Vibrio ezurae (DSM 17533, IAM 15061, LMG 19970)

Name: Vibrio ezurae (DSM 17533, IAM 15061, LMG 19970)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17311

Type strain

Strain Designation HDS1-1

Culture col. no. DSM 17533 IAM 15061 LMG 19970 CCUG 56779 NBRC 102218 3 more

NCBI tax ID(s) 1219080 252583

Special Collections DSMZ CCUG JCM CIP

History <- T. Sawabe IAM 15061 <-- T. Sawabe HDS1-1. CIP <- 2004, IAM <- T. Sawabe, Hokkaido Univ., Sapporo, Japan: strain HDS1-1

Links

Vibrio ezurae HDS1-1 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from gut of abalone Haliotis diversicolor aquatilis.

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

Name and taxonomic classification

SI-ID 85089

CAIM 905,LMG 19970,IAM 15061,IAM 15062,DSM 17533,NBRC 102218,JCM 21522,CIP 108520,JCM 21523,CCUG 56779

@ref 20215

Last LPSN update 2026-02-09 11:22:11

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Vibrio

Species Vibrio ezurae

Full scientific name Vibrio ezurae Sawabe et al. 2005

BacDive ID	Other strains from **Vibrio ezurae** (2)	Type strain
163218	V. ezurae JCM 21523, IAM 15062
163219	V. ezurae JCM 21524, IAM 15063, LMG 19979

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		100
125439	negative		99.4
119160	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7046	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
38279	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
119160	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7046	positive	growth	28	mesophilic
38279	positive	growth	30	mesophilic
61088	positive	growth	30	mesophilic
67770	positive	growth	25	mesophilic
119160	positive	growth	15-30
119160	negative	growth	5
119160	negative	growth	37
119160	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
61088	aerobe
119160	facultative anaerobe
125439	obligate aerobe	96.9

Spore formation

@ref	Spore formation	Confidence
125438		94.655
125439		99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119160	NaCl	positive	growth	2-8 %
119160	NaCl		growth	0 %
119160	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
119160	16947 ChEBI	citrate	-	carbon source
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
119160	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
119160	17234 ChEBI	glucose	+	fermentation
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
119160	17716 ChEBI	lactose	-	fermentation
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
119160	17632 ChEBI	nitrate	+	reduction
119160	17632 ChEBI	nitrate	+	respiration
119160	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
119160	132112 ChEBI	sodium thiosulfate	-	builds gas from
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68368	27897 ChEBI	tryptophan	+	energy source	from API 20E
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
119160	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test	Indole test
119160	15688 ChEBI	acetoin	-
68368	15688 ChEBI	acetoin	-			from API 20E
119160	17234 ChEBI	glucose		-
68368	35581 ChEBI	indole			+	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119160	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
119160	amylase	+
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
119160	beta-galactosidase	-	3.2.1.23
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119160	caseinase	-	3.4.21.50
119160	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68368	cytochrome oxidase	+	1.9.3.1	from API 20E
119160	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119160	gamma-glutamyltransferase	+	2.3.2.2
119160	gelatinase	-
68368	gelatinase	-		from API 20E
119160	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119160	lipase	-
68382	lipase (C 14)	-		from API zym
119160	lysine decarboxylase	-	4.1.1.18
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119160	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
119160	oxidase	+
119160	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
119160	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
119160	tween esterase	-
119160	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
7046	-	-	-	-	-	-	-	-	+	-	-	+	+	-	-	-	-	-	-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
119160	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
119160	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	#Stomach

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
7046	gut of abalone Haliotis diversicolor aquatilis	Haliotis diversicolor aquatilis	Kanagawa	Japan	JPN	Asia
61088	Cultured abalone gut (Halotis diversicolor aquat.)		Kanagawa	Japan	JPN	Asia	1999
67770	Gut of abalone (Haliotis aquatilis)	Haliotis aquatilis	Kanagawa Pref.	Japan	JPN	Asia
119160	Japonese abalones, gut, Haliotis diversicolor aquatilis			Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7046	1	Risk group (German classification) According to TRBA 466
119160	2	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
67770	Vezurae assembly for Vibrio ezurae HDS1-1	scaffold	GCA_003568985	252583.6	8033301637	252583	67.61
67770	ASM46718v1 assembly for Vibrio ezurae NBRC 102218	contig	GCA_000467185	1219080.4	2600255071	1219080	63.08

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Vibrio sp. LMG 19970 16S rRNA gene, strain LMG 19970	AJ316206	1429	170686
7046	Vibrio ezurae strain HDS1-1 16S ribosomal RNA gene, partial sequence	AY426980	1520	252583
124043	Vibrio ezurae gene for 16S rRNA, partial sequence, strain: NBRC 102218.	AB681732	1478	252583

GC content

@ref	GC-content (mol%)	Method
67770	43.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vibrio ezurae JCM 21522
NCBI: GCA_003568985

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	76.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vibrio ezurae NBRC 102218
PATRIC: 1219080.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	94.50	yes
125438	spore-forming	spore-formingⓘ	no	94.66	no
125438	aerobic	aerobicⓘ	no	70.48	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	no	67.59	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Prokaryotic viperins produce diverse antiviral molecules.	Bernheim A, Millman A, Ofir G, Meitav G, Avraham C, Avraham C, Shomar H, Rosenberg MM, Tal N, Melamed S, Amitai G, Sorek R.	Nature	10.1038/s41586-020-2762-2	2021
Phylogeny	Vibrio ishigakensis sp. nov., in Halioticoli clade isolated from seawater in Okinawa coral reef area, Japan.	Gao F, Al-Saari N, Rohul Amin AK, Sato K, Mino S, Suda W, Oshima K, Hattori M, Ohkuma M, Hargreaves PI, Meirelles PM, Thompson FL, Thompson C, Gomez-Gil B, Sawabe T, Sawabe T	Syst Appl Microbiol	10.1016/j.syapm.2016.04.002	2016
Phylogeny	Vibrio neonatus sp. nov. and Vibrio ezurae sp. nov. isolated from the gut of Japanese abalones.	Sawabe T, Hayashi K, Moriwaki J, Fukui Y, Thompson FL, Swings J, Christen R	Syst Appl Microbiol	10.1078/0723202041748154	2004

References

#7046	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17533
#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 )
#38279	; Curators of the CIP;
#61088	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56779
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#119160	Collection of Institut Pasteur ; Curators of the CIP; CIP 108520
#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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Vibrio ezurae (DSM 17533, IAM 15061, LMG 19970)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003568985

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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