Winogradskyella sediminis (DSM 28134, CGMCC 1.12601, LMG 28075)

Name: Winogradskyella sediminis (DSM 28134, CGMCC 1.12601, LMG 28075)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140167

Type strain

Strain Designation S5-23-3

Culture col. no. DSM 28134 CGMCC 1.12601 LMG 28075 S5-23-3

NCBI tax ID(s) 1382466

Special Collections DSMZ Literature strains

History <- R. Margesin, Inst. Microbiology, Univ. Innsbruck, Austria; S5-23-3 <- D.-C. Zhang, CAS, Inst. of Oceanology

Links

Winogradskyella sediminis S5-23-3 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from marine subsurface sediment.

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

Name and taxonomic classification

SI-ID 406287

LMG 28075,DSM 28134

@ref 20215

Last LPSN update 2026-02-09 11:33:32

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Winogradskyella

Species Winogradskyella sediminis

Full scientific name Winogradskyella sediminis Zhang et al. 2016

BacDive ID	Other strains from **Winogradskyella sediminis** (1)	Type strain
175340	W. sediminis RHA_55, DSM 116166

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
43099	negative	3 µm	0.7-0.8 µm	rod-shaped	gliding
125439	negative					99.7
125438						94
125438	negative					97.981

Colony morphology

@ref	Colony color	Colony shape	Medium used
43099	yellow	circular	marine agar (MA)

Pigmentation

@ref	Production	Name
43099		carotenoid pigment

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
43099	marine agar (MA)
42774	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
43099	Reasoner's 2A agar (R2A)
43099	tryptic soy agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)
42774	positive	growth	28
43099	positive	optimum	30
43099	positive	growth	1-30

Culture pH

@ref	Ability	Type	PH
43099	positive	optimum	7-8
43099	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
43099	aerobe
125439	obligate aerobe	98.5

Spore formation

@ref	Spore formation	Confidence
125439		98.5
125438		92.333

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43099	NaCl	positive	growth	2-6 %(w/v)
43099	Marine salts		growth	0 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43099	17128 ChEBI	adipate	+	assimilation
43099	2509 ChEBI	agar	-	degradation
43099	58187 ChEBI	alginate	+	degradation
43099	27613 ChEBI	amygdalin	+	oxidation
43099	18305 ChEBI	arbutin	-	oxidation
43099	15903 ChEBI	beta-d-glucose	+	assimilation
43099	85146 ChEBI	carboxymethylcellulose	-	degradation
43099		casein	+	degradation
43099	17057 ChEBI	cellobiose	-	oxidation
43099	17057 ChEBI	cellobiose	-	builds acid from
43099	16947 ChEBI	citrate	-	carbon source
43099	17108 ChEBI	D-arabinose	-	oxidation
43099	17108 ChEBI	D-arabinose	-	builds acid from
43099	18333 ChEBI	D-arabitol	-	oxidation
43099	28847 ChEBI	D-fucose	-	oxidation
43099	17634 ChEBI	D-glucose	-	fermentation
43099	17634 ChEBI	D-glucose	+	oxidation
43099	62318 ChEBI	D-lyxose	-	oxidation
43099	16899 ChEBI	D-mannitol	+	assimilation
43099	16899 ChEBI	D-mannitol	+	oxidation
43099	16024 ChEBI	D-mannose	+	assimilation
43099	16024 ChEBI	D-mannose	+	oxidation
43099	16988 ChEBI	D-ribose	-	oxidation
43099	17924 ChEBI	D-sorbitol	-	oxidation
43099	16443 ChEBI	D-tagatose	-	oxidation
43099	65327 ChEBI	D-xylose	-	oxidation
43099	27689 ChEBI	decanoate	-	assimilation
43099	16991 ChEBI	dna	+	degradation
43099	17113 ChEBI	erythritol	-	oxidation
43099	4853 ChEBI	esculin	+	hydrolysis
43099	16813 ChEBI	galactitol	-	oxidation
43099	28260 ChEBI	galactose	+	builds acid from
43099	5291 ChEBI	gelatin	+	hydrolysis
43099	28066 ChEBI	gentiobiose	+	oxidation
43099	17234 ChEBI	glucose	+	builds acid from
43099	17754 ChEBI	glycerol	-	oxidation
43099	28087 ChEBI	glycogen	+	oxidation
43099	15443 ChEBI	inulin	-	oxidation
43099	30849 ChEBI	L-arabinose	-	oxidation
43099	18403 ChEBI	L-arabitol	-	oxidation
43099	18287 ChEBI	L-fucose	-	oxidation
43099	62345 ChEBI	L-rhamnose	-	oxidation
43099	17266 ChEBI	L-sorbose	-	oxidation
43099	65328 ChEBI	L-xylose	-	oxidation
43099	17716 ChEBI	lactose	-	builds acid from
43099	25115 ChEBI	malate	+	assimilation
43099	17306 ChEBI	maltose	+	assimilation
43099	17306 ChEBI	maltose	+	oxidation
43099	17306 ChEBI	maltose	+	builds acid from
43099	29864 ChEBI	mannitol	+	builds acid from
43099	37684 ChEBI	mannose	+	builds acid from
43099	6731 ChEBI	melezitose	-	oxidation
43099	28053 ChEBI	melibiose	-	oxidation
43099	17268 ChEBI	myo-inositol	-	oxidation
43099	17268 ChEBI	myo-inositol	-	builds acid from
43099	17632 ChEBI	nitrate	-	reduction
43099	17309 ChEBI	pectin	-	degradation
43099	18401 ChEBI	phenylacetate	+	assimilation
43099	62969 ChEBI	polygalacturonic acid	-	degradation
43099	32032 ChEBI	potassium gluconate	-	assimilation
43099	16634 ChEBI	raffinose	-	oxidation
43099	16634 ChEBI	raffinose	-	builds acid from
43099	26546 ChEBI	rhamnose	-	builds acid from
43099	15963 ChEBI	ribitol	-	oxidation
43099	33942 ChEBI	ribose	-	builds acid from
43099	17814 ChEBI	salicin	-	oxidation
43099	17814 ChEBI	salicin	-	builds acid from
43099	53258 ChEBI	sodium citrate	+	assimilation
43099	30911 ChEBI	sorbitol	-	builds acid from
43099	27922 ChEBI	sorbose	-	builds acid from
43099	28017 ChEBI	starch	+	degradation
43099	28017 ChEBI	starch	+	oxidation
43099	17992 ChEBI	sucrose	-	oxidation
43099	17992 ChEBI	sucrose	-	builds acid from
43099	27082 ChEBI	trehalose	-	oxidation
43099	27082 ChEBI	trehalose	-	builds acid from
43099	32528 ChEBI	turanose	-	oxidation
43099	17151 ChEBI	xylitol	-	oxidation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43099	16136 ChEBI	hydrogen sulfide
43099	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43099	acid phosphatase	+	3.1.3.2
43099	alkaline phosphatase	+	3.1.3.1
43099	alpha-chymotrypsin	-	3.4.21.1
43099	alpha-fucosidase	-	3.2.1.51
43099	alpha-galactosidase	-	3.2.1.22
43099	alpha-glucosidase	-	3.2.1.20
43099	alpha-mannosidase	-	3.2.1.24
43099	arginine dihydrolase	-	3.5.3.6
43099	beta-galactosidase	-	3.2.1.23
43099	beta-glucosidase	-	3.2.1.21
43099	beta-glucuronidase	-	3.2.1.31
43099	catalase	+	1.11.1.6
43099	cystine arylamidase	-	3.4.11.3
43099	cytochrome oxidase	+	1.9.3.1
43099	esterase (C 4)	+
43099	esterase Lipase (C 8)	+
43099	leucine arylamidase	+	3.4.11.1
43099	lysine decarboxylase	-	4.1.1.18
43099	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43099	naphthol-AS-BI-phosphohydrolase	+
43099	ornithine decarboxylase	-	4.1.1.17
43099	trypsin	-	3.4.21.4
43099	tryptophan deaminase	-	4.1.99.1
43099	urease	-	3.5.1.5
43099	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

