Name: Vibrio aphrogenes CA-1004
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 139783

Type strain:

Species: Vibrio aphrogenes

Strain Designation: CA-1004

Culture col. no.: DSM 103759, JCM 31643

Strain history: T. Sawabe; Fac. of Fish. Sci., Hokkaido Univ., Japan; CA-1004.

NCBI tax ID(s): 1891186 (species)

SI-ID 405660

DSM 103759

Special Collections

DSMZ
JCM

Section

Vibrio aphrogenes CA-1004 is a bacterium that was isolated from surface of seaweed.

16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	*Vibrio*
	Species	**Vibrio aphrogenes**
	Full Scientific Name (LPSN)	Vibrio aphrogenes Tanaka et al. 2018

Information on culture and growth conditions Culture and growth conditions

[Ref.: #42391]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #42391]

Culture medium growth

[Ref.: #42391]

Culture medium link

Medium recipe at MediaDive

[Ref.: #42391]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #42391]			growth	28 °C
[Ref.: #67770]			growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	L-arabinose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	nitrate ChEBI	+	reduction	* from API 20E
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	dinitrogen ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	yes	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E
[Ref.: #68368]	nitrite ChEBI	yes	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	+	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	-	3.2.1.23	* from API 20E
[Ref.: #68368]	cytochrome oxidase	+	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #42391]	17668	-	+	-	-	-	+	-	-	-	-	-	+	+	-	-	-	-	-	+	-	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #42391]	Sample type/isolated from	surface of seaweed
[Ref.: #42391]	Geographic location (country and/or sea, region)	Mie Prefecture
[Ref.: #42391]	Country	Japan
[Ref.: #42391]	Country ISO 3 Code	JPN
[Ref.: #42391]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Surface of seaweed collected on the coast of Mie Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Algae	-
#Host	#Plants	#Aquatic plant
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX713151 (>99% sequence identity) for Vibrio from Microbeatlas

Aquatic Samples	74
Soil Samples	5
Animal Samples	66
Plant Samples	7
Total Samples	152

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #42391]	Vibrio aphrogenes strain CA-1004 16S ribosomal RNA gene, partial sequence	KX713151	1477	GenBank ENA	1891186 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Vibrio aphrogenes CA-1004	GCA_002157735	complete	GenBank ENA	1891186 tax ID
[Ref.: #66792]	Vibrio aphrogenes CA-1004	2791355440	draft	JGI IMG/M	1891186 tax ID	*

[Ref.: #67770]

GC-content

42.1 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Vibrio aphrogenes CA-1004 NCBI: GCA_002157735.2
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

Availability in culture collections External links

[Ref.: #42391]

Culture collection no.

DSM 103759, JCM 31643

[Ref.: #96226]

SI-ID 405660

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vibrio gangliei sp. nov., a novel member of Vibrionaceae isolated from sawdust in a pigpen.	Meng YC, Liu HC, Zhou YG, Cai M, Kang Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.002779	2018	*
Phylogeny	Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed.	Tanaka M, Endo S, Kotake F, Al-Saari N, Amin AKMR, Feng G, Mino S, Doi H, Ogura Y, Hayashi T, Suda W, Hattori M, Yumoto I, Sawabe T, Sawabe T, Araki T	PLoS One	10.1371/journal.pone.0180053	2017	*

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 )

#42391

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103759

#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;

#68368

Automatically annotated from API 20E .

#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 .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#96226

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID405660.1 )

* These data were automatically processed and therefore are not curated

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