Strain identifier

BacDive ID: 17228

Type strain: Yes

Species: Photobacterium leiognathi

Strain Designation: L1

Strain history: CIP <- 1966, H. Boisvert, Inst. Pasteur, Paris, France: strain L1

NCBI tax ID(s): 553611 (species)

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General

@ref: 15596

BacDive-ID: 17228

DSM-Number: 21260

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile

description: Photobacterium leiognathi L1 is a facultative anaerobe, mesophilic, motile bacterium that was isolated from light organ of teleostean fish Leiognathus equula.

NCBI tax id

  • NCBI tax id: 553611
  • Matching level: species

strain history

@refhistory
15596<- CIP <- H. Boisvert, Insitut Pasteur
418471966, H. Boisvert, Inst. Pasteur, Paris, France: strain L1
120577CIP <- 1966, H. Boisvert, Inst. Pasteur, Paris, France: strain L1

doi: 10.13145/bacdive17228.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Photobacterium
  • species: Photobacterium leiognathi
  • full scientific name: Photobacterium leiognathi Boisvert et al. 1967 (Approved Lists 1980)

@ref: 15596

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium leiognathi

full scientific name: Photobacterium leiognathi Boisvert et al. 1967

strain designation: L1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.913
6948099.989negative
120577yesnegativerod-shaped

colony morphology

  • @ref: 46454
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15596BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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 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
41847Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120577CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
15596positivegrowth28mesophilic
41847positivegrowth25mesophilic
46454positivegrowth30mesophilic
120577positivegrowth15-30
120577nogrowth5psychrophilic
120577nogrowth37mesophilic
120577nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120577
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
120577NaClpositivegrowth2-6 %
120577NaClnogrowth0 %
120577NaClnogrowth8 %
120577NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
12057716947citrate-carbon source
1205774853esculin-hydrolysis
12057717234glucose+fermentation
12057717716lactose-fermentation
12057717632nitrate+reduction
12057716301nitrite-reduction
120577132112sodium thiosulfate-builds gas from
12057717234glucose+degradation
12057717632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12057735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12057715688acetoin+
12057717234glucose+

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
120577oxidase+
120577beta-galactosidase-3.2.1.23
120577alcohol dehydrogenase+1.1.1.1
120577gelatinase-
120577amylase-
120577DNase+
120577caseinase-3.4.21.50
120577catalase+1.11.1.6
120577tween esterase-
120577gamma-glutamyltransferase-2.3.2.2
120577lecithinase-
120577lipase-
120577lysine decarboxylase-4.1.1.18
120577ornithine decarboxylase-4.1.1.17
120577phenylalanine ammonia-lyase-4.3.1.24
120577protease-
120577tryptophan deaminase-
120577urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120577-+++-+----++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
15596+-++---++-+-+/--+--+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120577+++-+--------------+-----------+-----------------+---------++--------------+---++-----+--+++-++----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
15596light organ of teleostean fish Leiognathus equulaLeiognathus equulaSingaporeMalaysiaMYSAsia
46454Light organ of teleostean fish (Legionathidae)
120577Animal, Teleostean fish, Leiognathus equula (light organ)SingaporeSGPAsia

isolation source categories

Cat1Cat2
#Host#Fishes
#Host Body-Site#Organ

taxonmaps

  • @ref: 69479
  • File name: preview.99_6042.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_318;97_354;98_4481;99_6042&stattab=map
  • Last taxonomy: Photobacterium leiognathi
  • 16S sequence: X74686
  • Sequence Identity:
  • Total samples: 2678
  • soil counts: 36
  • aquatic counts: 1903
  • animal counts: 733
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
155961Risk group (German classification)
1205771Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Photobacterium leiognathi 16S rRNA, partial sequenceD11184217ena553611
20218Photobacterium leiognathi 16S rRNAD11233178ena553611
20218Photobacterium leiognathi gene for 16S rRNA, partial sequenceD11282191ena553611
20218Photobacterium leiognathi gene for 16S rRNAD253091472ena553611
15596Photobacterium leiognathi (ATCC 25521T) gene for 16S ribosomal RNAX746861466ena658

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium leiognathi ATCC 25521GCA_003026235contigncbi553611
66792Photobacterium leiognathi ATCC 25521GCA_000950415contigncbi553611
66792Photobacterium leiognathi strain ATCC 25521553611.9wgspatric553611
66792Photobacterium leiognathi strain ATCC 25521553611.3wgspatric553611
66792Photobacterium leiognathi ATCC 255212814123196draftimg553611
66792Photobacterium leiognathi ATCC 255212878592099draftimg553611

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno99.024no
anaerobicno97.264no
halophileno61.997no
spore-formingno95.203no
glucose-utilyes88.208yes
thermophileno99.422no
aerobicyes61.365no
motileyes92.174no
glucose-fermentyes84.603yes
flagellatedyes85.219no

