Name: Vibrio azureus LC2-005
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17349

Type strain:

Species: Vibrio azureus

Strain Designation: LC2-005

Culture col. no.: DSM 23306, KCTC 22352, NBRC 104587

Strain history: <- NBRC <- S. Yoshizawa, Ocean Res. Inst., Univ. Tokyo, Japan; LC2-005

NCBI tax ID(s): 1219077 (strain), 512649 (species)

Section

Vibrio azureus LC2-005 is a mesophilic, Gram-negative, motile bacterium that was isolated from seawater.

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

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

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	*Vibrio*
	Species	**Vibrio azureus**
	Full Scientific Name (PNU)	Vibrio azureus Yoshizawa et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #29024]	Gram stain	negative
[Ref.: #29024]	Cell shape	rod-shaped
[Ref.: #29024]	Motility	yes

[Ref.: #29024]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16779]

Culture medium

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

[Ref.: #16779]

Culture medium growth

[Ref.: #16779]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #16779]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16779]	growth	28 °C
[Ref.: #29024]	growth	10-37 °C
[Ref.: #29024]	optimum	23.5 °C

[Ref.: #16779]	Temperature range	mesophilic
[Ref.: #29024]	Temperature range	psychrophilic

Information on physiology and metabolism Physiology and metabolism

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29024]		NaCl		growth	0.5-6	%
[Ref.: #29024]		NaCl		optimum	3.25	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29024]		glucose ChEBI	+	carbon source
[Ref.: #29024]		leucine ChEBI	+	carbon source

	Metabolite production	Metabolite
[Ref.: #29024]		indole ChEBI

	Physiological tests	Metabolite	Indole test
[Ref.: #29024]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #29024]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29024]	catalase	+	1.11.1.6
[Ref.: #29024]	cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	oxidative phosphorylation	53.85	49 of 91
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	degradation of sugar acids	28	7 of 25
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	vitamin B12 metabolism	23.53	8 of 34
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #16779]	Sample type/isolated from	seawater
[Ref.: #16779]	Geographic location (country and/or sea, region)	Kuroshio Region (32° 30' N 138° 00' E; depth: 200 m)
[Ref.: #16779]	Country	Japan
[Ref.: #16779]	Country ISO 3 Code	JPN
[Ref.: #16779]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16779]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #20218]	Vibrio azureus gene for 16S rRNA, partial sequence, strain: NBRC 104587	AB682211	1477	ENA	512649 tax ID	*
[Ref.: #16779]	Vibrio azureus gene for 16S rRNA, partial sequence, strain: LC2-005 (= NBRC 104587)	AB428897	1298	ENA	512649 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Vibrio azureus LC2-005	GCA_002849855	chromosome	GenBank	512649 tax ID	*
[Ref.: #66792]	Vibrio azureus NBRC 104587 NBRC 104587	GCA_000467165	contig	GenBank	1219077 tax ID	*
[Ref.: #66792]	Vibrio azureus NBRC 104587 NBRC 104587	GCA_000400265	scaffold	GenBank	1219077 tax ID	*
[Ref.: #66792]	Vibrio azureus NBRC 104587	1219077.3	wgs	PATRIC	1219077 tax ID	*
[Ref.: #66792]	Vibrio azureus NBRC 104587	1219077.9	wgs	PATRIC	1219077 tax ID	*
[Ref.: #66792]	Vibrio azureus strain LC2-005	512649.4		PATRIC	512649 tax ID	*

[Ref.: #16779]

GC-content

45.2 mol%

Availability in culture collections External links

[Ref.: #16779]

Culture collection no.

DSM 23306, KCTC 22352, NBRC 104587

[Ref.: #20218]

Associated Passport(s) in StrainInfo

843360, 843361

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vibrio azureus sp. nov., a luminous marine bacterium isolated from seawater.	Yoshizawa S, Wada M, Kita-Tsukamoto K, Ikemoto E, Yokota A, Kogure K	Int J Syst Evol Microbiol	10.1099/ijs.0.004283-0	2009	*
Metabolism	Vibrio azureus emits blue-shifted light via an accessory blue fluorescent protein.	Yoshizawa S, Karatani H, Wada M, Kogure K	FEMS Microbiol Lett	10.1111/j.1574-6968.2012.02507.x	2012	*
Genetics	Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences.	Urbanczyk H, Ogura Y, Hayashi T	Int J Syst Evol Microbiol	10.1099/ijs.0.051110-0	2013	*

References

#16779

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23306

#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 )

#29024

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 #25454 (see below)

#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 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#25454

IJSEM 1645 2009 ( DOI 10.1099/ijs.0.004283-0 , PubMed 19542136 )

* These data were automatically processed and therefore are not curated

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