: 31359
value: alkaline phosphatase
activity: +
ec: 3.1.3.1

Isolation, sampling and environmental information

isolation

@ref	sample type	country	origin.country	continent
6369	jeotgal, a traditional Korean fermented seafood	Republic of Korea	KOR	Asia
67771	From Jeotgal, a traditional Korean fermented seafood	Republic of Korea	KOR	Asia

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Seafood
#Engineered	#Food production	#Fermented

taxonmaps

@ref: 69479
File name: preview.99_279.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_80;96_193;97_209;98_234;99_279&stattab=map
Last taxonomy: Psychrobacter
16S sequence: AY639871
Sequence Identity:
Total samples: 7634
soil counts: 925
aquatic counts: 3187
animal counts: 3350
plant counts: 172

Safety information

risk assessment

@ref: 6369
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 6369
description: Psychrobacter cibarius strain JG-219 16S ribosomal RNA gene, partial sequence
accession: AY639871
length: 1494
database: ena
NCBI tax ID: 282669

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Psychrobacter cibarius DSM 16327	GCA_016107535	contig	ncbi	282669
66792	Psychrobacter cibarius strain DSM 16327	282669.8	wgs	patric	282669
66792	Salmonella enterica subsp. enterica serovar Newport NY_FSL S10-1060	GCA_002107465	contig	patric	108619

GC content

@ref: 6369
GC-content: 43.5

External links

@ref: 6369

culture collection no.: DSM 16327, KCTC 12256, CIP 108733

straininfo link

@ref	passport
20218	http://www.straininfo.net/strains/386590
20218	http://www.straininfo.net/strains/386592

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	15774627	Psychrobacter cibarius sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.	Jung SY, Lee MH, Oh TK, Park YH, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.63398-0	2005	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Psychrobacter/classification/genetics/growth & development/isolation & purification, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sequence Analysis, DNA	Genetics
Phylogeny	19502339	Psychrobacter fulvigenes sp. nov., isolated from a marine crustacean from the Sea of Japan.	Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.007195-0	2009	Animals, Bacterial Typing Techniques, Base Composition, Crustacea/microbiology, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, Psychrobacter/classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Species Specificity	Genetics

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed	ID_cross_reference
6369	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16327)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-16327
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
27672			10.1099/ijs.0.63398-0			15774627
31359	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information		28776041	27672
41750	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/6394
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67771	Curators of the KCTC		https://kctc.kribb.re.kr/En/Kctc
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)