Strain identifier

BacDive ID: 17221

Type strain: Yes

Species: Photobacterium phosphoreum

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

NCBI tax ID(s): 659 (species)

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General

@ref: 5999

BacDive-ID: 17221

DSM-Number: 15556

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

description: Photobacterium phosphoreum DSM 15556 is a facultative anaerobe, psychrophilic, motile bacterium that was isolated from Unknown source.

NCBI tax id

  • NCBI tax id: 659
  • Matching level: species

strain history

@refhistory
5999<- NCIMB <- ATCC <- F. H. Johnson <- A. J. Kluyver
67770IAM 14401 <-- ATCC 11040 <-- F. H. Johnson ("Bacterium phosphoreum") <-- A. J. Kluyver.
121807CIP <- 1988, ATCC <- F.J. Johnson, Bacterium phosphoreum <- A.J. Kluyver

doi: 10.13145/bacdive17221.20230509.8.1

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 phosphoreum
  • full scientific name: Photobacterium phosphoreum (Cohn 1878) Beijerinck 1889 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Micrococcus phosphoreus

@ref: 5999

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium phosphoreum

full scientific name: Photobacterium phosphoreum (Cohn 1878) Beijerinck 1889

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.116
6948099.988negative
121807nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41661Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
5999SEA WATER AGAR (DSMZ Medium 246)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium246.pdf
5999MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514f.pdf
121807CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5999positivegrowth22psychrophilic
41661positivegrowth25mesophilic
67770positivegrowth17psychrophilic
121807positivegrowth5-22psychrophilic
121807nogrowth30mesophilic
121807nogrowth37mesophilic
121807nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121807
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.986

halophily

@refsaltgrowthtested relationconcentration
121807NaClpositivegrowth2-6 %
121807NaClnogrowth0 %
121807NaClnogrowth8 %
121807NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1218074853esculin-hydrolysis
12180717234glucose-fermentation
12180717716lactose-fermentation
12180717632nitrate+reduction
12180716301nitrite-reduction
121807132112sodium thiosulfate-builds gas from
12180717234glucose-degradation
12180717632nitrate+respiration

metabolite production

  • @ref: 121807
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12180715688acetoin-
12180717234glucose-

enzymes

@refvalueactivityec
121807oxidase-
121807beta-galactosidase+3.2.1.23
121807alcohol dehydrogenase-1.1.1.1
121807gelatinase-
121807amylase-
121807caseinase-3.4.21.50
121807catalase+1.11.1.6
121807gamma-glutamyltransferase-2.3.2.2
121807lecithinase-
121807lipase+
121807lysine decarboxylase-4.1.1.18
121807ornithine decarboxylase-4.1.1.17
121807phenylalanine ammonia-lyase-4.3.1.24
121807protease-
121807tryptophan deaminase-
121807urease-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
121807-+++-+----+------+--

Isolation, sampling and environmental information

isolation

  • @ref: 121807
  • sample type: Unknown source

taxonmaps

  • @ref: 69479
  • File name: preview.99_518.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_318;97_354;98_399;99_518&stattab=map
  • Last taxonomy: Photobacterium
  • 16S sequence: X74687
  • Sequence Identity:
  • Total samples: 5263
  • soil counts: 73
  • aquatic counts: 2884
  • animal counts: 2251
  • plant counts: 55

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
59991Risk group (German classification)
1218071Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Photobacterium phosphoreum strain ATCC 11040 16S ribosomal RNA gene, partial sequenceAY3414371467ena659
20218Photobacterium phosphoreum 16S rRNAD11186212ena659
20218Photobacterium phosphoreum 16S rRNAD11235214ena659
20218Photobacterium phosphoreum 16S rRNAD11284191ena659
20218Photobacterium phosphoreum gene for 16S rRNAD253101465ena659
20218Photobacterium phosphoreum (ATCC 11040T) gene for 16S ribosomal RNAX746871457ena659
20218Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, complete sequenceAY779756320ena659
20218Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, complete sequenceAY779757351ena659
20218Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, complete sequenceAY779758391ena659
20218Photobacterium phosphoreum strain CIP102511 16S-23S ribosomal RNA intergenic spacer, tRNA-Ile and tRNA-Ala genes, complete sequenceAY779759610ena659
20218Photobacterium phosphoreum DNA, 16S-23S rRNA intergenic spacer and 23S rRNA, partial sequence, strain: IAM 14401AB255705290ena659
20218Photobacterium phosphoreum gene for 16S rRNA, partial sequence, strain: NBRC 103031AB6819111470ena659

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium phosphoreum strain ATCC 11040659.23wgspatric659
66792Photobacterium phosphoreum strain ATCC 11040659.4wgspatric659
66792Photobacterium phosphoreum strain JCM 21184659.11wgspatric659
66792Photobacterium phosphoreum ATCC 110402772190759draftimg659
66792Photobacterium phosphoreum ATCC 110402900322015draftimg659
67770Photobacterium phosphoreum ATCC 11040GCA_000949955contigncbi659
67770Photobacterium phosphoreum JCM 21184GCA_002954725scaffoldncbi659
67770Photobacterium phosphoreum ATCC 11040GCA_003026275contigncbi659

