Name: Beneckea nigripulchritudo 164
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17326

Type strain:

Species: Beneckea nigripulchritudo

Strain Designation: 164

Culture col. no.: DSM 21607, ATCC 27043, CAIM 323, CCUG 16376, CCUG 28586, CIP 103195, LMG 3896, NCIMB 1904

Strain history: CIP <- 1988, NCIB <- 1972, P. Baumann: strain 164, Beneckea nigripulchrituda

NCBI tax ID(s): 1051649 (strain), 28173 (species)

SI-ID 5108

LMG 3896, ATCC 27043, CCUG 16376, NCMB 1904, CCUG 28586, CECT 628, CIP 103195, NCIMB 1904, CCRC 12915, KCTC 2723, BCRC 12915, DSM 21607

Special Collections

Section

When using BacDive for research please cite our paper

Beneckea nigripulchritudo 164 is a mesophilic, Gram-negative, motile bacterium that was isolated from Sea water.

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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	Beneckea
	Species	Beneckea nigripulchritudo
	Full Scientific Name (LPSN)	Beneckea nigripulchritudo corrig. Baumann et al. 1971 (Approved Lists 1980)

	Synonym	Beneckea nigrapulchrituda
	Synonym	Beneckea nigrapulchritoda
	Synonym	**Vibrio nigripulchritudo**

Information on morphological and physiological properties Morphology

[Ref.: #121300]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %99.5
[Ref.: #125439]	Gram stain	negative Confidence in %98.2

[Ref.: #121300]	Cell shape	rod-shaped

[Ref.: #121300]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15841]

Culture medium

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

[Ref.: #15841]

Culture medium growth

[Ref.: #15841]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15841]

Culture medium composition

expand / minimize

[Ref.: #35504]

Culture medium

Marine agar (MA)

[Ref.: #35504]

Culture medium growth

[Ref.: #35504]

Culture medium composition

expand / minimize

[Ref.: #121300]

Culture medium

CIP Medium 13

[Ref.: #121300]

Culture medium growth

[Ref.: #121300]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #15841]		growth	28 °C
[Ref.: #35504]		growth	25 °C
[Ref.: #121300]		growth	15-41 °C
[Ref.: #121300]	no	growth	5 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #125439]

Oxygen tolerance

obligate aerobe Confidence in %97.9

[Ref.: #125439]

Ability of spore formation

no Confidence in %97.6

	Salt	Tested relation		Salt conc.
[Ref.: #121300]	NaCl		growth	2-6	%
[Ref.: #121300]	NaCl	no	growth	0	%
[Ref.: #121300]	NaCl	no	growth	8	%
[Ref.: #121300]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #121300]	citrate ChEBI	-	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	fermentation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #121300]	esculin ChEBI	-	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #121300]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #121300]	nitrite ChEBI	-	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #121300]		indole ChEBI	yes
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #121300]	acetoin ChEBI	-
[Ref.: #121300]	glucose ChEBI		-
[Ref.: #68369]	indole ChEBI			-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121300]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #121300]	amylase	+
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #121300]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121300]	caseinase	+	3.4.21.50
[Ref.: #121300]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121300]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #121300]	gelatinase	+
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #121300]	lecithinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121300]	lipase	+
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121300]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121300]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121300]	oxidase	+
[Ref.: #121300]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #121300]	protease	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121300]	tryptophan deaminase	-
[Ref.: #121300]	tween esterase	+
[Ref.: #121300]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #15841]	28336	+	-	+	-	-	+	+	+	-	-	+/-	+	-	+	-	-	+	+	+	+	+

