Zobellia galactanivorans (DSM 12802, CIP 106680, CCUG 47099)

Name: Zobellia galactanivorans (DSM 12802, CIP 106680, CCUG 47099)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5665

Type strain

Strain Designation Dsij

Culture col. no. DSM 12802 CIP 106680 CCUG 47099 Dsij KCTC 12921

NCBI tax ID(s) 63186

Special Collections DSMZ CCUG CIP KCTC

Links

Zobellia galactanivorans Dsij is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from red alga .

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

Name and taxonomic classification

SI-ID 49363

DSM 12802,CIP 106680,KCTC 12921,CCUG 47099,NCIMB 13871

@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 galactanivorans

Full scientific name Zobellia galactanivorans corrig. Barbeyron et al. 2001

Synonyms (1)

Zobellia galactanovorans

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119503	negative	rod-shaped
125439	negative		99.7
125438			91.75
125438	negative		99

Pigmentation

@ref	Production	Name
119503		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4827	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
38637	MEDIUM 308 - for Stappia stellulata and Ruegeria		Agar (15.000 g);Yeast extract (1.000 g);Peptone (5.000 g);Synthetic sea solution - M0527 (1000.000 ml)
119503	CIP Medium 308	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4827	positive	growth	35	mesophilic
38637	positive	growth	30	mesophilic
57507	positive	growth	25-28	mesophilic
119503	positive	growth	15-41
119503	negative	growth	5
119503	negative	growth	45

Physiology and metabolism

Oxygen tolerance

57507

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		96.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119503	4853 ChEBI	esculin	-	hydrolysis
119503	606565 ChEBI	hippurate	-	hydrolysis
119503	17632 ChEBI	nitrate	+	reduction
119503	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
119503	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119503	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
119503	15688 ChEBI	acetoin	-
119503	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119503	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
119503	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
119503	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
119503	caseinase	+	3.4.21.50
119503	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
119503	gamma-glutamyltransferase	+	2.3.2.2
119503	gelatinase	+
119503	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119503	lipase	-
68382	lipase (C 14)	-		from API zym
119503	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
119503	ornithine decarboxylase	-	4.1.1.17
119503	oxidase	+
119503	phenylalanine ammonia-lyase	-	4.3.1.24
119503	protease	+
68382	trypsin	+	3.4.21.4	from API zym
119503	tryptophan deaminase	-
119503	tween esterase	-
119503	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CMP-KDO biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	quinate degradation	100	2 of 2
66794	acetoin degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	kanosamine biosynthesis II	100	2 of 2
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	pentose phosphate pathway	100	11 of 11
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	proline metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	starch degradation	80	8 of 10
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	degradation of sugar acids	76	19 of 25
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	lactate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	d-xylose degradation	72.73	8 of 11
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	degradation of pentoses	71.43	20 of 28
66794	vitamin B1 metabolism	69.23	9 of 13
66794	lysine metabolism	69.05	29 of 42
66794	tryptophan metabolism	68.42	26 of 38
66794	lipid metabolism	67.74	21 of 31
66794	flavin biosynthesis	66.67	10 of 15
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	octane oxidation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	tyrosine metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	alanine metabolism	62.07	18 of 29
66794	methionine metabolism	61.54	16 of 26
66794	sulfate reduction	61.54	8 of 13
66794	arachidonate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	histidine metabolism	58.62	17 of 29
66794	mevalonate metabolism	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	nitrate assimilation	55.56	5 of 9
66794	carotenoid biosynthesis	54.55	12 of 22
66794	pantothenate biosynthesis	50	3 of 6
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	selenocysteine biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	isoprenoid biosynthesis	50	13 of 26
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	urea cycle	46.15	6 of 13
66794	oxidative phosphorylation	46.15	42 of 91
66794	metabolism of disaccharids	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	factor 420 biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	polyamine pathway	34.78	8 of 23
66794	cyanate degradation	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	catecholamine biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

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
119503	-	+	+	+	-	+	+	-	+	-	+	+	-	+	-	-	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Algae	#Red algae

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
4827	red alga (Delesseria sanguinea)	Delesseria sanguinea	Brittany, English Channel near Roscoff	France	FRA	Europe
119503	Red algae		Roscoff	France	FRA	Europe	1989

Taxonmaps

69479

Global distribution of 16S sequence AF208293 (>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
4827	1	Risk group (German classification) According to TRBA 466
119503	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	ASM97310v1 assembly for Zobellia galactanivorans DsiJT	complete	GCA_000973105	63186.3	2619619092	63186	98.53

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4827	Zobellia galactanovora 16S ribosomal RNA gene, partial sequence	AF208293	1483		63186

GC content

@ref	GC-content (mol%)	Method
4827	43-44	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: Zobellia galactanivorans strain Dsij
PATRIC: 63186.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.70	no
125439	motility	BacteriaNetⓘ	no	51.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	59.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Zobellia galactanivorans strain Dsij
PATRIC: 63186.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	95.26	yes
125438	spore-forming	spore-formingⓘ	no	88.93	no
125438	thermophilic	thermophileⓘ	no	99.10	yes
125438	aerobic	aerobicⓘ	yes	85.98	yes
125438	flagellated	motile2+ⓘ	no	91.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Unique alcohol dehydrogenases involved in algal sugar utilization by marine bacteria.	Brott S, Nam KH, Thomas F, Dutschei T, Reisky L, Behrens M, Grimm HC, Michel G, Schweder T, Bornscheuer UT.	Appl Microbiol Biotechnol	10.1007/s00253-023-12447-x	2023
Genetics	Mining of Microbial Genomes for the Novel Sources of Nitrilases.	Sharma N, Thakur N, Raj T, Savitri, Bhalla TC.	Biomed Res Int	10.1155/2017/7039245	2017
	Molecular cloning, expression, and functional characterization of the beta-agarase AgaB-4 from Paenibacillus agarexedens.	Chen ZW, Lin HJ, Huang WC, Hsuan SL, Lin JH, Wang JP.	AMB Express	10.1186/s13568-018-0581-8	2018
Biotechnology	Hyper-production and characterization of the iota-carrageenase useful for iota-carrageenan oligosaccharide production from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94T, and insight into the unusual catalytic mechanism.	Hatada Y, Mizuno M, Li Z, Ohta Y	Mar Biotechnol (NY)	10.1007/s10126-010-9312-0	2010
Phylogeny	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

#4827	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12802
#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 )
#38637	; Curators of the CIP;
#57507	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 47099
#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 )
#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 .
#119503	Collection of Institut Pasteur ; Curators of the CIP; CIP 106680
#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 galactanivorans (DSM 12802, CIP 106680, CCUG 47099)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000973105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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