External links

@ref: 15596

culture collection no.: CIP 665, DSM 21260, ATCC 25521, CAIM 327, CCUG 16229, CIP 66.5, LMG 4228, NCIMB 2193, WDCM 00113, CECT 4191

straininfo link

  • @ref: 86227
  • straininfo: 3833

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology1915359The lux genes of the luminous bacterial symbiont, Photobacterium leiognathi, of the ponyfish. Nucleotide sequence, difference in gene organization, and high expression in mutant Escherichia coli.Lee CY, Szittner RB, Meighen EAEur J Biochem10.1111/j.1432-1033.1991.tb16269.x1991Aldehyde Oxidoreductases/genetics/metabolism, Amino Acid Sequence, Base Sequence, Cloning, Molecular, Codon, DNA, Recombinant, Escherichia coli/*genetics, *Gene Expression, Luciferases/*genetics/metabolism, *Luminescent Measurements, Molecular Sequence Data, Mutation, Photobacterium/*genetics, Transformation, BacterialMetabolism
Enzymology3511030Strain variation in bacteriocuprein superoxide dismutase from symbiotic Photobacterium leiognathi.Dunlap PV, Steinman HMJ Bacteriol10.1128/jb.165.2.393-398.19861986Animals, Electrophoresis, Polyacrylamide Gel, Fishes, Immunologic Techniques, Iron, Photobacterium/*genetics, Species Specificity, Superoxide Dismutase/*genetics/immunology, SymbiosisPhylogeny
Genetics9345300The pkI gene encoding pyruvate kinase I links to the luxZ gene which enhances bioluminescence of the lux operon from Photobacterium leiognathi.Lin JW, Lu HC, Chen HY, Weng SFBiochem Biophys Res Commun10.1006/bbrc.1997.74611997Amino Acid Sequence, Bacterial Proteins/*metabolism, Base Sequence, *Luminescent Measurements, Molecular Sequence Data, Nucleic Acid Conformation, *Operon, Photobacterium/*enzymology/genetics, Pyruvate Kinase/*genetics, Restriction Mapping, Sequence Alignment, Species Specificity, Transcription, GeneticPhylogeny
Genetics9535753Characteristics analysis of the luzA gene encoding chaperone from Photobacterium leiognathi related to bioluminescence.Lin JW, Lin BJ, Chen HY, Weng SFBiochem Biophys Res Commun10.1006/bbrc.1998.83591998Amino Acid Sequence, Bacterial Proteins/*genetics, Base Sequence, Chromosome Mapping, *Genes, Bacterial, Genetic Complementation Test, Genetic Linkage, *Luminescent Measurements, Molecular Chaperones/*genetics, Molecular Sequence Data, Nucleic Acid Conformation, Photobacterium/*genetics, Regulatory Sequences, Nucleic Acid, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Superoxide Dismutase/geneticsTranscriptome
Enzymology9610381Characteristic analysis of the luxG gene encoding the probable flavin reductase that resides in the lux operon of Photobacterium leiognathi.Lin JW, Chao YF, Weng SFBiochem Biophys Res Commun10.1006/bbrc.1998.86411998Amino Acid Sequence, Bacterial Proteins/*genetics, Base Sequence, DNA, Bacterial/chemistry/genetics, FMN Reductase, *Genes, Bacterial, Molecular Sequence Data, NADH, NADPH Oxidoreductases/*genetics, Nucleic Acid Conformation, Operon, *Oxidoreductases, Photobacterium/*enzymology/*genetics, Sequence Homology, Amino Acid, Species SpecificityGenetics
Phylogeny10229952Polyphasic approach to the characterisation of marine luminous bacteria.Caccamo D, Di Cello F, Fani R, Gugliandolo C, Maugeri TLRes Microbiol10.1016/s0923-2508(99)80039-41999Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Luminescent Measurements, Molecular Sequence Data, Phenotype, Plasmids/genetics, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Restriction Mapping, Seawater/*microbiology, Sequence Analysis, DNA, Vibrionaceae/*classification/genetics/*isolation & purificationGenetics
Phylogeny15034641Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi.Ast JC, Dunlap PVArch Microbiol10.1007/s00203-004-0663-72004Animals, Fishes/microbiology, *Genes, Bacterial, Luminescent Measurements, Multigene Family, *Operon, Photobacterium/*classification/*genetics/isolation & purification, PhylogenyEnzymology
Phylogeny15774685Photobacterium rosenbergii sp. nov. and Enterovibrio coralii sp. nov., vibrios associated with coral bleaching.Thompson FL, Thompson CC, Naser S, Hoste B, Vandemeulebroecke K, Munn C, Bourne D, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.63370-02005Animals, Anthozoa/*metabolism/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, DNA-Directed RNA Polymerases/genetics, Genes, rRNA, Molecular Sequence Data, Phenotype, Photobacterium/*classification/genetics/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Sequence Analysis, DNA, Species Specificity, Vibrionaceae/*classification/genetics/metabolismMetabolism
Phylogeny17586644Natural merodiploidy of the lux-rib operon of Photobacterium leiognathi from coastal waters of Honshu, Japan.Ast JC, Urbanczyk H, Dunlap PVJ Bacteriol10.1128/JB.00672-0720073' Flanking Region/genetics, 5' Flanking Region/genetics, Bacterial Proteins/genetics, DNA, Bacterial/chemistry/genetics, DNA-Binding Proteins/genetics, *Diploidy, Gene Order, Genes, MDR, Geography, Japan, Luminescent Proteins/genetics, Membrane Proteins/genetics, Metabolic Networks and Pathways/genetics, Molecular Sequence Data, Operon, Photobacterium/*genetics/isolation & purification, Phylogeny, Riboflavin/biosynthesis, Sequence Analysis, DNA, Sequence Homology, Transcription Factors/genetics, Transposases/genetics, Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15596Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21260)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21260
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41847Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10226
46454Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 16229)https://www.ccug.se/strain?id=16229
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86227Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3833.1StrainInfo: A central database for resolving microbial strain identifiers
120577Curators of the CIPCollection of Institut Pasteur (CIP 66.5)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2066.5