Zeaxanthinibacter enoshimensis (DSM 18435, CCUG 53613, NBRC 101990)

Name: Zeaxanthinibacter enoshimensis (DSM 18435, CCUG 53613, NBRC 101990)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5729

Type strain

Strain Designation TD-ZE3

Culture col. no. DSM 18435 CCUG 53613 NBRC 101990 CIP 109560 TD-ZE3

NCBI tax ID(s) 392009

Special Collections DSMZ CCUG CIP Literature strains

History DSMZ <- K. Ueda, Nihon Univ., Fujisawa; TD-ZE3 <- D. Asker CIP <- 2007 CCUG <- 2006, D. Asker, K. Ueda, Nihon Univ., Fujisawa, Japan: strain TD-ZE3

Links

Zeaxanthinibacter enoshimensis TD-ZE3 is an aerobe, Gram-negative, motile bacterium that was isolated from shallow seawater.

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

Name and taxonomic classification

SI-ID 302777

CCUG 53613,NBRC 101990,DSM 18435,CIP 109560

@ref 20215

Last LPSN update 2026-05-29 08:26:14

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Zeaxanthinibacter

Species Zeaxanthinibacter enoshimensis

Full scientific name Zeaxanthinibacter enoshimensis Asker et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
31939	negative	2.55 µm	0.3 µm	rod-shaped	gliding
119033	negative			rod-shaped
125438						95
125438	negative					97.701

Colony morphology

59946

Incubation period1 day

Pigmentation

31939

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7550	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
42001	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
119033	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7550	positive	growth	30
31939	positive	growth	16-40
31939	positive	optimum	28-30
42001	positive	growth	37
59946	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
31939	positive	optimum	07-08
31939	positive	growth	5.5-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31939	aerobe
59946	aerobe
119033	obligate aerobe
125438	aerobe	90.029
125439	obligate anaerobe	94.423

Spore formation

@ref	Spore formation	Confidence
31939
125439		96.177

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31939	NaCl	positive	growth	01-07 %
31939	NaCl	positive	optimum	4 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31939	22599 ChEBI	arabinose	+	carbon source
31939	17057 ChEBI	cellobiose	+	carbon source
31939	4853 ChEBI	esculin	+	hydrolysis
31939	24265 ChEBI	gluconate	+	carbon source
31939	17234 ChEBI	glucose	+	carbon source
31939	17716 ChEBI	lactose	+	carbon source
31939	17306 ChEBI	maltose	+	carbon source
31939	37684 ChEBI	mannose	+	carbon source
31939	28053 ChEBI	melibiose	+	carbon source
31939	37657 ChEBI	methyl D-glucoside	+	carbon source
119033	17632 ChEBI	nitrate	-	reduction
119033	16301 ChEBI	nitrite	-	reduction
31939	16634 ChEBI	raffinose	+	carbon source
31939	17992 ChEBI	sucrose	+	carbon source
31939	27082 ChEBI	trehalose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119033	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
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
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	+	3.2.1.31	from API zym
31939	catalase	+	1.11.1.6
119033	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
31939	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119033	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
119033	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	kanosamine biosynthesis II	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	CMP-KDO biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	sulfopterin metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	folate polyglutamylation	100	1 of 1
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	starch degradation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	vitamin K metabolism	80	4 of 5
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	glycogen biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	tryptophan metabolism	73.68	28 of 38
66794	purine metabolism	73.4	69 of 94
66794	proline metabolism	72.73	8 of 11
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	tyrosine metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	arginine metabolism	70.83	17 of 24
66794	leucine metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	pyrimidine metabolism	68.89	31 of 45
66794	lipid metabolism	67.74	21 of 31
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	citric acid cycle	64.29	9 of 14
66794	lysine metabolism	64.29	27 of 42
66794	glutathione metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	glycogen metabolism	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	cellulose degradation	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	methionine metabolism	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	ribulose monophosphate pathway	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	isoprenoid biosynthesis	50	13 of 26
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	resorcinol degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of pentoses	46.43	13 of 28
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	carotenoid biosynthesis	40.91	9 of 22
66794	ascorbate metabolism	40.91	9 of 22
66794	oxidative phosphorylation	40.66	37 of 91
66794	gallate degradation	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	sulfate reduction	38.46	5 of 13
66794	degradation of sugar alcohols	37.5	6 of 16
66794	d-xylose degradation	36.36	4 of 11
66794	phenol degradation	35	7 of 20
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	pantothenate biosynthesis	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of sugar acids	32	8 of 25
66794	vitamin B1 metabolism	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	androgen and estrogen metabolism	25	4 of 16
66794	alginate biosynthesis	25	1 of 4
66794	arachidonic acid metabolism	22.22	4 of 18