43099

Fatty acid	Percentage	ECL
C15:0 iso	24.4
C15:1 iso G	19.5
C15:0 iso 3OH	12.9
C17:0 iso 3OH	10.5
C15:0 anteiso	6.2
C15:0 iso 2OH / C16:1ω7c	5
C16:0 iso 3OH	4
C15:0	3.7
C15:1 anteiso A	1.7
C17:0 2OH	1.5
C15:1ω6c	1.5
Unknown	1.4	13565
C15:0 3OH	1.3
C15:0 2OH	1.2
C17:1 iso ω9c	1.2

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture temperature	Isolation procedure
42774	marine subsurface sediment	Northern Yellow Sea (38° 03' N 122° 13' E)	China	CHN	Asia	38.05	122.217 38.05/122.217
43099	marine sediment sample	Northern Yellow Sea	China	CHN	Asia	38	122 38/122	marine agar 2216 (MA; Difco)	25	standard dilution plating method

Taxonmaps

69479

Global distribution of 16S sequence KF312887 (>99% sequence identity) for Winogradskyella sediminis subclade from Microbeatlas

Aquatic Samples	651
Soil Samples	18
Animal Samples	74
Plant Samples	7
Total Samples	750

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42774	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	ASM338735v1 assembly for Winogradskyella sediminis DSM 28134	scaffold	GCA_003387355	1382466.5	2739367661	1382466	72.15

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42774	Winogradskyella sediminis strain S5-23-3 16S ribosomal RNA gene, partial sequence	KF312887	1514		1382466

GC content

@ref	GC-content (mol%)	Method
42774	36.1	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Winogradskyella sediminis DSM 28134
NCBI: GCA_003387355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	no	61.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Winogradskyella sediminis DSM 28134
NCBI: GCA_003387355.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.98	yes
125438	anaerobic	anaerobicⓘ	no	97.49	yes
125438	aerobic	aerobicⓘ	yes	89.72	no
125438	spore-forming	spore-formingⓘ	no	92.33	no
125438	thermophilic	thermophileⓘ	no	96.94	yes
125438	flagellated	motile2+ⓘ	no	94.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Winogradskyella algae sp. nov., a marine bacterium isolated from the brown alga.	Kurilenko VV, Romanenko LA, Isaeva MP, Svetashev VI, Mikhailov VV	Antonie Van Leeuwenhoek	10.1007/s10482-018-1207-5	2018
Phylogeny	Winogradskyella sediminis sp. nov., isolated from marine sediment.	Zhang DC, Liu YX, Huang HJ, Weber K, Margesin R	Int J Syst Evol Microbiol	10.1099/ijsem.0.001157	2016

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 )
#42774	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28134
#43099	De-Chao Zhang, Yan-Xia Liu, Hai-Jun Huang, Karin Weber, Rosa Margesin: Winogradskyella sediminis sp. nov., isolated from marine sediment. IJSEM 66: 3157 - 3163 2016 ( DOI 10.1099/ijsem.0.001157 , PubMed 27189204 )
#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 .
#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 sediminis (DSM 28134, CGMCC 1.12601, LMG 28075)

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

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003387355

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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