Yoonia ponticola (DSM 101064, KCTC 42133, W-SW2)

Name: Yoonia ponticola (DSM 101064, KCTC 42133, W-SW2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131301

Type strain

Strain Designation W-SW2

Culture col. no. DSM 101064 KCTC 42133 W-SW2

NCBI tax ID(s) 1524255

Special Collections DSMZ KCTC

History <- KCTC <- J. H. Yoon, University of Science and Technology; W-SW2

Links

Yoonia ponticola W-SW2 is a bacterium that was isolated from seawater.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400380

KCTC 42133,NBRC 110409,DSM 101064

@ref 20215

Last LPSN update 2026-02-09 11:31:25

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Yoonia

Species Yoonia ponticola

Full scientific name Yoonia ponticola (Jung et al. 2014) Wang et al. 2022

Synonyms (1)

Loktanella ponticola

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99
125439	negative	98.3

Colony morphology

22528

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22528	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)
22528	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.2

Spore formation

@ref	Spore formation	Confidence
125439		98.8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
22528	catalase	+	1.11.1.6
22528	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
22528	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22528	seawater	Wando, South Sea	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KJ855314 (>99% sequence identity) for Loktanella ponticola subclade from Microbeatlas

Aquatic Samples	999
Soil Samples	5
Animal Samples	15
Plant Samples
Total Samples	1019

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22528	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1419939v1 assembly for Yoonia ponticola DSM 101064	scaffold	GCA_014199395	1524255.3	2828431062	1524255	71.99

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22528	Yoonia ponticola strain W-SW2 16S ribosomal RNA gene, partial sequence	KJ855314	1387		1524255

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Yoonia ponticola DSM 101064
NCBI: GCA_014199395

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	yes	71.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Loktanella ponticola DSM 101064
NCBI: GCA_014199395.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	96.31	no
125438	aerobic	aerobicⓘ	yes	79.81	no
125438	spore-forming	spore-formingⓘ	no	86.18	no
125438	thermophilic	thermophileⓘ	no	99.35	yes
125438	flagellated	motile2+ⓘ	no	58.51	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gymnodinialimonas ceratoperidinii gen. nov., sp. nov., isolated from rare marine dinoflagellate Ceratoperidinium margalefii.	Jiang Y, Peng Y, Shin HH, Kim HJ, Kim KH, Jiang L, Lee J, Li Z	Arch Microbiol	10.1007/s00203-022-02797-x	2022
Phylogeny	Loktanella ponticola sp. nov., isolated from seawater.	Jung YT, Park S, Park JM, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.068361-0	2014

References

#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 )
#22528	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101064
#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) .
#68369	Automatically annotated from API 20NE .
#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 .
#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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Yoonia ponticola (DSM 101064, KCTC 42133, W-SW2)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014199395

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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