Strain identifier

BacDive ID: 157258

Type strain: Yes

Species: Staphylococcus edaphicus

Strain Designation: P5085

Strain history: CIP <- 2018, CCM <- 2016, I. Sedlacek, Mazaryk Univ., Brno, Czech Republic

NCBI tax ID(s): 1955013 (species)

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General

@ref: 64323

BacDive-ID: 157258

DSM-Number: 104441

keywords: genome sequence, Bacteria, aerobe, Gram-positive

description: Staphylococcus edaphicus P5085 is an aerobe, Gram-positive bacterium that was isolated from Fragments of black porus stone.

NCBI tax id

  • NCBI tax id: 1955013
  • Matching level: species

strain history

@refhistory
64323<- I. Sedlacek; Masaryk University, Brno, CZECH REPUBLIC; P5085<-I. Sedlácek; CCM, Masaryk University, Czech Republic
118996CIP <- 2018, CCM <- 2016, I. Sedlacek, Mazaryk Univ., Brno, Czech Republic

doi: 10.13145/bacdive157258.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Staphylococcus
  • species: Staphylococcus edaphicus
  • full scientific name: Staphylococcus edaphicus Pant??ek et al. 2018

@ref: 64323

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Clostridiales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus edaphicus

full scientific name: Staphylococcus edaphicus Pant??ek et al. 2018

strain designation: P5085

type strain: yes

Morphology

cell morphology

  • @ref: 118996
  • gram stain: negative
  • cell shape: coccus-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64323COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
64323TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
118996CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
64323positivegrowth37
63798positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 63798
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 99

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837516199urea+hydrolysis
6837529016arginine-hydrolysis
6837518257ornithine-degradation
683754853esculin-hydrolysis
6837517634D-glucose+fermentation
6837515824D-fructose+fermentation
6837517306maltose+fermentation
6837517716lactose-fermentation
6837527082trehalose-fermentation
6837516899D-mannitol+fermentation
6837516634raffinose-fermentation
6837516988D-ribose-fermentation
6837517057cellobiose-fermentation
6837517632nitrate+reduction
6837517992sucrose+fermentation
6837559640N-acetylglucosamine+fermentation
6837532528turanose-fermentation
6837522599arabinose-fermentation

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is resistant: yes
  • resistance conc.: 1.8 µg

metabolite production

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: no

metabolite tests

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68375beta-glucuronidase+3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
68375alkaline phosphatase-3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase-3.2.1.23
68375beta-glucosidase-3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68375urease+3.5.1.5

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
64323+---+++/-+--+---+-----+++--+

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinent
63798Fragments of black porus stone2016Ross Island,Lachman CapeAntarcticaATAAustralia and Oceania
64323fragments of black porous stone (top of the hill)James Ross Island (57° 47' 11" W, 63° 46' 58" S)AntarcticaATAAustralia and Oceania
118996Environment, Fragments of black porus stoneLachman Cap, J. Ross IslandAntarcticaATAAntarctica

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

  • @ref: 118996
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus edaphicus CCM 8730GCA_002614725contigncbi1955013
66792Staphylococcus edaphicus strain CCM 8730 strain CCM 50851955013.3wgspatric1955013
66792Staphylococcus edaphicus CCM 87302802429263draftimg1955013

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno99no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes81.283no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no99.434yes
69480spore-formingspore-formingAbility to form endo- or exosporesno69.837no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes60.933no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.517yes
69480flagellatedmotile2+Ability to perform flagellated movementno80no

External links

@ref: 64323

culture collection no.: DSM 104441, CCM 8730, CCUG 72269, CIP 111603

straininfo link

  • @ref: 110355
  • straininfo: 401196

literature

  • topic: Phylogeny
  • Pubmed-ID: 29079617
  • title: Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments.
  • authors: Pantucek R, Sedlacek I, Indrakova A, Vrbovska V, Maslanova I, Kovarovic V, Svec P, Kralova S, Kristofova L, Keklakova J, Petras P, Doskar J
  • journal: Appl Environ Microbiol
  • DOI: 10.1128/AEM.01746-17
  • year: 2018
  • mesh: Adaptation, Biological/*genetics, Antarctic Regions, *Extreme Cold Weather, *Extreme Environments, Genes, Bacterial/*physiology, Genomic Islands/*physiology, Staphylococcus/*classification/genetics/physiology

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
63798Curators of the CCUGhttps://www.ccug.se/strain?id=72269Culture Collection University of Gothenburg (CCUG) (CCUG 72269)
64323Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104441Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104441)
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
68375Automatically annotated from API ID32STA
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
110355Reimer, 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-ID401196.1
118996Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111603Collection of Institut Pasteur (CIP 111603)