Epibacterium ulvae (DSM 24752, LMG 26464, U95)

Name: Epibacterium ulvae (DSM 24752, LMG 26464, U95)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24523

Type strain

Strain Designation U95

Culture col. no. DSM 24752 LMG 26464 U95

NCBI tax ID(s) 1156985

Special Collections DSMZ Literature strains

Links

Epibacterium ulvae U95 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from surface of the marine green alga Ulva australis collected from a rocky intertidal zone.

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

Name and taxonomic classification

SI-ID 377580

LMG 26464,DSM 24752

@ref 20215

Last LPSN update 2025-12-16 09:52:52

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Epibacterium

Species Epibacterium ulvae

Full scientific name Epibacterium ulvae Penesyan et al. 2013

Synonyms (1)

Tritonibacter ulvae

BacDive ID	Other strains from **Epibacterium ulvae** (1)	Type strain
24524	E. ulvae U82, DSM 24753, LMG 26463

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30714	negative	2.5 µm	0.5 µm	rod-shaped
125439	negative				99.2
125438	negative				98.5

Colony morphology

21250

Incubation period3-7 days

Pigmentation

30714

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21250	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)	Range
21250	positive	growth	25	mesophilic
30714	positive	growth	12-34
30714	positive	optimum	25	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30714	positive	optimum	7.5
30714	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30714	aerobe
125439	obligate aerobe	97.8

Spore formation

@ref	Spore formation	Confidence
125439		99.2
125438		93.159

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30714	NaCl	positive	growth	01-06 %
30714	NaCl	positive	optimum	2.5 %

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
30714	16947 ChEBI	citrate	+	carbon source
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
30714	28757 ChEBI	fructose	+	carbon source
30714	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
30714	17234 ChEBI	glucose	+	carbon source
30714	17754 ChEBI	glycerol	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
30714	24996 ChEBI	lactate	+	carbon source
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
30714	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
30714	29864 ChEBI	mannitol	+	carbon source
30714	37684 ChEBI	mannose	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
30714	17272 ChEBI	propionate	+	carbon source
30714	30031 ChEBI	succinate	+	carbon source
30714	17992 ChEBI	sucrose	+	carbon source
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
21250	catalase	+	1.11.1.6
30714	catalase	+	1.11.1.6
30714	cytochrome oxidase	+	1.9.3.1
21250	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	+	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CMP-KDO biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	Entner Doudoroff pathway	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	vitamin B1 metabolism	92.31	12 of 13
66794	myo-inositol biosynthesis	90	9 of 10
66794	alanine metabolism	89.66	26 of 29
66794	serine metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	pyrimidine metabolism	88.89	40 of 45
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	flavin biosynthesis	86.67	13 of 15
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	NAD metabolism	83.33	15 of 18
66794	purine metabolism	82.98	78 of 94
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	tyrosine metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	non-pathway related	76.32	29 of 38
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	arginine metabolism	75	18 of 24
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	lysine metabolism	73.81	31 of 42
66794	methionine metabolism	73.08	19 of 26
66794	pentose phosphate pathway	72.73	8 of 11
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	oxidative phosphorylation	68.13	62 of 91
66794	IAA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	d-mannose degradation	66.67	6 of 9
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	polyamine pathway	65.22	15 of 23
66794	lipid metabolism	64.52	20 of 31
66794	degradation of sugar acids	64	16 of 25
66794	vitamin B6 metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	carnitine metabolism	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	hydrogen production	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	histidine metabolism	55.17	16 of 29
66794	phenol degradation	55	11 of 20
66794	degradation of pentoses	53.57	15 of 28
66794	phenylmercury acetate degradation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	catecholamine biosynthesis	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	resorcinol degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	d-xylose degradation	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	lipoate biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	ketogluconate metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	mevalonate metabolism	28.57	2 of 7
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4

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
21250	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Tidal flat
#Host	#Algae	#Green algae

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
21250	surface of the marine green alga Ulva australis collected from a rocky intertidal zone	Ulva australis	near Sydney (33° 51'09''S, 151° 16'00''E), Clovelly, Sharks Point	Australia	AUS	Australia and Oceania	33.8525	151.267 33.8525/151.267

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21250	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	ASM279679v1 assembly for Epibacterium ulvae U95	scaffold	GCA_002796795	1156985.5		1156985	73.87
66792	IMG-taxon 2622736501 annotated assembly for Epibacterium ulvae U95	contig	GCA_900102795	1156985.4	2622736501	1156985	73.27

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21250	Epibacterium ulvae strain U95 16S ribosomal RNA gene, partial sequence	JN935021	1326		1156985

GC content

@ref	GC-content (mol%)	Method
21250	52.6	high performance liquid chromatography (HPLC)
30714	52.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Epibacterium ulvae U95
NCBI: GCA_002796795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	yes	79.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Epibacterium ulvae U95
NCBI: GCA_002796795.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	93.77	no
125438	aerobic	aerobicⓘ	yes	80.33	yes
125438	spore-forming	spore-formingⓘ	no	93.16	no
125438	thermophilic	thermophileⓘ	no	96.83	yes
125438	flagellated	motile2+ⓘ	yes	70.96	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Genetics	Genome sequence of Epibacterium ulvae strain DSM 24752(T), an indigoidine-producing, macroalga-associated member of the marine Roseobacter group.	Breider S, Sehar S, Berger M, Thomas T, Brinkhoff T, Egan S	Environ Microbiome	10.1186/s40793-019-0343-5	2019
Phylogeny	Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga.	Penesyan A, Breider S, Schumann P, Tindall BJ, Egan S, Brinkhoff T	Int J Syst Evol Microbiol	10.1099/ijs.0.042838-0	2012

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 )
#21250	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24752
#30714	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 #27045 (see below)
#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 )
#68369	Automatically annotated from API 20NE .
#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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Epibacterium ulvae (DSM 24752, LMG 26464, U95)

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

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002796795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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