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #121300]	350	not determinedn.d.	+	-	-	+	-	-	+	+	-	-	-	+	-	+	+	-	-	-	+	+	-	-	-	-	+	-	-	-	-	-	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	+	-	-	+	+	-	-	+	+	-	-	-	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121300]	7419	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	+	-	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	purine metabolism	88.3	83 of 94
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	4-hydroxyphenylacetate degradation	80	8 of 10
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	degradation of sugar acids	80	20 of 25
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	oxidative phosphorylation	73.63	67 of 91
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	O-antigen biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	ascorbate metabolism	59.09	13 of 22
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	phenol degradation	55	11 of 20
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	grixazone biosynthesis	50	1 of 2
[Ref.: #66794]	d-xylose degradation	45.45	5 of 11
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #15841]	Sample type/isolated from	Sea water

[Ref.: #121300]	Sample type/isolated from	Environment, Seawater enriched with chitin
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X74717 (>99% sequence identity) for Vibrio from Microbeatlas

Aquatic Samples	192
Soil Samples	22
Animal Samples	17
Plant Samples
Total Samples	231

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

[Ref.: #15841]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121300]	Biosafety level	2	Risk group (French classification)

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

16S Sequence information:

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

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #15841]	V.nigripulchritudo (ATCC 27043T) gene for 16S ribosomal RNA	X74717	1434	GenBank ENA	1051649 tax ID
[Ref.: #20218]	Vibrio nigripulchritudo 16S ribosomal RNA gene, partial sequence	HM771352	1470	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo DNA, 16S-23S ribosomal RNA intergenic spacer, type G, including tRNA-Glu, strain: ATCC 27043	AB515338	468	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo DNA, 16S-23S ribosomal RNA intergenic spacer, type GLV, including tRNA-Glu, tRNA-Lys, tRNA-Val, strain: ATCC 27043	AB515339	723	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo DNA, 16S-23S ribosomal RNA intergenic spacer, type GLAV, including tRNA-Glu, tRNA-Lys, tRNA-Ala, tRNA-Val, strain: ATCC 27043	AB515340	762	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo 16S rRNA	D11213	218	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo 16S rRNA	D11262	214	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo 16S rRNA	D11311	191	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo DNA, 16S-23S rRNA intergenic spacer and 23S rRNA, partial sequence, strain: ATCC 27043	AB255726	291	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu gene, complete sequence	AF413009	492	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu and tRNA-Val genes, complete sequence	AF413010	729	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu and tRNA-Val genes, complete sequence	AF413011	766	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu, tRNA-Ala, and tRNA-Val genes, complete sequence	AF413012	800	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ala gene, complete sequence	AF413013	472	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ala gene, complete sequence	AF413014	474	GenBank ENA	1051649 tax ID	*
[Ref.: #20218]	Vibrio nigripulchritudo strain ATCC 27043 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence	AF413015	571	GenBank ENA	1051649 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Vibrio nigripulchritudo ATCC 27043	GCA_000222685	contig	GenBank ENA	1051649 tax ID	*
[Ref.: #66792]	Vibrio nigripulchritudo ATCC 27043	1051649.3	wgs	PATRIC	1051649 tax ID	*
[Ref.: #66792]	Vibrio nigripulchritudo ATCC 27043	2512047078	draft	JGI IMG/M	1051649 tax ID	*

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Vibrio nigripulchritudo ATCC 27043 PATRIC: 1051649.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99.5	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.205	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	86.744	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	64.549	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.5	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	87.256	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vibrio nigripulchritudo ATCC 27043 NCBI: GCA_000222685
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	62.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.9

Availability in culture collections External links

[Ref.: #15841]

Culture collection no.

DSM 21607, ATCC 27043, CAIM 323, CCUG 16376, CCUG 28586, CIP 103195, LMG 3896, NCIMB 1904

[Ref.: #86326]

SI-ID 5108

References

#15841

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21607

#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 )

#35504 ; Curators of the CIP;

#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 )

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#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 .

#86326

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-ID5108.1 )

#121300 Collection of Institut Pasteur ; Curators of the CIP; CIP 103195

#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 .

* These data were automatically processed and therefore are not curated

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Vibrio nigripulchritudo ATCC 27043

Vibrio nigripulchritudo ATCC 27043

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