Winogradskyella echinorum (KCTC 22026, LMG 24757, KMM 6211)

Name: Winogradskyella echinorum (KCTC 22026, LMG 24757, KMM 6211)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133461

Type strain

Culture col. no. KCTC 22026 LMG 24757 KMM 6211

NCBI tax ID(s) 538189

Special Collections KCTC Literature strains

History <- OI Nedashkovskaya, Pacific Institute of Bioorganic Chemistry, Russia

Links

Winogradskyella echinorum KCTC 22026 is an aerobe, spore-forming, Gram-negative bacterium that was isolated from sea urchin.

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

Name and taxonomic classification

SI-ID 264789

LMG 24757,KCTC 22026,CECT 7944

@ref 20215

Last LPSN update 2026-02-09 11:31:57

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Winogradskyella

Species Winogradskyella echinorum

Full scientific name Winogradskyella echinorum Nedashkovskaya et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
29068	negative	1.95 µm	0.45 µm	rod-shaped	gliding
67771				rod-shaped	gliding
67771	negative
125439	negative					99.7
125438						94
125438	negative					98.981

Pigmentation

29068

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
29068	positive	growth	04-37
29068	positive	optimum	20.5
67771	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29068	aerobe
67771	aerobe
125439	obligate aerobe	98.7

Spore formation

@ref	Spore formation	Confidence
29068
125439		97.6
125438		92.833

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29068	NaCl	positive	growth	01-06 %
29068	NaCl	positive	optimum	3.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29068	4853 ChEBI	esculin	+	hydrolysis
29068	17234 ChEBI	glucose	+	carbon source
29068	37684 ChEBI	mannose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29068	alkaline phosphatase	+	3.1.3.1
29068	catalase	+	1.11.1.6
29068	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Echinodermata

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
29068	sea urchin
67771	From the sea urchin `Strongylocentrotus intermedius`	Troitsa Bay, Gulf of Peter the Great, East Sea	Russia	RUS	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1428408v1 assembly for Winogradskyella echinorum KCTC 22026	contig	GCA_014284085	538189.3	8067559796	538189	77.73
66792	ASM1429736v1 assembly for Winogradskyella echinorum KCTC 22026	contig	GCA_014297365	538189.4	2995634087	538189	77.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29068	Winogradskyella echinorum strain KMM 6211 16S ribosomal RNA gene, partial sequence	EU727254	1478		538189
124043	Winogradskyella echinorum strain KMM 6211 16S ribosomal RNA gene, partial sequence.	PQ248462	601		538189

GC content

29068

GC-content (mol%)33.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Winogradskyella echinorum KCTC 22026
NCBI: GCA_014284085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.60	no
125439	motility	BacteriaNetⓘ	no	66.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Winogradskyella echinorum strain KCTC 22026
PATRIC: 538189.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.98	no
125438	anaerobic	anaerobicⓘ	no	98.12	no
125438	spore-forming	spore-formingⓘ	no	92.83	no
125438	aerobic	aerobicⓘ	yes	88.59	yes
125438	thermophilic	thermophileⓘ	no	98.16	no
125438	flagellated	motile2+ⓘ	no	94.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Characterization of Pustular Mats and Related Rivularia-Rich Laminations in Oncoids From the Laguna Negra Lake (Argentina).	Mlewski EC, Pisapia C, Gomez F, Lecourt L, Soto Rueda E, Benzerara K, Menez B, Borensztajn S, Jamme F, Refregiers M, Gerard E.	Front Microbiol	10.3389/fmicb.2018.00996	2018
Phylogeny	Winogradskyella litoriviva sp. nov., isolated from coastal seawater.	Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV, Kim SJ, Rhee SK, Mikhailov VV.	Int J Syst Evol Microbiol	10.1099/ijsem.0.000470	2015
Phylogeny	Winogradskyella ouciana sp. nov., isolated from the hadal seawater of the Mariana Trench.	He X, Liu R, Liang J, Li Y, Zhao X, Ran L, Ahmad W, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijsem.0.004687	2021
Phylogeny	Winogradskyella jejuensis sp. nov., a marine bacterium isolated from a brown alga Carpopeltis affinis.	Kim JY, Oh DC	J Microbiol	10.1007/s12275-012-2447-0	2012
Phylogeny	Winogradskyella damuponensis sp. nov., isolated from seawater.	Lee DH, Cho SJ, Kim SM, Lee SB	Int J Syst Evol Microbiol	10.1099/ijs.0.041384-0	2012
Phylogeny	Winogradskyella ulvae sp. nov., an epiphyte of a Pacific seaweed, and emended descriptions of the genus Winogradskyella and Winogradskyella thalassocola, Winogradskyella echinorum, Winogradskyella exilis and Winogradskyella eximia.	Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV	Int J Syst Evol Microbiol	10.1099/ijs.0.032219-0	2011
Phylogeny	Winogradskyella flava sp. nov., isolated from the brown alga, Sargassum fulvellum.	Lee JH, Kang JW, Shin SB, Seong CN	Int J Syst Evol Microbiol	10.1099/ijsem.0.002161	2017
Phylogeny	Winogradskyella eckloniae sp. nov., a marine bacterium isolated from the brown alga Ecklonia cava.	Kim JY, Park SH, Seo GY, Kim YJ, Oh DC	Int J Syst Evol Microbiol	10.1099/ijs.0.000334	2015
Phylogeny	Winogradskyella pulchriflava sp. nov., isolated from marine sediment.	Kim SJ, Choi YR, Park SJ, Kim JG, Shin KS, Roh DH, Rhee SK	Int J Syst Evol Microbiol	10.1099/ijs.0.049502-0	2013
Phylogeny	Winogradskyella echinorum sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius.	Nedashkovskaya OI, Vancanneyt M, Kim SB, Zhukova NV	Int J Syst Evol Microbiol	10.1099/ijs.0.005421-0	2009

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 )
#25498	IJSEM 1465 2009 ( DOI 10.1099/ijs.0.005421-0 , PubMed 19502336 )
#29068	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 #25498
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Winogradskyella echinorum (KCTC 22026, LMG 24757, KMM 6211)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014284085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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