Photobacterium iliopiscarium (DSM 9896, ATCC 51760, PS1)

Name: Photobacterium iliopiscarium (DSM 9896, ATCC 51760, PS1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17224

Type strain

Strain Designation PS1

Culture col. no. DSM 9896 ATCC 51760 PS1 CIP 104755 KCTC 12376

NCBI tax ID(s) 56192

Special Collections DSMZ KCTC CIP

History DSMZ <- A.M. Onarheim, Fiskeriforskning, Tromsö CIP <- 1996, ATCC <- A.M. Onarheim

Links

Photobacterium iliopiscarium PS1 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from pyloric ceca of herring.

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

Name and taxonomic classification

SI-ID 10417

LMG 16848,ATCC 51760,DSM 9896,LMG 19543,CAIM 909,CIP 104755,NCIMB 13355,KCTC 12376

@ref 20215

Last LPSN update 2026-05-29 08:28:57

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Photobacterium

Species Photobacterium iliopiscarium

Full scientific name Photobacterium iliopiscarium (Onarheim et al. 1995) Urakawa et al. 1999

Synonyms (1)

Vibrio iliopiscarius

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125439	negative		97.173
125438	negative		99
120048	negative	oval-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3757	REACTIVATION WITH LIQUID MEDIUM 115 (DSMZ Medium 115a)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 115 (DSMZ Medium 115a) Composition: Agar 15.0 g/l (optional) NaCl 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39087	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
3757	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
120048	CIP Medium 13	Medium recipe at CIP
120048	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3757	positive	growth	20
39087	positive	growth	15
120048	positive	growth	5-22
120048	negative	growth	30
120048	negative	growth	37
120048	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
120048	facultative anaerobe
125439	obligate aerobe	98.298

Spore formation

@ref	Spore formation	Confidence
125439		99.858

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120048	NaCl	positive	growth	2-6 %
120048	NaCl		growth	0 %
120048	NaCl		growth	8 %
120048	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68369	29016 ChEBI	arginine	+	hydrolysis	from API 20NE
68368	29016 ChEBI	arginine	+	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
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
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
120048	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
120048	17632 ChEBI	nitrate	+	reduction
120048	17632 ChEBI	nitrate	+	respiration
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
120048	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68369	35581 ChEBI	indole	from API 20NE
120048	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
120048	15688 ChEBI	acetoin		-
120048	17234 ChEBI	glucose			-
68369	35581 ChEBI	indole	-			from API 20NE
68368	35581 ChEBI	indole	-			from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120048	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
120048	amylase	+
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68368	arginine dihydrolase	+	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
120048	beta-galactosidase	-	3.2.1.23
68368	beta-galactosidase	-	3.2.1.23	from API 20E
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
120048	caseinase	-	3.4.21.50
120048	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
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
120048	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120048	gamma-glutamyltransferase	-	2.3.2.2
120048	gelatinase	-
68369	gelatinase	-		from API 20NE
68368	gelatinase	-		from API 20E
120048	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
120048	lipase	+
68382	lipase (C 14)	-		from API zym
120048	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
120048	ornithine decarboxylase	-	4.1.1.17
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
120048	oxidase	+
120048	phenylalanine ammonia-lyase	-	4.3.1.24
120048	protease	-
68382	trypsin	-	3.4.21.4	from API zym
120048	tryptophan deaminase	-
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
120048	tween esterase	-
120048	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

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
3757	-	+	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
3757	-	+	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
3757	-	+	+	-	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
120048	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+	-	-

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
3757	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Fishes	-
#Host Body-Site	#Gastrointestinal tract	#Stomach

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3757	pyloric ceca of herring	Tromsö	Norway	NOR	Europe
120048	Herring, pyloric ceca		Norway	NOR	Europe

Taxonmaps

69479

Global distribution of 16S sequence AY643710 (>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
3757	1	Risk group (German classification) According to TRBA 466
120048	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
66792	ASM302639v1 assembly for Photobacterium iliopiscarium ATCC 51760	contig	GCA_003026395	56192.15	2868861791	56192	69.65
66792	CFSAN029431_01.0 assembly for Photobacterium iliopiscarium ATCC 51760	contig	GCA_000950265	56192.4	2751185812	56192	18.04

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Photobacterium iliopiscarium gene for 16S ribosomal RNA, partial sequence	AB000278	1410	56192
20218	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence	AY643710	1467	56192
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642160	1467	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642161	1467	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642162	1451	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642163	1467	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642164	1467	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642165	1467	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642166	1467	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642167	1467	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642168	1455	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642169	1467	318456
124043	Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequence.	AY642170	1467	318456

GC content

@ref	GC-content (mol%)	Method
3757	39	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM302639v1 assembly for Photobacterium iliopiscarium ATCC 51760
BV-BRC: 56192.15

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	97.17	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.30	no
125439	motility	BacteriaNetⓘ	yes	63.89	no
125439	spore_formation	BacteriaNetⓘ	no	99.86	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium iliopiscarium strain ATCC 51760
PATRIC: 56192.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	92.41	no
125438	spore-forming	spore-formingⓘ	no	87.21	no
125438	aerobic	aerobicⓘ	no	68.47	no
125438	thermophilic	thermophileⓘ	no	97.49	no
125438	flagellated	motile2+ⓘ	yes	82.47	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
Genetics	The Microbiota of the Outer Gut Mucus Layer of the Migrating Northeast Arctic Cod (Gadus morhua) as Determined by Shotgun DNA Sequencing.	Le Doujet T, Haugen P.	Microorganisms	10.3390/microorganisms12112204	2024
	Functional characterization of diverse type I-F CRISPR-associated transposons.	Roberts A, Nethery MA, Barrangou R.	Nucleic Acids Res	10.1093/nar/gkac985	2022
Genetics	Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua).	Le Doujet T, De Santi C, Klemetsen T, Hjerde E, Willassen NP, Haugen P.	Microbiome	10.1186/s40168-019-0681-y	2019
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
Phylogeny	Reassessment of the taxonomic position of Vibrio iliopiscarius (Onarheim et al. 1994) and proposal for Photobacterium iliopiscarium comb. nov.	Urakawa H, Kita-Tsukamoto K, Ohwada K	Int J Syst Bacteriol	10.1099/00207713-49-1-257	1999
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

References

#3757	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9896
#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 )
#39087	; 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) .
#68368	Automatically annotated from API 20E .
#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 .
#120048	Collection of Institut Pasteur ; Curators of the CIP; CIP 104755
#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 iliopiscarium (DSM 9896, ATCC 51760, PS1)

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 20E

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003026395

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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