Veronia nyctiphanis (DSM 24592, CAIM 600, CECT 7578)

Name: Veronia nyctiphanis (DSM 24592, CAIM 600, CECT 7578)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 157681

Type strain

Strain Designation 42Xb2

Culture col. no. DSM 24592 CAIM 600 CECT 7578 42Xb2

NCBI tax ID(s) 1278244 1902814

Special Collections DSMZ

Links

Veronia nyctiphanis 42Xb2 is a mesophilic prokaryote that was isolated from stomach of infected female of euphausid .

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 394963

DSM 24592,CAIM 600,CECT 7578

@ref 20215

Last LPSN update 2025-12-16 10:07:51

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Veronia

Species Veronia nyctiphanis

Full scientific name Veronia nyctiphanis Gomez-Gil et al. 2022

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99.8
125439	negative	99.4

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
64250	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)	Range
64250	positive	growth	28	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		91.915
125439		99.4

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
64250	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Arthropoda	#Crustacea
#Host Body-Site	#Gastrointestinal tract	#Stomach

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
64250	stomach of infected female of euphausid (Nyctiphanes simplex)	Gulf of Baja California	Mexico	MEX	North America

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	CAIM600T.1 assembly for Veronia nyctiphanis CAIM 600	scaffold	GCA_004116385	1278244.5	2894575800	1278244	32.45
66792	Enterovibrio sp. CAIM 600	contig		1278244.4		1278244	31.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64250	Vibrio sp. 42Xb2 16S ribosomal RNA gene, partial sequence	EU440061	845		1278244
124043	Enterovibrio sp. CAIM 600 16S ribosomal RNA gene, partial sequence.	JX129353	1445		1278244

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Veronia nyctiphanis CAIM 600
NCBI: GCA_004116385

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	80.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.40	no
125439	motility	BacteriaNetⓘ	yes	70.70	no
125439	spore_formation	BacteriaNetⓘ	no	99.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Veronia nyctiphanis CAIM 600
NCBI: GCA_004116385.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.80	no
125438	anaerobic	anaerobicⓘ	no	96.05	no
125438	aerobic	aerobicⓘ	yes	54.04	no
125438	spore-forming	spore-formingⓘ	no	91.92	no
125438	thermophilic	thermophileⓘ	no	99.50	no
125438	flagellated	motile2+ⓘ	yes	89.27	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Veronia nyctiphanis gen. nov., sp. nov., Isolated from the Stomach of the Euphausiid Nyctiphanes simplex (Hansen, 1911) in the Gulf of California, and Reclassification of Enterovibrio pacificus as Veronia pacifica comb. nov.	Gomez-Gil B, Gonzalez-Castillo A, Aguilar-Mendez MJ, Lopez-Cortes A, Gomez-Gutierrez J, Roque A, Lang E, Enciso-Ibarra J	Curr Microbiol	10.1007/s00284-021-02627-1	2021

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 )
#64250	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24592
#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) .
#68369	Automatically annotated from API 20NE .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Veronia nyctiphanis (DSM 24592, CAIM 600, CECT 7578)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_004116385

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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