Photobacterium ganghwense (DSM 22954, IMSNU 60287, JCM 12487)

Name: Photobacterium ganghwense (DSM 22954, IMSNU 60287, JCM 12487)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17233

Type strain

Strain Designation FR1311

Culture col. no. DSM 22954 IMSNU 60287 JCM 12487 KCTC 12328 FR1311 3 more

NCBI tax ID(s) 320778

Special Collections DSMZ JCM KCTC CIP Literature strains

Links

Photobacterium ganghwense FR1311 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from sea water.

Gram-negative motile ovoid-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 232818

DSM 22954,KCTC 12328,JCM 12487,CIP 109254,CECT 7641

@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 ganghwense

Full scientific name Photobacterium ganghwense Park et al. 2006

BacDive ID	Other strains from **Photobacterium ganghwense** (1)	Type strain
169571	P. ganghwense C2.2, DSM 109767

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
31562	negative	1.3-2 µm	0.8-1.2 µm	ovoid-shaped
67771	negative
125438	negative
125439	negative

Pigmentation

31562

Productionyes

Multimedia

@ref:	16632
multimedia content:	DSM_22954.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_22954.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16632	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16632	positive	growth	28	mesophilic
31562	positive	growth	10-45
31562	positive	optimum	35	mesophilic
67770	positive	growth	25	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
31562	positive	optimum	08-09
31562	positive	growth	05-11

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31562	facultative anaerobe
67771	aerobe

Spore formation

@ref	Spore formation
31562
125439

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31562	NaCl	positive	growth	01-07 %
31562	NaCl	positive	optimum	2 %

Observation

@ref	Observation
31562	aggregates in chains
67770	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31562	17128 ChEBI	adipate	+	carbon source
31562	16947 ChEBI	citrate	+	carbon source
31562	27689 ChEBI	decanoate	+	carbon source
31562	24265 ChEBI	gluconate	+	carbon source
31562	17234 ChEBI	glucose	+	carbon source
31562	25115 ChEBI	malate	+	carbon source
31562	29864 ChEBI	mannitol	+	carbon source
31562	37684 ChEBI	mannose	+	carbon source
31562	506227 ChEBI	N-acetylglucosamine	+	carbon source
31562	18401 ChEBI	phenylacetate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31562	catalase	+	1.11.1.6
31562	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	enterobactin biosynthesis	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	biotin biosynthesis	100	4 of 4
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	butanoate fermentation	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	starch degradation	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	ubiquinone biosynthesis	100	7 of 7
66794	photosynthesis	92.86	13 of 14
66794	heme metabolism	92.86	13 of 14
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	vitamin B6 metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	pyrimidine metabolism	86.67	39 of 45
66794	purine metabolism	86.17	81 of 94
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	gallate degradation	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	citric acid cycle	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	urea cycle	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	non-pathway related	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	histidine metabolism	68.97	20 of 29
66794	lipid metabolism	67.74	21 of 31
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	nitrate assimilation	66.67	6 of 9
66794	methionine metabolism	65.38	17 of 26
66794	lysine metabolism	64.29	27 of 42
66794	oxidative phosphorylation	63.74	58 of 91
66794	arginine metabolism	62.5	15 of 24
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	cellulose degradation	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	polyamine pathway	56.52	13 of 23
66794	degradation of hexoses	55.56	10 of 18
66794	d-mannose degradation	55.56	5 of 9
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	denitrification	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	phenol degradation	45	9 of 20
66794	allantoin degradation	44.44	4 of 9
66794	degradation of sugar alcohols	43.75	7 of 16
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	degradation of pentoses	42.86	12 of 28
66794	glycine betaine biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	metabolism of disaccharids	36.36	4 of 11
66794	vitamin B12 metabolism	35.29	12 of 34
66794	methane metabolism	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of sugar acids	32	8 of 25
66794	coenzyme M biosynthesis	30	3 of 10
66794	ascorbate metabolism	27.27	6 of 22
66794	d-xylose degradation	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
16632	sea water	Ganghwa Island (37°35'39.1'' N 126°27'24.5'' E)	Republic of Korea	KOR	Asia	37.5942	126.457 37.5942/126.457
67770	Seawater	Ganghwa Island	Republic of Korea	KOR	Asia
67771	From seawater	Kangwha	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY960847 (>99% sequence identity) for Photobacterium ganghwense subclade from Microbeatlas

Aquatic Samples	241
Soil Samples	44
Animal Samples	93
Plant Samples	4
Total Samples	382

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16632	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	ASM302559v1 assembly for Photobacterium ganghwense JCM 12487	contig	GCA_003025595	320778.6	2868869919	320778	67.9
66792	ASM102945v1 assembly for Photobacterium ganghwense DSM 22954	contig	GCA_001029455	320778.3	2713896764	320778	51.64

Genome browser: GCA_003025595

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16632	Photobacterium ganghwense strain FR1311 16S ribosomal RNA gene, partial sequence	AY960847	1474		320778

GC content

@ref	GC-content (mol%)
16632	44.0
31562	44
67770	44

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photobacterium ganghwense JCM 12487
NCBI: GCA_003025595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.70	no
125439	motility	BacteriaNetⓘ	yes	82.90	no
125439	gram_stain	BacteriaNetⓘ	negative	97.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	84.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium ganghwense strain DSM 22954
PATRIC: 320778.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	yes
125438	anaerobic	anaerobicⓘ	no	96.38	yes
125438	spore-forming	spore-formingⓘ	no	84.65	no
125438	aerobic	aerobicⓘ	no	58.13	no
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	89.51	no

Literature

Title	Authors	Journal	DOI	Year
Biocide-Resistant Escherichia coli ST540 Co-Harboring ESBL, dfrA14 Confers QnrS-Dependent Plasmid-Mediated Quinolone Resistance.	Bharathi SV, Rajamohan G.	Antibiotics (Basel)	10.3390/antibiotics11121724	2022
Out of the Abyss: Genome and Metagenome Mining Reveals Unexpected Environmental Distribution of Abyssomicins.	Iglesias A, Latorre-Perez A, Stach JEM, Porcar M, Pascual J.	Front Microbiol	10.3389/fmicb.2020.00645	2020
Environmental Impact of Tributyltin-Resistant Marine Bacteria in the Indigenous Microbial Population of Tributyltin-Polluted Surface Sediments.	Mimura H, Yagi M, Yoshida K	Biocontrol Sci	10.4265/bio.22.89	2017
Photobacterium ganghwense sp. nov., a halophilic bacterium isolated from sea water.	Park YD, Baik KS, Seong CN, Bae KS, Kim S, Chun J	Int J Syst Evol Microbiol	10.1099/ijs.0.63811-0	2006

References

#16632	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22954
#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 )
#31562	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 #27852 (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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 ganghwense (DSM 22954, IMSNU 60287, JCM 12487)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003025595

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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