Photobacterium jeanii (DSM 100339, CAIM 1817, LMG 25436)

Name: Photobacterium jeanii (DSM 100339, CAIM 1817, LMG 25436)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130749

Type strain

Strain Designation R-2567

Culture col. no. DSM 100339 CAIM 1817 LMG 25436 R-2567 UFRJ R-789

NCBI tax ID(s) 858640

Special Collections DSMZ Literature strains

History <- CAIM <- L. A. Chimetto, Department of Genetics, Evolution and Bioagents, State University of Campinas, Brazil

Links

Photobacterium jeanii R-2567 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from mucus of apparently healthy coral zoanthid Palythoa caribaeorum.

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

Name and taxonomic classification

SI-ID 362871

DSM 100339,CAIM 1817,LMG 25436

@ref 20215

Last LPSN update 2026-02-09 11:31:18

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Photobacterium

Species Photobacterium jeanii

Full scientific name Photobacterium jeanii Chimetto et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29747	negative	2-2.5 µm	01-02 µm	ovoid-shaped
125439	negative				99.6
125438	negative				100

Pigmentation

29747

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21727	REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto 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 Na2CO3 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

Culture temp

@ref	Growth	Type	Temperature (°C)
21727	positive	growth	28
29747	positive	growth	20-35
29747	positive	optimum	20-35

Culture pH

@ref	Ability	Type	PH
29747	positive	optimum	7
29747	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29747	facultative anaerobe
125439	obligate aerobe	96.8

Spore formation

@ref	Spore formation	Confidence
29747
125439		99.8

Observation

29747

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
29747	22599 ChEBI	arabinose	+	carbon source
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
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
29747	29864 ChEBI	mannitol	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
29747	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
29747	26546 ChEBI	rhamnose	+	carbon source
29747	30911 ChEBI	sorbitol	+	carbon source
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

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
29747	acid phosphatase	+	3.1.3.2
29747	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
29747	catalase	+	1.11.1.6
29747	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	+		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	ubiquinone biosynthesis	100	7 of 7
66794	vitamin K metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	starch degradation	100	10 of 10
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	photosynthesis	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	lipid A biosynthesis	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	purine metabolism	81.91	77 of 94
66794	vitamin B6 metabolism	81.82	9 of 11
66794	cellulose degradation	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	chorismate metabolism	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	urea cycle	69.23	9 of 13
66794	lipid metabolism	67.74	21 of 31
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	citric acid cycle	64.29	9 of 14
66794	oxidative phosphorylation	63.74	58 of 91
66794	non-pathway related	63.16	24 of 38
66794	arginine metabolism	62.5	15 of 24
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	lysine metabolism	61.9	26 of 42
66794	methionine metabolism	61.54	16 of 26
66794	gallate degradation	60	3 of 5
66794	glycine metabolism	60	6 of 10
66794	glycine betaine biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	tyrosine metabolism	57.14	8 of 14
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	proline metabolism	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	sulfate reduction	53.85	7 of 13
66794	tryptophan metabolism	52.63	20 of 38
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	sulfopterin metabolism	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	phenol degradation	50	10 of 20
66794	butanoate fermentation	50	2 of 4
66794	nitrate assimilation	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	3-phenylpropionate degradation	40	6 of 15
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	ketogluconate metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	methane metabolism	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	cyanate degradation	33.33	1 of 3
66794	vitamin B12 metabolism	32.35	11 of 34
66794	degradation of sugar acids	32	8 of 25
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	d-xylose degradation	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	degradation of sugar alcohols	25	4 of 16
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	carotenoid biosynthesis	22.73	5 of 22

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
21727	+	-	+	+	-	-	+	+	+	-	+	-	+	+/-	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Invertebrates (Other)	#Cnidaria (Corals)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
21727	mucus of apparently healthy coral zoanthid Palythoa caribaeorum	Palythoa caribaeorum	São Paulo, São Sebastião channel, Preta beach	Brazil	BRA	Middle and South America

Taxonmaps

69479

Global distribution of 16S sequence GU065210 (>99% sequence identity) for Photobacterium jeanii subclade from Microbeatlas

Aquatic Samples	68
Soil Samples	2
Animal Samples	56
Plant Samples
Total Samples	126

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21727	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM302549v1 assembly for Photobacterium jeanii DSM 100339	contig	GCA_003025495	858640.7	2900308143	858640	68.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
29747	Photobacterium jeanii strain R-40507 16S ribosomal RNA gene, partial sequence	GU065209	1523		858640
21727	Photobacterium jeanii strain R-40508 16S ribosomal RNA gene, partial sequence	GU065210	1523		858640

GC content

29747

GC-content (mol%)45.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photobacterium jeanii DSM 100339
NCBI: GCA_003025495

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.80	no
125439	motility	BacteriaNetⓘ	yes	84.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium jeanii strain DSM 100339
PATRIC: 858640.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	yes
125438	anaerobic	anaerobicⓘ	no	97.50	yes
125438	aerobic	aerobicⓘ	no	69.76	yes
125438	spore-forming	spore-formingⓘ	no	89.33	no
125438	thermophilic	thermophileⓘ	no	99.50	no
125438	flagellated	motile2+ⓘ	yes	89.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Photobacterium jeanii sp. nov., isolated from corals and zoanthids.	Chimetto LA, Cleenwerck I, Thompson CC, Brocchi M, Willems A, De Vos P, Thompson FL	Int J Syst Evol Microbiol	10.1099/ijs.0.019968-0	2010

References

#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 )
#21727	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100339
#26129	IJSEM 2843 2010 ( DOI 10.1099/ijs.0.019968-0 , PubMed 20081016 )
#29747	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 #26129
#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 )
#68369	Automatically annotated from API 20NE .
#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 jeanii (DSM 100339, CAIM 1817, LMG 25436)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003025495

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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