Zobellia uliginosa (DSM 2061, ATCC 14397, IAM 14312)

Name: Zobellia uliginosa (DSM 2061, ATCC 14397, IAM 14312)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5664

Type strain

Strain Designation 553 (843)

Culture col. no. DSM 2061 ATCC 14397 IAM 14312 IFO 14962 NBRC 14962 9 more

NCBI tax ID(s) 143224

Special Collections DSMZ CCUG JCM CIP

Links

Zobellia uliginosa 553 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from seawater.

Gram-negative rod-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 2837

LMG 3809,ATCC 14397,DSM 2061,NCMB 1863,CECT 4277,IAM 14312,IFO 14962,CIP 104808,CCUG 33448,NCIMB 1863,KCTC 2916,CCUG 47100,NBRC 14962,JCM 21152

@ref 20215

Last LPSN update 2025-12-16 09:48:07

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Zobellia

Species Zobellia uliginosa

Full scientific name Zobellia uliginosa (ZoBell and Upham 1944) Barbeyron et al. 2001

Synonyms (4)

"Agarbacterium uliginosum"
Cytophaga uliginosa
Flavobacterium uliginosum
Cellulophaga uliginosa

Morphology

Cell morphology

@ref	Gram stain	Cell shape
123712	negative	rod-shaped
125438
125438	negative
125439	negative

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
697	SEAWATER YEAST PEPTONE AGAR (DSMZ Medium 243)	Medium recipe at MediaDive	Name: SEAWATER YEAST PEPTONE AGAR (DSMZ Medium 243) Composition: Agar 12.0 g/l Peptone 5.0 g/l Yeast extract 3.0 g/l Sea water Distilled water
37581	MEDIUM 167 - for Cytophaga uliginosa, Demetria terragena and Marinococcus al bus		Distilled water make up to (1000.000 ml);Sodium chloride (50.000 g);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);
123712	CIP Medium 167	Medium recipe at CIP
123712	CIP Medium 234	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
697	positive	growth	26	mesophilic
37581	positive	growth	25	mesophilic
67770	positive	growth	25	mesophilic
123712	positive	growth	15-37
123712	negative	growth	5
123712	negative	growth	41
123712	negative	growth	45

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		90.265
125439		99.2

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
123712	4853 ChEBI	esculin	-	hydrolysis
123712	606565 ChEBI	hippurate	-	hydrolysis
123712	17632 ChEBI	nitrate	+	reduction
123712	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is antibiotic	Is sensitive	Is resistant
123712	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123712	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
123712	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
123712	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123712	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
123712	gamma-glutamyltransferase	+	2.3.2.2
123712	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
123712	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123712	ornithine decarboxylase	-	4.1.1.17
123712	oxidase	+
123712	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
123712	tryptophan deaminase	-
123712	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
123712	-	+	+	+	-	+	+	-	+	-	+	+	+	+	-	+	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type
697	seawater
67770	Marine bottom sediment

Taxonmaps

69479

Global distribution of 16S sequence AB680724 (>99% sequence identity) for Zobellia from Microbeatlas

Aquatic Samples	434
Soil Samples	69
Animal Samples	18
Plant Samples	8
Total Samples	529

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
697	1	Risk group (German classification) According to TRBA 466
123712	1	Risk group (French 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	IMG-taxon 2681813510 annotated assembly for Zobellia uliginosa DSM 2061	contig	GCA_900156625	143224.8	2681813510	143224	73.38

Genome browser: GCA_900156625

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Zobellia uliginosa gene for 16S rRNA, partial sequence, strain: NBRC 14962	AB680724	1449	143224
697	Zobellia uliginosa strain ATCC 14397 16S ribosomal RNA gene, partial sequence	M62799	1527	143224
124043	Zobellia uliginosa gene for 16S ribosomal RNA, partial sequence, strain: NCIMB 1863.	D12674	1260	143224

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Zobellia uliginosa DSM 2061
NCBI: GCA_900156625

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	no	58.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	64.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Zobellia uliginosa strain DSM 2061
PATRIC: 143224.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	96.16	no
125438	spore-forming	spore-formingⓘ	no	90.27	no
125438	aerobic	aerobicⓘ	yes	84.71	no
125438	thermophilic	thermophileⓘ	no	98.96	no
125438	flagellated	motile2+ⓘ	no	92.25	no

Literature

Title	Authors	Journal	DOI	Year
Glitter-like iridescence within the bacteroidetes especially Cellulophaga spp.: optical properties and correlation with gliding motility.	Kientz B, Ducret A, Luke S, Vukusic P, Mignot T, Rosenfeld E.	PLoS One	10.1371/journal.pone.0052900	2012
Isolation of sulfonosphingolipids from the rosette-inducing bacterium Zobellia uliginosa and evaluation of their rosette-inducing activity.	Peng CC, Dormanns N, Regestein L, Beemelmanns C.	RSC Adv	10.1039/d3ra04314b	2023
Total Synthesis and Functional Evaluation of IORs, Sulfonolipid-based Inhibitors of Cell Differentiation in Salpingoeca rosetta.	Raguz L, Peng CC, Rutaganira FUN, Kruger T, Stanisic A, Jautzus T, Kries H, Kniemeyer O, Brakhage AA, King N, Beemelmanns C.	Angew Chem Int Ed Engl	10.1002/anie.202209105	2022
A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals.	Alegado RA, Brown LW, Cao S, Dermenjian RK, Zuzow R, Fairclough SR, Clardy J, King N.	Elife	10.7554/elife.00013	2012
Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov.	Barbeyron T, L'Haridon S, Corre E, Kloareg B, Potin P	Int J Syst Evol Microbiol	10.1099/00207713-51-3-985	2001

References

#697	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2061
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#37581	; Curators of the CIP;
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#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 .
#123712	Collection of Institut Pasteur ; Curators of the CIP; CIP 104808
#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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Zobellia uliginosa (DSM 2061, ATCC 14397, IAM 14312)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900156625

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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