Vibrio taketomensis (DSM 106943, CAIM 1928, JCM 33434)

Name: Vibrio taketomensis (DSM 106943, CAIM 1928, JCM 33434)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158992

Type strain

Strain Designation C4III282

Culture col. no. DSM 106943 CAIM 1928 JCM 33434 C4III282

NCBI tax ID(s) 2572923

Special Collections DSMZ JCM

History <- T. Sawabe, Inst. Low Temperature Sci., Hokkaido Univ., Sapporo, Japan; C4III282 <- T. Sawabe; Hokkaido Univ., Japan; C4III282.

Links

Vibrio taketomensis C4III282 is a bacterium that was isolated from seawater.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401188

CAIM 1928,JCM 33434,DSM 106943

@ref 20215

Last LPSN update 2026-02-09 11:38:29

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Vibrio

Species Vibrio taketomensis

Full scientific name Vibrio taketomensis Tanaka et al. 2021

BacDive ID	Other strains from **Vibrio taketomensis** (1)	Type strain
158991	V. taketomensis C4III291, DSM 106942, CAIM 1929

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	100
125439	negative	96.6

Multimedia

@ref:	65815
multimedia content:	DSM_106943.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_106943.jpg
caption:	DSM 106942 on medium 514f at 25 °C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
65815	MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)		Medium recipe at MediaDive	Name: MARINE BROTH (ROTH CP73) (DSMZ Medium 514f) Composition: NaCl 19.4 g/l Agar 15.0 g/l MgCl2 8.8 g/l 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)
65815	positive	growth	25
67770	positive	growth	25

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.4

Spore formation

@ref	Spore formation	Confidence
125438		90.415
125439		97.4

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
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
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
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
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

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
65815	+	-	+	+	-	-	-	-	+	-	+	-	+	+	+	+	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
65815	seawater	Taketomi, Okinawa, Exclusive economic zone (24° 20' 18.1'' N, 124° 25' 56.5'' E)	Japan	JPN	Asia	24.3384	124.099 24.3384/124.099
67770	Seawater from a site off the Taketomicoral coral reef	Okinawa	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC469309 (>99% sequence identity) for Vibrio from Microbeatlas

Aquatic Samples	733
Soil Samples	42
Animal Samples	407
Plant Samples	80
Total Samples	1262

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM993816v1 assembly for Vibrio taketomensis C4III282	complete	GCA_009938165	2572923.3	2908849201	2572923	94.41

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
65815	Vibrio taketomensis C4III282 gene for 16S ribosomal RNA, partial sequence	LC469309	1501		2572923

GC content

@ref	GC-content (mol%)	Method
65815	44.3	sequence analysis
67770	44.3	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vibrio taketomensis C4III282
NCBI: GCA_009938165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.40	no
125439	motility	BacteriaNetⓘ	yes	73.60	no
125439	gram_stain	BacteriaNetⓘ	negative	96.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vibrio taketomensis C4III282
NCBI: GCA_009938165.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	95.59	no
125438	aerobic	aerobicⓘ	no	69.91	no
125438	spore-forming	spore-formingⓘ	no	90.42	no
125438	thermophilic	thermophileⓘ	no	99.07	yes
125438	flagellated	motile2+ⓘ	yes	88.37	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vibrio taketomensis sp. nov. by genome taxonomy.	Tanaka M, Hongyu B, Jiang C, Mino S, Milet Meirelles P, Thompson F, Gomez-Gil B, Sawabe T	Syst Appl Microbiol	10.1016/j.syapm.2019.126048	2019

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 )
#65815	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 106943
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 .
#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 taketomensis (DSM 106943, CAIM 1928, JCM 33434)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_009938165

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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