Name: Photobacterium ganghwense FR1311
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17233

Type strain:

Species: Photobacterium ganghwense

Strain Designation: FR1311

Culture col. no.: DSM 22954, IMSNU 60287, JCM 12487, KCTC 12328, CIP 109254, DSM 22358, NCIMB 14495

Strain history: <- J Chun, Seoul National Univ.

NCBI tax ID(s): 320778 (species)

SI-ID 232818

KCTC 12328, JCM 12487, CIP 109254, CECT 7641

Other strains from Photobacterium ganghwense

P. ganghwense C2.2, DSM 109767

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	*Photobacterium*
	Species	**Photobacterium ganghwense**
	Full Scientific Name (LPSN)	Photobacterium ganghwense Park et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31562]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #31562]	Cell length	1.3-2 µm

[Ref.: #31562]	Cell width	0.8-1.2 µm

[Ref.: #31562]	Cell shape	ovoid-shaped

[Ref.: #31562]	Motility	yes

[Ref.: #31562]

Pigment production

yes

Multimedia content

[Ref.: #16632]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16632]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #16632]

Culture medium growth

[Ref.: #16632]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16632]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16632]	growth	28 °C
[Ref.: #31562]	growth	10-45 °C
[Ref.: #31562]	optimum	35 °C
[Ref.: #67770]	growth	25 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #16632]	Temperature range	mesophilic
[Ref.: #31562]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31562]			optimum	08-09
[Ref.: #31562]			growth	05-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31562]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31562]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31562]		NaCl		growth	01-07	%
[Ref.: #31562]		NaCl		optimum	2	%

[Ref.: #31562]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31562]	adipate ChEBI	+	carbon source
[Ref.: #31562]	citrate ChEBI	+	carbon source
[Ref.: #31562]	decanoate ChEBI	+	carbon source
[Ref.: #31562]	gluconate ChEBI	+	carbon source
[Ref.: #31562]	glucose ChEBI	+	carbon source
[Ref.: #31562]	malate ChEBI	+	carbon source
[Ref.: #31562]	mannitol ChEBI	+	carbon source
[Ref.: #31562]	mannose ChEBI	+	carbon source
[Ref.: #31562]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31562]	phenylacetate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31562]		catalase	+	1.11.1.6
[Ref.: #31562]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	heme metabolism	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]	vitamin B6 metabolism	90.91	10 of 11
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	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]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	purine metabolism	86.17	81 of 94
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	vitamin B12 metabolism	35.29	12 of 34
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
		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.: #16632]	Sample type/isolated from	sea water
[Ref.: #16632]	Geographic location (country and/or sea, region)	Ganghwa Island (37°35'39.1'' N 126°27'24.5'' E)
[Ref.: #16632]	Country	Republic of Korea
[Ref.: #16632]	Country ISO 3 Code	KOR
[Ref.: #16632]	Continent	Asia
[Ref.: #16632]	Geographic location	37.5942°/126.4570°

[Ref.: #67770]	Sample type/isolated from	Seawater
[Ref.: #67770]	Geographic location (country and/or sea, region)	Ganghwa Island
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From seawater
[Ref.: #67771]	Geographic location (country and/or sea, region)	Kangwha
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #16632]

Biosafety level

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.: #16632]	Photobacterium ganghwense strain FR1311 16S ribosomal RNA gene, partial sequence	AY960847	1474	ENA	320778 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]	Photobacterium ganghwense JCM 12487	GCA_003025595	contig	GenBank	320778 tax ID	*
[Ref.: #66792]	Photobacterium ganghwense DSM 22954	GCA_001029455	contig	GenBank	320778 tax ID	*
[Ref.: #66792]	Photobacterium ganghwense strain DSM 22954	320778.3	wgs	PATRIC	320778 tax ID	*
[Ref.: #66792]	Photobacterium ganghwense strain JCM 12487	320778.6	wgs	PATRIC	320778 tax ID	*
[Ref.: #66792]	Photobacterium ganghwense DSM 22954	2713896764	draft	JGI IMG/M	320778 tax ID	*
[Ref.: #66792]	Photobacterium ganghwense JCM 12487	2868869919	draft	JGI IMG/M	320778 tax ID	*

[Ref.: #16632]	GC-content	44.0 mol%
[Ref.: #31562]	GC-content	44 mol%
[Ref.: #67770]	GC-content	44 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Photobacterium ganghwense strain DSM 22954 PATRIC: 320778.3
[Ref.: #69480]	gram-positive	no	98.794	yes
[Ref.: #69480]	anaerobic	no	96.561	yes
[Ref.: #69480]	halophile	no	63.888	no
[Ref.: #69480]	spore-forming	no	93.663	yes
[Ref.: #69480]	glucose-util	yes	93.161	yes
[Ref.: #69480]	motile	yes	91.498	yes
[Ref.: #69480]	flagellated	yes	91.303	no
[Ref.: #69480]	thermophile	no	99.744	yes
[Ref.: #69480]	aerobic	yes	73.358	no
[Ref.: #69480]	glucose-ferment	yes	85.378	no

Availability in culture collections External links

[Ref.: #16632]

Culture collection no.

DSM 22954, IMSNU 60287, JCM 12487, KCTC 12328, CIP 109254, DSM 22358, NCIMB 14495

[Ref.: #86232]

SI-ID 232818

Literature:

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	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	*
Phylogeny	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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#86232

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-ID232818.1 )

#27852

IJSEM 745 2006 ( DOI 10.1099/ijs.0.63811-0 , PubMed 16585687 )

* These data were automatically processed and therefore are not curated

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Photobacterium ganghwense strain DSM 22954

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