Name: Photobacterium phosphoreum DSM 15556
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17221

Type strain:

Species: Photobacterium phosphoreum

Culture col. no.: DSM 15556, ATCC 11040, NCIMB 1282, JCM 21184, BCRC 13804, CECT 4192, CIP 102511, HAMBI 1726, IAM 14401, KCTC 12377, LMG 4233, NBRC 103031, CIP 75.9

Strain history: CIP <- 1988, ATCC <- F.J. Johnson, Bacterium phosphoreum <- A.J. Kluyver

NCBI tax ID(s): 659 (species)

SI-ID 3838

LMG 4233, ATCC 11040, NCMB 1282, CIP 102511, NCIMB 1282, CIP 75.09, CECT 4192, CCRC 13804, DSM 15556, BCRC 13804, KCTC 12377, HAMBI 1726, IAM 14401, JCM 21184, NBRC 103031

Special Collections

Other strains from Photobacterium phosphoreum

Section

Photobacterium phosphoreum DSM 15556 is a facultative anaerobe, Gram-negative bacterium that was isolated from Unknown source.

Gram-negative
facultative anaerobe
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 phosphoreum**
	Full Scientific Name (LPSN)	Photobacterium phosphoreum (Cohn 1878) Beijerinck 1889 (Approved Lists 1980)

Synonym

"Micrococcus phosphoreus"

Information on morphological and physiological properties Morphology

[Ref.: #121807]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99

[Ref.: #121807]	Cell shape	rod-shaped

[Ref.: #121807]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #41661]

Culture medium

Marine agar (MA)

[Ref.: #41661]

Culture medium growth

[Ref.: #41661]

Culture medium composition

expand / minimize

[Ref.: #5999]

Culture medium

SEA WATER AGAR (DSMZ Medium 246)

[Ref.: #5999]

Culture medium growth

[Ref.: #5999]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #5999]

Culture medium

MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)

[Ref.: #5999]

Culture medium growth

[Ref.: #5999]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #121807]

Culture medium

CIP Medium 13

[Ref.: #121807]

Culture medium growth

[Ref.: #121807]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5999]		growth	22 °C
[Ref.: #41661]		growth	25 °C
[Ref.: #67770]		growth	17 °C
[Ref.: #121807]		growth	5-22 °C
[Ref.: #121807]	no	growth	30 °C
[Ref.: #121807]	no	growth	37 °C
[Ref.: #121807]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #121807]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Salt	Tested relation		Salt conc.
[Ref.: #121807]	NaCl		growth	2-6	%
[Ref.: #121807]	NaCl	no	growth	0	%
[Ref.: #121807]	NaCl	no	growth	8	%
[Ref.: #121807]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #121807]	esculin ChEBI	-	hydrolysis
[Ref.: #121807]	glucose ChEBI	-	fermentation
[Ref.: #121807]	glucose ChEBI	-	degradation
[Ref.: #121807]	lactose ChEBI	-	fermentation
[Ref.: #121807]	nitrate ChEBI	+	reduction
[Ref.: #121807]	nitrate ChEBI	+	respiration
[Ref.: #121807]	nitrite ChEBI	-	reduction
[Ref.: #121807]	sodium thiosulfate ChEBI	-	builds gas from

	Metabolite production	Metabolite	Production
[Ref.: #121807]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #121807]		acetoin ChEBI	-
[Ref.: #121807]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121807]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #121807]	amylase	-
[Ref.: #121807]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #121807]	caseinase	-	3.4.21.50
[Ref.: #121807]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121807]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #121807]	gelatinase	-
[Ref.: #121807]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #121807]	lipase	+
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #121807]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #121807]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121807]	oxidase	-
[Ref.: #121807]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #121807]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121807]	tryptophan deaminase	-
[Ref.: #121807]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121807]	7114	-	+	+	+	-	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #121807]	Sample type/isolated from	Unknown source
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence X74687 (>99% sequence identity) for Photobacterium from Microbeatlas

Aquatic Samples	2884
Soil Samples	73
Animal Samples	2251
Plant Samples	55
Total Samples	5263

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

[Ref.: #5999]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121807]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

