Strain identifier

BacDive ID: 17224

Type strain: Yes

Species: Photobacterium iliopiscarium

Strain Designation: PS1

Strain history: CIP <- 1996, ATCC <- A.M. Onarheim

NCBI tax ID(s): 56192 (species)

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General

@ref: 3757

BacDive-ID: 17224

DSM-Number: 9896

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, psychrophilic, Gram-negative, motile, oval-shaped

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

NCBI tax id

  • NCBI tax id: 56192
  • Matching level: species

strain history

@refhistory
3757<- A.M. Onarheim, Fiskeriforskning, Tromsö
120048CIP <- 1996, ATCC <- A.M. Onarheim

doi: 10.13145/bacdive17224.20230509.8.1

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 iliopiscarium
  • full scientific name: Photobacterium iliopiscarium (Onarheim et al. 1995) Urakawa et al. 1999

  • synonyms

    • @ref: 20215
    • synonym: Vibrio iliopiscarius

@ref: 3757

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium iliopiscarium

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

strain designation: PS1

type strain: yes

Morphology

cell morphology

  • @ref: 120048
  • gram stain: negative
  • cell shape: oval-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3757REACTIVATION WITH LIQUID MEDIUM 115 (DSMZ Medium 115a)yeshttps://mediadive.dsmz.de/medium/115aName: 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
39087Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
3757MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514f.pdf
120048CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
120048CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
39087positivegrowth15psychrophilic
3757positivegrowth20psychrophilic
120048positivegrowth5-22psychrophilic
120048nogrowth30mesophilic
120048nogrowth37mesophilic
120048nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120048
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
120048NaClpositivegrowth2-6 %
120048NaClnogrowth0 %
120048NaClnogrowth8 %
120048NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-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
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836829016arginine+hydrolysis
1200484853esculin-hydrolysis
12004817632nitrate+reduction
12004816301nitrite-reduction
12004817632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836835581indoleno
6836816136hydrogen sulfideno
12004835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
6836835581indole-
12004815688acetoin-
12004817234glucose-

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
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
120048oxidase+
120048beta-galactosidase-3.2.1.23
120048alcohol dehydrogenase+1.1.1.1
120048gelatinase-
120048amylase+
120048DNase-
120048caseinase-3.4.21.50
120048catalase+1.11.1.6
120048tween esterase-
120048gamma-glutamyltransferase-2.3.2.2
120048lecithinase+
120048lipase+
120048lysine decarboxylase-4.1.1.18
120048ornithine decarboxylase-4.1.1.17
120048phenylalanine ammonia-lyase-4.3.1.24
120048protease-
120048tryptophan deaminase-
120048urease-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
120048-+++-+----++-----+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
3757-++------+-+---------
3757-+---------+/----------
3757-++------+-+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3757+-++---++------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
3757pyloric ceca of herringTromsöNorwayNOREurope
120048Herring, pyloric cecaNorwayNOREurope

isolation source categories

Cat1Cat2Cat3
#Host#Fishes
#Host Body-Site#Gastrointestinal tract#Stomach

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: AY643710
  • 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
37571Risk group (German classification)
1200481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Photobacterium iliopiscarium gene for 16S ribosomal RNA, partial sequenceAB0002781410ena56192
20218Photobacterium iliopiscarium strain ATCC 51760 16S ribosomal RNA gene, partial sequenceAY6437101467ena56192

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium iliopiscarium ATCC 51760GCA_003026395contigncbi56192
66792Photobacterium iliopiscarium ATCC 51760GCA_000950265contigncbi56192
66792Photobacterium iliopiscarium strain ATCC 5176056192.4wgspatric56192
66792Photobacterium iliopiscarium strain ATCC 5176056192.15wgspatric56192
66792Photobacterium iliopiscarium ATCC 517602868861791draftimg56192
66792Photobacterium iliopiscarium ATCC 517602751185812draftimg56192

GC content

  • @ref: 3757
  • GC-content: 39
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno99.025no
anaerobicno97.762no
halophileno58.201no
spore-formingno95.686no
glucose-utilyes89.596yes
aerobicyes65.681no
thermophileno98.887no
motileyes90.332no
flagellatedyes79.858no
glucose-fermentyes85.282no

External links

@ref: 3757

culture collection no.: DSM 9896, ATCC 51760, CIP 104755, KCTC 12376

straininfo link

  • @ref: 86223
  • straininfo: 10417

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10028270Reassessment of the taxonomic position of Vibrio iliopiscarius (Onarheim et al. 1994) and proposal for Photobacterium iliopiscarium comb. nov.Urakawa H, Kita-Tsukamoto K, Ohwada KInt J Syst Bacteriol10.1099/00207713-49-1-2571999Base Sequence, Molecular Sequence Data, Photobacterium/*classification, Phylogeny, Vibrio/*classificationGenetics
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
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3757Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 9896)https://www.dsmz.de/collection/catalogue/details/culture/DSM-9896
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
39087Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16698
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)
68368Automatically annotated from API 20E
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
86223Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10417.1StrainInfo: A central database for resolving microbial strain identifiers
120048Curators of the CIPCollection of Institut Pasteur (CIP 104755)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104755