Name: Enterovibrio nigricans DSM 22720
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17218

Type strain:

Species: Enterovibrio nigricans

Culture col. no.: DSM 22720, CAIM 661, CECT 7320, DAl 1-1-5

Strain history: <- M. J. Pujalte, Departamento de Microbiología y Ecologia, Universidad de Valencia, Spain

NCBI tax ID(s): 1121868 (strain), 504469 (species)

SI-ID 362303

CECT 7320

Special Collections

Section

When using BacDive for research please cite our paper

Enterovibrio nigricans DSM 22720 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from head kidney of Sparus aurata.

Gram-negative
motile
rod-shaped
facultative anaerobe
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	*Enterovibrio*
	Species	**Enterovibrio nigricans**
	Full Scientific Name (LPSN)	Enterovibrio nigricans Pascual et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28935]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %100
[Ref.: #125439]	Gram stain	negative Confidence in %98.7

[Ref.: #28935]	Cell length	1.25 µm

[Ref.: #28935]	Cell width	0.55 µm

[Ref.: #28935]	Cell shape	rod-shaped

[Ref.: #28935]	Motility	yes

[Ref.: #28935]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16479]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #16479]

Culture medium growth

[Ref.: #16479]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16479]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16479]	growth	28 °C
[Ref.: #28935]	growth	15-28 °C
[Ref.: #28935]	optimum	21.5 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28935]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97.5

[Ref.: #125439]

Ability of spore formation

no Confidence in %98.9

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28935]		NaCl		growth	0.9-6	%
[Ref.: #28935]		NaCl		optimum	3.45	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[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.: #28935]	glucose ChEBI	+	carbon source
[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.: #28935]	mannose ChEBI	+	carbon source
[Ref.: #28935]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #28935]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #28935]	sucrose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #28935]	tween 80 ChEBI	+	carbon source
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

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

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	+	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #28935]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

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.: #16479]	27995	+	-	+	+	-	+	-	-	+/-	-	+/-	-	+/-	-	-	-	-	-	-	-	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[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]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	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]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	peptidoglycan biosynthesis	66.67	10 of 15
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	arachidonic acid metabolism	50	9 of 18
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		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.: #16479]	Sample type/isolated from	head kidney of Sparus aurata
[Ref.: #16479]	Host species	Sparus aurata
[Ref.: #16479]	Geographic location (country and/or sea, region)	Mediterranean coast, Alcanar
[Ref.: #16479]	Country	Spain
[Ref.: #16479]	Country ISO 3 Code	ESP
[Ref.: #16479]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Fishes	-
#Host Body-Site	#Urogenital tract	#Kidney

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM942722 (>99% sequence identity) for Enterovibrio nigricans subclade from Microbeatlas

Aquatic Samples	205
Soil Samples	20
Animal Samples	98
Plant Samples
Total Samples	323

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

[Ref.: #16479]	Pathogenicity (animal)	yes, in single cases
[Ref.: #16479]	Biosafety level	1	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.: #16479]	Enterovibrio nigricans partial 16S rRNA gene, type strain DAL 1-1-5T	AM942722	1493	GenBank ENA	504469 tax ID

Genome sequence information:

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

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Enterovibrio nigricans DSM 22720	GCA_900167155	scaffold	GenBank ENA	1121868 tax ID	*
[Ref.: #66792]	Enterovibrio nigricans CAIM 661	GCA_002835505	contig	GenBank ENA	504469 tax ID	*
[Ref.: #66792]	Enterovibrio nigricans DSM 22720 strain DSM 22720	1121868.4	wgs	PATRIC	1121868 tax ID	*
[Ref.: #66792]	Enterovibrio nigricans strain CAIM 661	504469.3	wgs	PATRIC	504469 tax ID	*
[Ref.: #66792]	Enterovibrio nigricans DSM 22720	2568526010	draft	JGI IMG/M	1121868 tax ID	*
[Ref.: #66792]	Enterovibrio nigricans CAIM 661	2834490561	draft	JGI IMG/M	504469 tax ID	*

[Ref.: #16479]

GC-content

47.9 mol%

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: Enterovibrio nigricans DSM 22720 DSM 22720 NCBI: GCA_900167155.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	100	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	92.825	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	62.531	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	89.117	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.875	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	86.783	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Enterovibrio nigricans DSM 22720 NCBI: GCA_900167155
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	80.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.5

Availability in culture collections External links

[Ref.: #16479]

Culture collection no.

DSM 22720, CAIM 661, CECT 7320, DAl 1-1-5

[Ref.: #86217]

SI-ID 362303

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Enterovibrio nigricans sp. nov., reclassification of Vibrio calviensis as Enterovibrio calviensis comb. nov. and emended description of the genus Enterovibrio Thompson et al. 2002.	Pascual J, Macian MC, Arahal DR, Garay E, Pujalte MJ	Int J Syst Evol Microbiol	10.1099/ijs.0.001990-0	2009	*

References

#16479

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22720

#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 )

#28935

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 #25374 (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 )

#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 .

#86217

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-ID362303.1 )

#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 .

#25374

IJSEM 698 2009 ( DOI 10.1099/ijs.0.001990-0 , PubMed 19329591 )

* These data were automatically processed and therefore are not curated

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Enterovibrio nigricans DSM 22720 DSM 22720

Enterovibrio nigricans DSM 22720

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Change proposal