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

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Photobacterium phosphoreum strain ATCC 11040 16S ribosomal RNA gene, partial sequence	AY341437	1467	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum 16S rRNA	D11186	212	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum 16S rRNA	D11235	214	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum 16S rRNA	D11284	191	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum gene for 16S rRNA	D25310	1465	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum (ATCC 11040T) gene for 16S ribosomal RNA	X74687	1457	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, complete sequence	AY779756	320	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, complete sequence	AY779757	351	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, complete sequence	AY779758	391	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence	AY779759	610	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum DNA, 16S-23S rRNA intergenic spacer and 23S rRNA, partial sequence, strain: IAM 14401	AB255705	290	GenBank ENA	659 tax ID	*
[Ref.: #20218]	Photobacterium phosphoreum gene for 16S rRNA, partial sequence, strain: NBRC 103031	AB681911	1470	GenBank ENA	659 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.: #67770]	Photobacterium phosphoreum ATCC 11040	GCA_003026275	contig	GenBank ENA	659 tax ID
[Ref.: #67770]	Photobacterium phosphoreum ATCC 11040	GCA_000949955	contig	GenBank ENA	659 tax ID
[Ref.: #67770]	Photobacterium phosphoreum JCM 21184	GCA_002954725	scaffold	GenBank ENA	659 tax ID
[Ref.: #66792]	Photobacterium phosphoreum strain ATCC 11040	659.4	wgs	PATRIC	659 tax ID	*
[Ref.: #66792]	Photobacterium phosphoreum strain JCM 21184	659.11	wgs	PATRIC	659 tax ID	*
[Ref.: #66792]	Photobacterium phosphoreum ATCC 11040	2772190759	draft	JGI IMG/M	659 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Photobacterium phosphoreum JCM 21184 NCBI: GCA_002954725.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Photobacterium phosphoreum strain ATCC 11040 PATRIC: 659.23
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.114	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.143	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	69.714	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.5	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	85.878	no

Availability in culture collections External links

[Ref.: #5999]

Culture collection no.

DSM 15556, ATCC 11040, NCIMB 1282, JCM 21184, BCRC 13804, CECT 4192, CIP 102511, HAMBI 1726, IAM 14401, KCTC 12377, LMG 4233, NBRC 103031, CIP 75.9

[Ref.: #86220]

SI-ID 3838

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Metabolism	A new HPTLC platformed luminescent biosensor system for facile screening of captan residue in fruits.	Chen Y, Huang C, Hellmann B, Jin Z, Xu X, Xiao G	Food Chem	10.1016/j.foodchem.2019.125691	2019	*
Phylogeny	Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater.	Huang Z, Dong C, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001142	2016	*
Phylogeny	Photobacterium piscicola sp. nov., isolated from marine fish and spoiled packed cod.	Figge MJ, Cleenwerck I, van Uijen A, De Vos P, Huys G, Robertson L	Syst Appl Microbiol	10.1016/j.syapm.2014.05.003	2014	*
Phylogeny	Historical microbiology: revival and phylogenetic analysis of the luminous bacterial cultures of M. W. Beijerinck.	Figge MJ, Robertson LA, Ast JC, Dunlap PV	FEMS Microbiol Ecol	10.1111/j.1574-6941.2011.01177.x	2011	*
Phylogeny	Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes.	Ast JC, Cleenwerck I, Engelbeen K, Urbanczyk H, Thompson FL, De Vos P, Dunlap PV	Int J Syst Evol Microbiol	10.1099/ijs.0.65153-0	2007	*
Phylogeny	Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae).	Dunlap PV, Ast JC	Appl Environ Microbiol	10.1128/AEM.71.2.930-939.2005	2005	*
Metabolism	Characteristic analysis of the ampC gene encoding beta-lactamase from Photobacterium phosphoreum.	Lin JW, Weng SF, Chao YF, Chung YT	Biochem Biophys Res Commun	10.1016/j.bbrc.2004.11.065	2005	*
Enzymology	Highly repetitive tRNA(Pro)-tRNA(His) gene cluster from Photobacterium phosphoreum.	Giroux S, Beaudet J, Cedergren R	J Bacteriol	10.1128/jb.170.12.5601-5606.1988	1988	*

References

#5999

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15556

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#41661 ; Curators of the CIP;

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68382

Automatically annotated from API zym .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86220

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-ID3838.1 )

#121807 Collection of Institut Pasteur ; Curators of the CIP; CIP 102511
* These data were automatically processed and therefore are not curated

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Photobacterium phosphoreum JCM 21184

Photobacterium phosphoreum strain ATCC 11040

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