Vibrio variabilis (DSM 26147, CAIM 1454, LMG 25438)

Name: Vibrio variabilis (DSM 26147, CAIM 1454, LMG 25438)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17363

Type strain

Strain Designation R-40492

Culture col. no. DSM 26147 CAIM 1454 LMG 25438 R-40492

NCBI tax ID(s) 990271

Special Collections DSMZ

History <- LMG <- I. Cleenwerck, BCCM/LMG <- L. Chimetto, Universidade Estadual de Campinas, Brazil

Links

Vibrio variabilis R-40492 is a mesophilic prokaryote that was isolated from mucus of the zoanthid Palythoa caribaeorum.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 361316

DSM 26147,CAIM 1454,LMG 25438

@ref 20215

Last LPSN update 2026-02-09 11:22:12

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Vibrio

Species Vibrio variabilis

Full scientific name Vibrio variabilis Chimetto et al. 2011

BacDive ID	Other strains from **Vibrio variabilis** (1)	Type strain
162443	V. variabilis JCM 19239

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.7
125438	negative	99

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18169	REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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
18169	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.3

Spore formation

@ref	Spore formation	Confidence
125439		99.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	starch degradation	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	threonine metabolism	100	10 of 10
66794	Entner Doudoroff pathway	100	10 of 10
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	vitamin K metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	aerobactin biosynthesis	100	1 of 1
66794	4-hydroxyphenylacetate degradation	100	10 of 10
66794	tetrahydrofolate metabolism	100	14 of 14
66794	ubiquinone biosynthesis	100	7 of 7
66794	folate polyglutamylation	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	photosynthesis	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	vitamin B6 metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	pyrimidine metabolism	88.89	40 of 45
66794	isoleucine metabolism	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	degradation of sugar alcohols	87.5	14 of 16
66794	purine metabolism	87.23	82 of 94
66794	heme metabolism	85.71	12 of 14
66794	urea cycle	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	gallate degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	degradation of hexoses	77.78	14 of 18
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	alanine metabolism	75.86	22 of 29
66794	acetate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	degradation of pentoses	75	21 of 28
66794	flavin biosynthesis	73.33	11 of 15
66794	metabolism of disaccharids	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	tryptophan metabolism	71.05	27 of 38
66794	non-pathway related	71.05	27 of 38
66794	arginine metabolism	70.83	17 of 24
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	phenol degradation	70	14 of 20
66794	oxidative phosphorylation	69.23	63 of 91
66794	histidine metabolism	68.97	20 of 29
66794	degradation of sugar acids	68	17 of 25
66794	lipid metabolism	67.74	21 of 31
66794	acetoin degradation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	enterobactin biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	lysine metabolism	66.67	28 of 42
66794	citric acid cycle	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	methionine metabolism	61.54	16 of 26
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	glycine betaine biosynthesis	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	polyamine pathway	56.52	13 of 23
66794	nitrate assimilation	55.56	5 of 9
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	androgen and estrogen metabolism	50	8 of 16
66794	phenylmercury acetate degradation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	catecholamine biosynthesis	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	ascorbate metabolism	40.91	9 of 22
66794	3-phenylpropionate degradation	40	6 of 15
66794	O-antigen biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	vitamin B12 metabolism	35.29	12 of 34
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Cnidaria (Corals)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
18169	mucus of the zoanthid Palythoa caribaeorum	Palythoa caribaeorum	São Paulo, São Sebastião Channel, Portinho Beach	Brazil	BRA	Middle and South America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18169	1	Risk group (German 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	ASM326378v1 assembly for Vibrio variabilis CAIM 1454	contig	GCA_003263785	990271.24	8117303900	990271	31.38
66792	Vibrio variabilis strain CAIM 1454	contig		990271.12		990271	23.7

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18169	Vibrio variabilis strain R-40492 16S ribosomal RNA (16S rRNA) gene, partial sequence	GU929924	1328		990271

GC content

18169

GC-content (mol%)46.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vibrio variabilis CAIM 1454
NCBI: GCA_003263785

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.10	no
125439	motility	BacteriaNetⓘ	yes	79.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vibrio variabilis strain CAIM 1454
PATRIC: 990271.12

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	93.12	no
125438	aerobic	aerobicⓘ	no	57.97	no
125438	spore-forming	spore-formingⓘ	no	87.86	no
125438	thermophilic	thermophileⓘ	no	99.00	no
125438	flagellated	motile2+ⓘ	yes	89.38	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms.	Zhang X, Liang Y, Zheng K, Wang Z, Dong Y, Liu Y, Ren L, Wang H, Han Y, McMinn A, Sung YY, Mok WJ, Wong LL, He J, Wang M.	Front Microbiol	10.3389/fmicb.2023.1161265	2023
Genetics	Description and Genome-Based Analysis of Vibrio chaetopteri sp. nov., a New Species of the Mediterranei Clade Isolated from a Marine Polychaete.	Kurilenko V, Bystritskaya E, Otstavnykh N, Velansky P, Lichmanuk D, Savicheva Y, Romanenko L, Isaeva M.	Microorganisms	10.3390/microorganisms13030638	2025
	Vibrio sinus sp. nov., a marine bacterium isolated from coastal seawater.	Wang W, Zhao W, Cao B, Liu R, Cheng H, Tian P, Xiao J, Xu Z, Wang X, Niu W.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005676	2023
Phylogeny	Vibrio ulleungensis sp. nov., isolated from Mytilus coruscus.	Moon YL, Park JS	Int J Syst Evol Microbiol	10.1099/ijsem.0.005136	2021
Phylogeny	Vibrio agarilyticus sp. nov., an agar-digesting marine bacterium isolated from coastal seawater in Daya Bay (Guangdong, China).	Wang X, Guo F, Tian P, Yu S, Xue CX, Wang W, Xiao J, Niu W	Int J Syst Evol Microbiol	10.1099/ijsem.0.004647	2021
Phylogeny	Vibrio hannami sp. nov., Isolated from Seawater.	Lee GE, Im WT, Park JS	Curr Microbiol	10.1007/s00284-017-1376-x	2017
Phylogeny	Vibrio variabilis sp. nov. and Vibrio maritimus sp. nov., isolated from Palythoa caribaeorum.	Chimetto LA, Cleenwerck I, Moreira APB, Brocchi M, Willems A, De Vos P, Thompson FL	Int J Syst Evol Microbiol	10.1099/ijs.0.026997-0	2011
Phylogeny	Vibrio ostreae sp. nov., a novel gut bacterium isolated from a Yellow Sea oyster.	Muhammad N, Nguyen TTH, Lee YJ, Ko J, Avila F, Kim SG	Int J Syst Evol Microbiol	10.1099/ijsem.0.005586	2022

References

#18169	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26147
#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 )
#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 )
#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 variabilis (DSM 26147, CAIM 1454, LMG 25438)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003263785

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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