Strain identifier

BacDive ID: 130750

Type strain: Yes

Species: Photobacterium sanctipauli

Strain history: <- CAIM <- A. P. B. Moreira et al., Institute of Biology, Federal University of Rio de Janeiro

NCBI tax ID(s): 1342794 (species)

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General

@ref: 21728

BacDive-ID: 130750

DSM-Number: 100436

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Photobacterium sanctipauli DSM 100436 is a mesophilic, motile bacterium that was isolated from bleached coral Madracis decactis.

NCBI tax id

  • NCBI tax id: 1342794
  • Matching level: species

strain history

  • @ref: 21728
  • history: <- CAIM <- A. P. B. Moreira et al., Institute of Biology, Federal University of Rio de Janeiro

doi: 10.13145/bacdive130750.20230509.8.1

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 sanctipauli
  • full scientific name: Photobacterium sanctipauli Moreira et al. 2015

@ref: 21728

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Photobacterium

species: Photobacterium sanctipauli

full scientific name: Photobacterium sanctipauli Moreira et al. 2015

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes96.636
6948099.962negative

Culture and growth conditions

culture medium

  • @ref: 21728
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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 NaHCO3 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

  • @ref: 21728
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.943

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

metabolite production

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

metabolite tests

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

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21728--++-+-++-++--+------

Isolation, sampling and environmental information

isolation

  • @ref: 21728
  • sample type: bleached coral Madracis decactis
  • host species: Madracis decactis
  • geographic location: St Peter and St Paul Archipelago, Mid-Atlantic Ridge
  • country: Brazil
  • origin.country: BRA
  • continent: Middle and South America
  • latitude: 0.9333
  • longitude: -29.3667

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Cnidaria (Corals)

taxonmaps

  • @ref: 69479
  • File name: preview.99_60437.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_3204;97_33379;98_42899;99_60437&stattab=map
  • Last taxonomy: Photobacterium sanctipauli subclade
  • 16S sequence: KC751088
  • Sequence Identity:
  • Total samples: 140
  • aquatic counts: 121
  • animal counts: 19

Sequence information

16S sequences

  • @ref: 21728
  • description: Photobacterium sanctipauli strain A-394 16S ribosomal RNA gene, partial sequence
  • accession: KC751088
  • length: 1505
  • database: ena
  • NCBI tax ID: 1342794

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Photobacterium sanctipauli DSM 100436GCA_003026495contigncbi1342794
66792Photobacterium sanctipauli strain DSM 1004361342794.7wgspatric1342794
66792Photobacterium sanctipauli DSM 1004362902482210draftimg1342794

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.985no
gram-positiveno98.696no
anaerobicno96.232no
halophileno58.673no
spore-formingno93.427no
thermophileno99.801yes
glucose-utilyes90.428no
aerobicyes74.249no
flagellatedyes80.496no
glucose-fermentyes86.196yes

External links

@ref: 21728

culture collection no.: DSM 100436, CAIM 1892, LMG 27910

straininfo link

  • @ref: 89247
  • straininfo: 403282

literature

  • topic: Phylogeny
  • Pubmed-ID: 25024905
  • title: Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil.
  • authors: Moreira AP, Duytschaever G, Chimetto Tonon LA, Froes AM, de Oliveira LS, Amado-Filho GM, Francini-Filho RB, De Vos P, Swings J, Thompson CC, Thompson FL
  • journal: PeerJ
  • DOI: 10.7717/peerj.427
  • year: 2014

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
21728Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100436Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100436)
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
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
89247Reimer, 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-ID403282.1