Photobacterium phosphoreum (DSM 15556, ATCC 11040, NCIMB 1282)

Name: Photobacterium phosphoreum (DSM 15556, ATCC 11040, NCIMB 1282)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17221

Type strain

Culture col. no. DSM 15556 ATCC 11040 NCIMB 1282 NBRC 103031 LMG 4233 8 more

NCBI tax ID(s) 659

Special Collections DSMZ JCM KCTC CIP

Links

Photobacterium phosphoreum DSM 15556 is a facultative anaerobe, psychrophilic, Gram-negative prokaryote of the family Vibrionaceae.

Gram-negative rod-shaped facultative anaerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 3838

LMG 4233,ATCC 11040,NCMB 1282,CAIM:328,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

@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 phosphoreum

Full scientific name Photobacterium phosphoreum (Cohn 1878) Beijerinck 1889 (Approved Lists 1980)

Synonyms (1)

"Micrococcus phosphoreus"

BacDive ID	Other strains from **Photobacterium phosphoreum** (3)	Type strain
138223	P. phosphoreum NZ11D, CIP 105612
143014	P. phosphoreum CCUG 16288, ATCC 35081
162911	P. phosphoreum JCM 20393, IAM 12085

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		99
125439	negative		91
121807	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
41661	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
5999	SEA WATER AGAR (DSMZ Medium 246)	Medium recipe at MediaDive	Name: SEA WATER AGAR (DSMZ Medium 246) Composition: Agar 20.0 g/l Peptone 10.0 g/l Beef extract 10.0 g/l Tap water Sea water
5999	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
121807	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5999	positive	growth	22	psychrophilic
41661	positive	growth	25	mesophilic
67770	positive	growth	17	psychrophilic
121807	positive	growth	5-22	psychrophilic
121807	negative	growth	30
121807	negative	growth	37
121807	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
121807	facultative anaerobe
125439	facultative anaerobe	96.9

Spore formation

@ref	Spore formation	Confidence
125439		99.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121807	NaCl	positive	growth	2-6 %
121807	NaCl		growth	0 %
121807	NaCl		growth	8 %
121807	NaCl		growth	10 %

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
121807	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
121807	17234 ChEBI	glucose	-	fermentation
121807	17234 ChEBI	glucose	-	degradation
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
121807	17716 ChEBI	lactose	-	fermentation
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
121807	17632 ChEBI	nitrate	+	reduction
121807	17632 ChEBI	nitrate	+	respiration
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
121807	16301 ChEBI	nitrite	-	reduction
121807	132112 ChEBI	sodium thiosulfate	-	builds gas from
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
121807	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
121807	15688 ChEBI	acetoin		-
121807	17234 ChEBI	glucose			-
68369	35581 ChEBI	indole	-			from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121807	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
121807	amylase	-
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
121807	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121807	caseinase	-	3.4.21.50
121807	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121807	gamma-glutamyltransferase	-	2.3.2.2
121807	gelatinase	-
68369	gelatinase	-		from API 20NE
121807	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121807	lipase	+
68382	lipase (C 14)	-		from API zym
121807	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
121807	ornithine decarboxylase	-	4.1.1.17
121807	oxidase	-
121807	phenylalanine ammonia-lyase	-	4.3.1.24
121807	protease	-
68382	trypsin	-	3.4.21.4	from API zym
121807	tryptophan deaminase	-
121807	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121807	-	+	+	+	-	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-

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
5999	+	-	+	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5999	1	Risk group (German classification) According to TRBA 466
121807	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM295472v1 assembly for Photobacterium phosphoreum JCM 21184	scaffold	GCA_002954725	659.11	8111233322	659	62.96
67770	ASM302627v1 assembly for Photobacterium phosphoreum ATCC 11040	contig	GCA_003026275	659.23	2900322015	659	61.44
67770	CFSAN029438_01.0 assembly for Photobacterium phosphoreum ATCC 11040	contig	GCA_000949955	659.4	2772190759	659	42.56

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Photobacterium phosphoreum strain ATCC 11040 16S ribosomal RNA gene, partial sequence	AY341437	1467	659
20218	Photobacterium phosphoreum 16S rRNA	D11186	212	659
20218	Photobacterium phosphoreum 16S rRNA	D11235	214	659
20218	Photobacterium phosphoreum 16S rRNA	D11284	191	659
20218	Photobacterium phosphoreum gene for 16S rRNA	D25310	1465	659
20218	Photobacterium phosphoreum (ATCC 11040T) gene for 16S ribosomal RNA	X74687	1457	659
20218	Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, complete sequence	AY779756	320	659
20218	Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, complete sequence	AY779757	351	659
20218	Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, complete sequence	AY779758	391	659
20218	Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequence	AY779759	610	659
20218	Photobacterium phosphoreum DNA, 16S-23S rRNA intergenic spacer and 23S rRNA, partial sequence, strain: IAM 14401	AB255705	290	659
20218	Photobacterium phosphoreum gene for 16S rRNA, partial sequence, strain: NBRC 103031	AB681911	1470	659

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photobacterium phosphoreum JCM 21184
NCBI: GCA_002954725

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	no	57.40	no
125439	gram_stain	BacteriaNetⓘ	negative	91.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	96.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium phosphoreum strain ATCC 11040
PATRIC: 659.23