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.776no
anaerobicno97.895no
halophileno52.735no
spore-formingno94.245no
glucose-utilyes90.897no
thermophileno99.336no
flagellatedyes79.304no
motileyes89.933no
aerobicyes82.342no
glucose-fermentyes83.918no

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

straininfo link

  • @ref: 86220
  • straininfo: 3838

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology3056906Highly repetitive tRNA(Pro)-tRNA(His) gene cluster from Photobacterium phosphoreum.Giroux S, Beaudet J, Cedergren RJ Bacteriol10.1128/jb.170.12.5601-5606.19881988Base Sequence, Blotting, Southern, Cloning, Molecular, Escherichia coli/genetics, *Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Hybridization, Photobacterium/*genetics, Promoter Regions, Genetic, RNA, Transfer, Amino Acid-Specific/*genetics, RNA, Transfer, His/*genetics, RNA, Transfer, Pro/*genetics, Repetitive Sequences, Nucleic Acid, Terminator Regions, Genetic, Transcription, GeneticGenetics
Metabolism15596133Characteristic analysis of the ampC gene encoding beta-lactamase from Photobacterium phosphoreum.Lin JW, Weng SF, Chao YF, Chung YTBiochem Biophys Res Commun10.1016/j.bbrc.2004.11.0652005Amino Acid Sequence, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/*genetics/metabolism/pharmacology, Base Sequence, Cloning, Molecular, Drug Resistance, Bacterial/genetics/physiology, Molecular Sequence Data, Photobacterium/drug effects/*genetics/metabolism, Phylogeny, Time Factors, beta-Lactamases/*genetics/metabolism/pharmacologyEnzymology
Phylogeny15691950Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae).Dunlap PV, Ast JCAppl Environ Microbiol10.1128/AEM.71.2.930-939.20052005Animals, Base Sequence, DNA Gyrase/genetics, DNA, Ribosomal/analysis, Evolution, Molecular, Fishes/anatomy & histology/*microbiology, Light, Luminescent Measurements, Luminescent Proteins/genetics/*metabolism, Molecular Sequence Data, Photobacterium/*classification/*genetics/isolation & purification, *Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *SymbiosisGenetics
Phylogeny17766874Photobacterium 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 PVInt J Syst Evol Microbiol10.1099/ijs.0.65153-02007Animal Structures/microbiology, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Catalase/biosynthesis, Chromosomes, Bacterial, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Circular, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fishes/*microbiology/physiology, Flagella, Genes, rRNA, Locomotion/physiology, Luminescence, Luminescent Proteins/*biosynthesis, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Nucleic Acid Hybridization, Oxidoreductases/biosynthesis, Photobacterium/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Skin/microbiology, *SymbiosisGenetics
Phylogeny22066815Historical microbiology: revival and phylogenetic analysis of the luminous bacterial cultures of M. W. Beijerinck.Figge MJ, Robertson LA, Ast JC, Dunlap PVFEMS Microbiol Ecol10.1111/j.1574-6941.2011.01177.x2011Bacterial Typing Techniques, DNA, Bacterial/genetics, France, Genes, Bacterial, Genetic Variation, Japan, *Luminescence, Mexico, Microbial Viability, Multilocus Sequence Typing, Norway, Photobacterium/*classification/genetics/isolation & purification, *Phylogeny, Seawater/microbiology, Sequence Analysis, DNA, Uruguay, Vibrio/*classification/genetics/isolation & purificationEnzymology
Phylogeny24951451Photobacterium piscicola sp. nov., isolated from marine fish and spoiled packed cod.Figge MJ, Cleenwerck I, van Uijen A, De Vos P, Huys G, Robertson LSyst Appl Microbiol10.1016/j.syapm.2014.05.0032014Amplified Fragment Length Polymorphism Analysis, Animals, Aquatic Organisms/microbiology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Food Microbiology, Gadiformes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Photobacterium/*classification/genetics/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNABiotechnology
Phylogeny27154455Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater.Huang Z, Dong C, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0011422016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/chemistry, Phospholipids/chemistry, *Phylogeny, Polyesters/chemistry, RNA, Ribosomal, 16S/genetics, Salinity, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, Vibrionaceae/*classification/genetics/isolation & purificationTranscriptome
Metabolism31679853A 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 GFood Chem10.1016/j.foodchem.2019.1256912019Biosensing Techniques/*methods, Captan/*analysis, Chromatography, Thin Layer, Fruit/chemistry/metabolism, Fungicides, Industrial/*analysis, Malus/chemistry/metabolism, Photobacterium/chemistry/isolation & purification, Silica Gel/chemistryBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5999Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15556)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15556
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
41661Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14206
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86220Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3838.1StrainInfo: A central database for resolving microbial strain identifiers
121807Curators of the CIPCollection of Institut Pasteur (CIP 102511)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102511