Strain identifier

BacDive ID: 130749

Type strain: Yes

Species: Photobacterium jeanii

Strain Designation: R-2567

Strain history: <- CAIM <- L. A. Chimetto, Department of Genetics, Evolution and Bioagents, State University of Campinas, Brazil

NCBI tax ID(s): 858640 (species)

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General

@ref: 21727

BacDive-ID: 130749

DSM-Number: 100339

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, ovoid-shaped

description: Photobacterium jeanii R-2567 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from mucus of apparently healthy coral zoanthid Palythoa caribaeorum.

NCBI tax id

  • NCBI tax id: 858640
  • Matching level: species

strain history

  • @ref: 21727
  • history: <- CAIM <- L. A. Chimetto, Department of Genetics, Evolution and Bioagents, State University of Campinas, Brazil

doi: 10.13145/bacdive130749.20230509.8.1

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 jeanii
  • full scientific name: Photobacterium jeanii Chimetto et al. 2010

@ref: 21727

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium jeanii

full scientific name: Photobacterium jeanii Chimetto et al. 2010

strain designation: R-2567

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29747negative2-2.5 µm01-02 µmovoid-shapedyes
69480yes97.507
69480negative99.991

pigmentation

  • @ref: 29747
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21727
  • 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
21727positivegrowth28mesophilic
29747positivegrowth20-35
29747positiveoptimum20-35

culture pH

@refabilitytypepH
29747positivegrowth7
29747positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29747
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
29747no
69481no100
69480no99.971

observation

  • @ref: 29747
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2974722599arabinose+carbon source
2974729864mannitol+carbon source
2974726546rhamnose+carbon source
2974730911sorbitol+carbon source
2974717632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29747acid phosphatase+3.1.3.2
29747alkaline phosphatase+3.1.3.1
29747catalase+1.11.1.6
29747cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21727+-++--+++-+-++/----+--+

Isolation, sampling and environmental information

isolation

  • @ref: 21727
  • sample type: mucus of apparently healthy coral zoanthid Palythoa caribaeorum
  • host species: Palythoa caribaeorum
  • geographic location: São Paulo, São Sebastião channel, Preta beach
  • country: Brazil
  • origin.country: BRA
  • continent: Middle and South America

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Cnidaria (Corals)

taxonmaps

  • @ref: 69479
  • File name: preview.99_47320.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_318;97_354;98_34140;99_47320&stattab=map
  • Last taxonomy: Photobacterium jeanii subclade
  • 16S sequence: GU065210
  • Sequence Identity:
  • Total samples: 126
  • soil counts: 2
  • aquatic counts: 68
  • animal counts: 56

Safety information

risk assessment

  • @ref: 21727
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
29747Photobacterium jeanii strain R-40507 16S ribosomal RNA gene, partial sequenceGU0652091523nuccore858640
21727Photobacterium jeanii strain R-40508 16S ribosomal RNA gene, partial sequenceGU0652101523ena858640

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium jeanii DSM 100339GCA_003025495contigncbi858640
66792Photobacterium jeanii strain DSM 100339858640.7wgspatric858640
66792Photobacterium jeanii DSM 1003392900308143draftimg858640

GC content

  • @ref: 29747
  • GC-content: 45.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes91.431yes
flagellatedyes85.685no
gram-positiveno99.085yes
anaerobicno94.043yes
halophileno73.027no
spore-formingno94.473no
thermophileno99.651yes
glucose-utilyes90.287yes
aerobicno68.396yes
glucose-fermentyes84.509yes

External links

@ref: 21727

culture collection no.: DSM 100339, CAIM 1817, LMG 25436, UFRJ R-789

straininfo link

  • @ref: 89246
  • straininfo: 362871

literature

  • topic: Phylogeny
  • Pubmed-ID: 20081016
  • title: Photobacterium jeanii sp. nov., isolated from corals and zoanthids.
  • authors: Chimetto LA, Cleenwerck I, Thompson CC, Brocchi M, Willems A, De Vos P, Thompson FL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.019968-0
  • year: 2010
  • mesh: Animals, Anthozoa/*microbiology, Australia, Bacterial Typing Techniques, Base Composition, Brazil, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Photobacterium/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
21727Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100339Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100339)
29747Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172612928776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
68369Automatically annotated from API 20NE
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
89246Reimer, 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-ID362871.1