Pseudidiomarina salinarum (DSM 21900, CCUG 54359, KCTC 12971)

Name: Pseudidiomarina salinarum (DSM 21900, CCUG 54359, KCTC 12971)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6236

Type strain

Strain Designation ISL-52

Culture col. no. DSM 21900 CCUG 54359 KCTC 12971 ISL-52

NCBI tax ID(s) 435908

Special Collections DSMZ CCUG KCTC Literature strains

History DSMZ <- CCUG <- J. H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea KCTC <- JH Yoon, KRIBB

Links

Pseudidiomarina salinarum ISL-52 is an aerobe, Gram-negative, motile bacterium that was isolated from marine solar saltern.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398644

KCTC 12971,DSM 21900,CCUG 54359

@ref 20215

Last LPSN update 2026-05-29 08:26:21

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Idiomarinaceae

Genus Pseudidiomarina

Species Pseudidiomarina salinarum

Full scientific name Pseudidiomarina salinarum (Yoon et al. 2007) Jean et al. 2009

Synonyms (1)

Idiomarina salinarum

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32249	negative	2.25 µm	0.45 µm	rod-shaped
67771	negative
125438	negative				98.494

Colony morphology

60150

Incubation period3 days

Pigmentation

32249

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16028	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	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

Culture temp

@ref	Growth	Type	Temperature (°C)
16028	positive	growth	37
32249	positive	growth	04-42
32249	positive	optimum	33.5
60150	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH
32249	positive	optimum	7.5
32249	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32249	aerobe
67771	aerobe
125439	aerobe	94.947

Spore formation

@ref	Spore formation	Confidence
125439		94.598
125438		93.563

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32249	NaCl	positive	growth	0.5-14 %
32249	NaCl	positive	optimum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32249	17632 ChEBI	nitrate	+	reduction
32249	53423 ChEBI	tween 40	+	carbon source
32249	53425 ChEBI	tween 60	+	carbon source
32249	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32249	alkaline phosphatase	+	3.1.3.1
32249	catalase	+	1.11.1.6
32249	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	alanine metabolism	75.86	22 of 29
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	sulfopterin metabolism	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	threonine metabolism	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	pyrimidine metabolism	68.89	31 of 45
66794	lipid metabolism	67.74	21 of 31
66794	arginine metabolism	66.67	16 of 24
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	citric acid cycle	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	phenylalanine metabolism	61.54	8 of 13
66794	non-pathway related	60.53	23 of 38
66794	tryptophan metabolism	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	lysine metabolism	57.14	24 of 42
66794	propanol degradation	57.14	4 of 7
66794	vitamin B6 metabolism	54.55	6 of 11
66794	glycolysis	52.94	9 of 17
66794	polyamine pathway	52.17	12 of 23
66794	quinate degradation	50	1 of 2
66794	acetate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	cysteine metabolism	50	9 of 18
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	d-mannose degradation	44.44	4 of 9
66794	arachidonic acid metabolism	44.44	8 of 18
66794	valine metabolism	44.44	4 of 9
66794	heme metabolism	42.86	6 of 14
66794	methionine metabolism	42.31	11 of 26
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	phenylacetate degradation (aerobic)	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	vitamin B1 metabolism	38.46	5 of 13
66794	pentose phosphate pathway	36.36	4 of 11
66794	phenol degradation	35	7 of 20
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	oxidative phosphorylation	32.97	30 of 91
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	glycine metabolism	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	degradation of pentoses	25	7 of 28
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	butanoate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Condition	#Saline	-
#Engineered	#Industrial	#Industrial production
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
16028	marine solar saltern	Yellow Sea	Republic of Korea	KOR	Asia
60150	Marine solar saltern		Republic of Korea	KOR	Asia	2005
67771	From saltern field	the Yellow Sea	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16028	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
66792	ASM398710v1 assembly for Pseudidiomarina salinarum ISL-52	contig	GCA_003987105	435908.5		435908	75
66792	ASM75371v1 assembly for Pseudidiomarina salinarum ISL-52	contig	GCA_000753715	435908.3	2609460261	435908	73.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16028	Idiomarina salinarum strain ISL-52 16S ribosomal RNA gene, partial sequence	EF486355	1497		435908

GC content

16028

GC-content (mol%)53.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM75371v1 assembly for Pseudidiomarina salinarum ISL-52
NCBI: GCA_000753715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.95	no
125439	gram_stain	BacteriaNetⓘ	negative	86.75	no
125439	motility	BacteriaNetⓘ	yes	69.18	no
125439	spore_formation	BacteriaNetⓘ	no	94.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudidiomarina salinarum ISL-52
NCBI: GCA_003987105.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	yes
125438	anaerobic	anaerobicⓘ	no	97.27	no
125438	aerobic	aerobicⓘ	yes	82.27	yes
125438	spore-forming	spore-formingⓘ	no	93.56	no
125438	thermophilic	thermophileⓘ	no	95.93	yes
125438	flagellated	motile2+ⓘ	no	56.42	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Idiomarina halophila sp. nov., isolated from a solar saltern sediment.	Lee JC, Kim YS, Yun BS, Whang KS	Int J Syst Evol Microbiol	10.1099/ijs.0.000094	2015
Phylogeny	Idiomarina atlantica sp. nov., a marine bacterium isolated from the deep sea sediment of the North Atlantic Ocean.	Du J, Lai Q, Liu Y, Du Y, Liu X, Sun F, Shao Z	Antonie Van Leeuwenhoek	10.1007/s10482-014-0337-7	2014
Phylogeny	Idiomarina planktonica sp. nov., isolated from a saline lake.	Zhong ZP, Liu Y, Liu HC, Wang F, Song L, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.065938-0	2014
Phylogeny	Idiomarina maris sp. nov., a marine bacterium isolated from sediment.	Zhang YJ, Zhang XY, Zhao HL, Zhou MY, Li HJ, Gao ZM, Chen XL, Dang HY, Zhang YZ	Int J Syst Evol Microbiol	10.1099/ijs.0.027896-0	2011
Phylogeny	Idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer Pseudidiomarina aestuarii to the genus Idiomarina as Idiomarina aestuarii comb. nov.	Wang L, Lai Q, Fu Y, Chen H, Wang W, Wang J, Sun F, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.022970-0	2010
Phylogeny	Idiomarina salinarum sp. nov., isolated from a marine solar saltern in Korea.	Yoon JH, Jung SY, Jung YT, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.65189-0	2007

References

#16028	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21900
#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 )
#28490	IJSEM 2503 2007 ( DOI 10.1099/ijs.0.65189-0 , PubMed 17978209 )
#32249	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28490
#60150	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54359
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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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Pseudidiomarina salinarum (DSM 21900, CCUG 54359, KCTC 12971)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003987105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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