Strain identifier

BacDive ID: 17240

Type strain: Yes

Species: Photobacterium aphoticum

Strain Designation: M46

Strain history: <- MJ Pujalte, Univ. of Valencia, Spain

NCBI tax ID(s): 754436 (species)

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General

@ref: 18146

BacDive-ID: 17240

DSM-Number: 25995

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Photobacterium aphoticum M46 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface seawater.

NCBI tax id

  • NCBI tax id: 754436
  • Matching level: species

strain history

@refhistory
18146<- CECT <- M. J. Pujalte, Univ. Valencia, Spain
67771<- MJ Pujalte, Univ. of Valencia, Spain

doi: 10.13145/bacdive17240.20230509.8.1

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 aphoticum
  • full scientific name: Photobacterium aphoticum Lucena et al. 2011

@ref: 18146

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium aphoticum

full scientific name: Photobacterium aphoticum Lucena et al. 2011

strain designation: M46

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
67771negative
69480yes94.246
69480negative99.926

Culture and growth conditions

culture medium

  • @ref: 18146
  • name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514c
  • composition: 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

@refgrowthtypetemperaturerange
18146positivegrowth28mesophilic
67771positivegrowth26mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.474

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose+fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
18146++---------+++---+--+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
18146surface seawaterValencia, Malvarrosa Beach (39° 28' 29'' N 0° 19' 23'' W)SpainESPEurope39.4747-0.3231
67771From surface sea waterMediterranean coast in Malvarrosa beach, ValenciaSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_4872.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_504;97_2921;98_3647;99_4872&stattab=map
  • Last taxonomy: Photobacterium aphoticum subclade
  • 16S sequence: FN796493
  • Sequence Identity:
  • Total samples: 1603
  • soil counts: 45
  • aquatic counts: 994
  • animal counts: 553
  • plant counts: 11

Safety information

risk assessment

  • @ref: 18146
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18146
  • description: Photobacterium aphoticum partial 16S rRNA gene, strain CECT 7614
  • accession: FN796493
  • length: 1529
  • database: ena
  • NCBI tax ID: 754436

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium aphoticum DSM 25995GCA_001029435contigncbi754436
66792Photobacterium aphoticum KCTC 23057GCA_014652075scaffoldncbi754436
66792Photobacterium aphoticum DSM 25995GCA_003025575contigncbi754436
66792Photobacterium aphoticum strain DSM 25995754436.4wgspatric754436
66792Photobacterium aphoticum strain DSM 25995754436.6wgspatric754436
66792Photobacterium aphoticum strain KCTC 23057754436.8wgspatric754436
66792Photobacterium aphoticum DSM 259952900340083draftimg754436
66792Photobacterium aphoticum DSM 259952671180362draftimg754436

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.679no
flagellatedyes86.598no
gram-positiveno99.043yes
anaerobicno95.133no
aerobicyes59.91yes
halophileno71.283no
spore-formingno93.329no
thermophileno98.899yes
glucose-utilyes93.329no
glucose-fermentyes87.104no

External links

@ref: 18146

culture collection no.: DSM 25995, CECT 7614, KCTC 23057

straininfo link

  • @ref: 86238
  • straininfo: 377770

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20675441Photobacterium aphoticum sp. nov., isolated from coastal water.Lucena T, Ruvira MA, Pascual J, Garay E, Macian MC, Arahal DR, Pujalte MJInt J Syst Evol Microbiol10.1099/ijs.0.025171-02010Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Photobacterium/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, SpainGenetics
Phylogeny24096359Photobacterium aquae sp. nov., isolated from a recirculating mariculture system.Liu Y, Liu LZ, Song L, Zhou YG, Qi FJ, Liu ZPInt J Syst Evol Microbiol10.1099/ijs.0.055020-02013Animals, *Aquaculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, Perciformes, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, Photobacterium/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18146Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25995)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25995
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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68368Automatically annotated from API 20E
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
86238Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID377770.1StrainInfo: A central database for resolving microbial strain identifiers