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	95.11	yes
125438	spore-forming	spore-formingⓘ	no	89.14	no
125438	aerobic	aerobicⓘ	no	69.71	yes
125438	thermophilic	thermophileⓘ	no	97.50	yes
125438	flagellated	motile2+ⓘ	yes	85.88	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus.	Minich JJ, Petrus S, Michael JD, Michael TP, Knight R, Allen EE.	mSphere	10.1128/msphere.00401-20	2020
Pathogenicity	Comparison of Microtox and Xenoassay light as a near real time river monitoring assay for heavy metals.	Halmi MI, Jirangon H, Johari WL, Rachman AR, Shukor MY, Syed MA.	ScientificWorldJournal	10.1155/2014/834202	2014
Enzymology	Quantitative detection of Listeria monocytogenes in biofilms by real-time PCR.	Guilbaud M, de Coppet P, Bourion F, Rachman C, Prevost H, Dousset X.	Appl Environ Microbiol	10.1128/aem.71.4.2190-2194.2005	2005
Enzymology	Simultaneous detection of marine fish pathogens by using multiplex PCR and a DNA microarray.	Gonzalez SF, Krug MJ, Nielsen ME, Santos Y, Call DR.	J Clin Microbiol	10.1128/jcm.42.4.1414-1419.2004	2004
	Evolution of a tRNA operon in gamma purple bacteria.	Giroux S, Cedergren R.	J Bacteriol	10.1128/jb.171.12.6446-6454.1989	1989
	Biodiversity among luminescent symbionts from squid of the genera Uroteuthis, Loliolus and Euprymna (Mollusca: Cephalopoda).	Guerrero-Ferreira RC, Nishiguchi MK.	Cladistics	10.1111/j.1096-0031.2007.00155.x	2007
	Tandemly repeated tRNA pseudogenes in photobacterium.	Giroux S, Cedergren R.	Proc Natl Acad Sci U S A	10.1073/pnas.85.23.9101	1988
	Rapid, quantitative PCR monitoring of growth of Clostridium botulinum type E in modified-atmosphere-packaged fish.	Kimura B, Kawasaki S, Nakano H, Fujii T.	Appl Environ Microbiol	10.1128/aem.67.1.206-216.2001	2001
Enzymology	Infaunal burrows are enrichment zones for Vibrio parahaemolyticus.	Gamble MD, Lovell CR.	Appl Environ Microbiol	10.1128/aem.02897-10	2011
Enzymology	Identification of the genes encoding NAD(P)H-flavin oxidoreductases that are similar in sequence to Escherichia coli Fre in four species of luminous bacteria: Photorhabdus luminescens, Vibrio fischeri, Vibrio harveyi, and Vibrio orientalis.	Zenno S, Saigo K.	J Bacteriol	10.1128/jb.176.12.3544-3551.1994	1994
Phylogeny	Diversity and dynamics of a north atlantic coastal Vibrio community.	Thompson JR, Randa MA, Marcelino LA, Tomita-Mitchell A, Lim E, Polz MF, Polz MF.	Appl Environ Microbiol	10.1128/aem.70.7.4103-4110.2004	2004
Biotechnology	Detection of Salmonella spp. in oysters by PCR.	Bej AK, Mahbubani MH, Boyce MJ, Atlas RM.	Appl Environ Microbiol	10.1128/aem.60.1.368-373.1994	1994
Metabolism	Degradation of uric acid by certain aerobic bacteria.	Rouf MA, Lomprey RF.	J Bacteriol	10.1128/jb.96.3.617-622.1968	1968
Metabolism	Bacteria mediate methylation of iodine in marine and terrestrial environments.	Amachi S, Kamagata Y, Kanagawa T, Muramatsu Y.	Appl Environ Microbiol	10.1128/aem.67.6.2718-2722.2001	2001
Enzymology	Development of a rapid real-time PCR method as a tool to quantify viable Photobacterium phosphoreum bacteria in salmon (Salmo salar) steaks.	Mace S, Mamlouk K, Chipchakova S, Prevost H, Joffraud JJ, Dalgaard P, Pilet MF, Dousset X.	Appl Environ Microbiol	10.1128/aem.03677-12	2013
	Effects of Amino Acid Decarboxylase Genes and pH on the Amine Formation of Enteric Bacteria From Chinese Traditional Fermented Fish (Suan Yu).	Yang Q, Meng J, Zhang W, Liu L, He L, Deng L, Zeng X, Ye C.	Front Microbiol	10.3389/fmicb.2020.01130	2020
	Inhibitory Effects of High-Hydrostatic-Pressure Processing on Growth and Histamine Formation of Histamine-Forming Bacteria in Yellowfin Tuna Meat during Storage.	Huang CH, Hsieh CY, Lee YC, Ou TY, Chang TH, Lee SH, Tseng CH, Tsai YH.	Biology (Basel)	10.3390/biology11050702	2022
	Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences.	Gould AL, Henderson JB.	Microb Genom	10.1099/mgen.0.001161	2023
Metabolism	Comparative genomics of Photobacterium species from terrestrial and marine habitats.	Fuertes-Perez S, Vogel RF, Hilgarth M.	Curr Res Microb Sci	10.1016/j.crmicr.2021.100087	2021
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	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	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
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	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

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;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 .
#121807	Collection of Institut Pasteur ; Curators of the CIP; CIP 102511
#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 phosphoreum (DSM 15556, ATCC 11040, NCIMB 1282)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002954725

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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