Photobacterium aphoticum (DSM 25995, CECT 7614, KCTC 23057)

Name: Photobacterium aphoticum (DSM 25995, CECT 7614, KCTC 23057)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17240

Type strain

Strain Designation M46

Culture col. no. DSM 25995 CECT 7614 KCTC 23057 M46

NCBI tax ID(s) 754436

Special Collections DSMZ KCTC

Links

Photobacterium aphoticum M46 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from surface seawater.

Gram-negative aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 377770

CAIM 1839,CECT 7614,KCTC 23057,DSM 25995

@ref 20215

Last LPSN update 2025-12-16 09:51:02

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Photobacterium

Species Photobacterium aphoticum

Full scientific name Photobacterium aphoticum Lucena et al. 2011

Morphology

Cell morphology

@ref	Gram stain
67771	negative
125438	negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18146	REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto 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 Na2CO3 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
18146	positive	growth	28	mesophilic
67771	positive	growth	26	mesophilic

Physiology and metabolism

Oxygen tolerance

67771

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		95

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	+	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	+	fermentation	from API 20E
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
68368	15688 ChEBI	acetoin	-	from API 20E
68368	35581 ChEBI	indole		from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68368	cytochrome oxidase	+	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	threonine metabolism	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	ubiquinone biosynthesis	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	butanoate fermentation	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	NAD metabolism	94.44	17 of 18
66794	photosynthesis	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	vitamin B6 metabolism	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	citric acid cycle	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	degradation of sugar alcohols	81.25	13 of 16
66794	hydrogen production	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	purine metabolism	78.72	74 of 94
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	alanine metabolism	72.41	21 of 29
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	non-pathway related	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	histidine metabolism	68.97	20 of 29
66794	lipid metabolism	67.74	21 of 31
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	glutathione metabolism	64.29	9 of 14
66794	oxidative phosphorylation	62.64	57 of 91
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	cysteine metabolism	61.11	11 of 18
66794	myo-inositol biosynthesis	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	arginine metabolism	58.33	14 of 24
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	tyrosine metabolism	57.14	8 of 14
66794	degradation of pentoses	57.14	16 of 28
66794	tryptophan metabolism	55.26	21 of 38
66794	proline metabolism	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	methionine metabolism	53.85	14 of 26
66794	ketogluconate metabolism	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	toluene degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	nitrate assimilation	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	d-xylose degradation	36.36	4 of 11
66794	phenol degradation	35	7 of 20
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of hexoses	33.33	6 of 18
66794	arachidonic acid metabolism	33.33	6 of 18
66794	degradation of sugar acids	32	8 of 25
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	vitamin B12 metabolism	29.41	10 of 34
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	alginate biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	methanogenesis from CO2	25	3 of 12
66794	androgen and estrogen metabolism	25	4 of 16
66794	catecholamine biosynthesis	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
18146	+	+	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	+	-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
18146	surface seawater	Valencia, Malvarrosa Beach (39° 28' 29'' N 0° 19' 23'' W)	Spain	ESP	Europe	39.4747	-0.3231 39.4747/-0.3231
67771	From surface sea water	Mediterranean coast in Malvarrosa beach, Valencia	Spain	ESP	Europe

Taxonmaps

69479

Global distribution of 16S sequence FN796493 (>99% sequence identity) for Photobacterium aphoticum subclade from Microbeatlas

Aquatic Samples	994
Soil Samples	45
Animal Samples	553
Plant Samples	11
Total Samples	1603

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18146	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1465207v1 assembly for Photobacterium aphoticum KCTC 23057	scaffold	GCA_014652075	754436.8	8110945092	754436	64.45
124043	ASM4243000v1 assembly for Photobacterium aphoticum KCTC 23057	scaffold	GCA_042430005			754436	61.55
66792	ASM102943v1 assembly for Photobacterium aphoticum DSM 25995	contig	GCA_001029435	754436.4	2671180362	754436	52.06
66792	ASM302557v1 assembly for Photobacterium aphoticum DSM 25995	contig	GCA_003025575	754436.6	2900340083	754436	24.86

Genome browser: GCA_014652075

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
18146	Photobacterium aphoticum partial 16S rRNA gene, strain CECT 7614	FN796493	1529	754436
124043	Photobacterium aphoticum strain KCTC 23057 16S ribosomal RNA gene, partial sequence.	MT758090	1340	754436
124043	Photobacterium aphoticum strain KCTC 23057 16S ribosomal RNA gene, partial sequence.	MT759889	1340	754436

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photobacterium aphoticum KCTC 23057
NCBI: GCA_014652075

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.00	no
125439	motility	BacteriaNetⓘ	yes	70.80	no
125439	gram_stain	BacteriaNetⓘ	negative	87.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium aphoticum KCTC 23057
NCBI: GCA_014652075.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.92	yes
125438	anaerobic	anaerobicⓘ	no	93.81	no
125438	aerobic	aerobicⓘ	no	55.27	yes
125438	spore-forming	spore-formingⓘ	no	85.85	no
125438	thermophilic	thermophileⓘ	no	96.49	yes
125438	flagellated	motile2+ⓘ	yes	86.43	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Photobacterium aquae sp. nov., isolated from a recirculating mariculture system.	Liu Y, Liu LZ, Song L, Zhou YG, Qi FJ, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.055020-0	2013
Phylogeny	Photobacterium aphoticum sp. nov., isolated from coastal water.	Lucena T, Ruvira MA, Pascual J, Garay E, Macian MC, Arahal DR, Pujalte MJ	Int J Syst Evol Microbiol	10.1099/ijs.0.025171-0	2010

References

#18146	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25995
#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 )
#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 )
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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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Photobacterium aphoticum (DSM 25995, CECT 7614, KCTC 23057)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014652075

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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