Strain identifier

BacDive ID: 131276

Type strain: Yes

Species: Photobacterium aquae

Strain Designation: AE6

Strain history: Z.-P. Liu AE6.

NCBI tax ID(s): 1195763 (species)

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General

@ref: 22503

BacDive-ID: 131276

DSM-Number: 100848

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

description: Photobacterium aquae AE6 is a Gram-negative bacterium that was isolated from recirculating mariculture system.

NCBI tax id

  • NCBI tax id: 1195763
  • Matching level: species

strain history

@refhistory
22503<- JCM <- Z.-P. Liu, State Key Lab. Microbial Resources, Inst. Microbiol., Chinese Academy of Sciences, Beijing; AE6
67770Z.-P. Liu AE6.

doi: 10.13145/bacdive131276.20240916.9.1

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 aquae
  • full scientific name: Photobacterium aquae Liu et al. 2014

@ref: 22503

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium aquae

full scientific name: Photobacterium aquae Liu et al. 2014

strain designation: AE6

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 100

Culture and growth conditions

culture medium

  • @ref: 22503
  • 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

@refgrowthtypetemperature
22503positivegrowth28
67770positivegrowth30

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

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
22503-+--------++--------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudehost species
22503recirculating mariculture systemTianjinChinaCHNAsia38.8469117.62
67770Water from a grouper (Epinephelus malabaricas) culture tank in the recirculating mariculture system in TianjinChinaCHNAsiaEpinephelus malabaricas

isolation source categories

Cat1Cat2Cat3
#Engineered
#Environmental#Aquatic#Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_837.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_504;97_578;98_665;99_837&stattab=map
  • Last taxonomy: Photobacterium
  • 16S sequence: JQ948040
  • Sequence Identity:
  • Total samples: 453
  • soil counts: 33
  • aquatic counts: 283
  • animal counts: 130
  • plant counts: 7

Safety information

risk assessment

  • @ref: 22503
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22503
  • description: Photobacterium aquae strain AE6 16S ribosomal RNA gene, partial sequence
  • accession: JQ948040
  • length: 1366
  • database: nuccore
  • NCBI tax ID: 1195763

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium aquae strain CGMCC 1.121591195763.3wgspatric1195763
66792Photobacterium aquae CGMCC 1.121592713896763draftimg1195763
67770Photobacterium aquae CGMCC 1.12159GCA_001029445contigncbi1195763

GC content

  • @ref: 22503
  • GC-content: 47.1

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno100no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.862no
69480spore-formingspore-formingAbility to form endo- or exosporesno88.318no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no61.895no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.928yes
69480flagellatedmotile2+Ability to perform flagellated movementyes87.16no

External links

@ref: 22503

culture collection no.: DSM 100848, CGMCC 1.12159, JCM 18480

straininfo link

  • @ref: 89720
  • straininfo: 401457

literature

  • topic: Phylogeny
  • Pubmed-ID: 24096359
  • title: Photobacterium aquae sp. nov., isolated from a recirculating mariculture system.
  • authors: Liu Y, Liu LZ, Song L, Zhou YG, Qi FJ, Liu ZP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.055020-0
  • year: 2013
  • mesh: Animals, *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/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
22503Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100848Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100848)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89720Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID401457.1