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
119033	-	+	+	+	-	+	+	+	+	+	+	+	-	-	+	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
7550	shallow seawater		Pacific coastline of Japan near Enoshima Island	Japan	JPN	Asia
59946	Seawater	2005-04-10	near the Enoshima Island	Japan	JPN	Asia
119033	Environment, Sea water		Enoshima Island	Japan	JPN	Asia	2005

Taxonmaps

69479

Global distribution of 16S sequence AB681649 (>99% sequence identity) for Zeaxanthinibacter enoshimensis subclade from Microbeatlas

Aquatic Samples	1198
Soil Samples	35
Animal Samples	28
Plant Samples	1
Total Samples	1262

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7550	1	Risk group (German classification) According to TRBA 466
119033	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	ASM436286v1 assembly for Zeaxanthinibacter enoshimensis DSM 18435	scaffold	GCA_004362865	392009.4	2731639225	392009	77.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Zeaxanthinibacter enoshimensis gene for 16S rRNA, partial sequence, strain: NBRC 101990	AB681649	1452		392009
7550	Zeaxanthinibacter enoshimensis gene for 16S rRNA, partial sequence	AB264057	1431		392009

GC content

7550

GC-content (mol%)46.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM436286v1 assembly for Zeaxanthinibacter enoshimensis DSM 18435
NCBI: GCA_004362865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	94.42	no
125439	gram_stain	BacteriaNetⓘ	negative	78.65	no
125439	motility	BacteriaNetⓘ	no	82.97	no
125439	spore_formation	BacteriaNetⓘ	no	96.18	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Zeaxanthinibacter enoshimensis DSM 18435
NCBI: GCA_004362865.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.70	yes
125438	anaerobic	anaerobicⓘ	no	97.78	yes
125438	aerobic	aerobicⓘ	yes	90.03	yes
125438	spore-forming	spore-formingⓘ	no	89.25	no
125438	thermophilic	thermophileⓘ	no	97.44	no
125438	flagellated	motile2+ⓘ	no	95.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Bacillus pinisoli sp. nov., Isolated from Soil of a Decayed Pine Tree.	Huang Y, Cai H, Qin S, Yang L, Zhou Y, Wu J, Chen X, Jiang M, Jiang Y, Ihsan YN.	Curr Microbiol	10.1007/s00284-022-03130-x	2022
Phylogeny	Zeaxanthinibacter aestuarii sp. nov., isolated from estuary sediment and emended description of the genus Zeaxanthinibacter Asker et al. 2007.	Lee Y, Jeong HI, Jeong SE, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.001185	2016
Phylogeny	Zeaxanthinibacter enoshimensis gen. nov., sp. nov., a novel zeaxanthin-producing marine bacterium of the family Flavobacteriaceae, isolated from seawater off Enoshima Island, Japan.	Asker D, Beppu T, Ueda K	Int J Syst Evol Microbiol	10.1099/ijs.0.64682-0	2007

References

#7550	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18435
#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 )
#28195	IJSEM 837 2007 ( DOI 10.1099/ijs.0.64682-0 , PubMed 17392216 )
#31939	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 #28195
#42001	; Curators of the CIP;
#59946	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53613
#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 .
#119033	Collection of Institut Pasteur ; Curators of the CIP; CIP 109560
#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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Zeaxanthinibacter enoshimensis (DSM 18435, CCUG 53613, NBRC 101990)

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

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_004362865

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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