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Strain identifier

BacDive ID: 159066

Type strain: Yes

Species: Staphylococcus debuckii

Strain history: <- S. Naushad, Univ. Calgary, Canada; SDB 2975

NCBI tax ID(s): 2044912 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 7.1 (current version):
version 7:
version 6:
version 5:
version 7.1 (current version)

General

@ref: 65889

BacDive-ID: 159066

DSM-Number: 105892

keywords: 16S sequence, Bacteria, mesophilic, Gram-positive, coccus-shaped, colony-forming

description: Staphylococcus debuckii DSM 105892 is a mesophilic, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from bovine milk.

NCBI tax id

  • NCBI tax id: 2044912
  • Matching level: species

strain history: <- S. Naushad, Univ. Calgary, Canada; SDB 2975

doi: 10.13145/bacdive159066.20221219.7.1

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 debuckii
  • full scientific name: Staphylococcus debuckii Naushad et al. 2019

@ref: 65889

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus debuckii

full scientific name: Staphylococcus debuckii Naushad et al. 2019

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
67898positivecoccus-shapedno
69480positive96.84

colony morphology

  • @ref: 67898
  • colony size: 1-2 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 1 days
  • medium used: 5 % defibrinted sheep blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65889TRYPTICASE 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
65889COLUMBIA 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

culture temp

@refgrowthtypetemperaturerange
65889positivegrowth37mesophilic
67898nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
67898no
69480no95.081

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
67898NaClnogrowth15 %
67898NaClpositivegrowth0-10 %
69480halophilic97.857

observation

@refobservation
67898Cells appear mostly in pairs or small clusters.
67898Strains are haemolytic.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6789817632nitrate+reduction
6789816199urea+assimilation
6789816467L-arginine+assimilation
6789850144sodium pyruvate+assimilation
67898320061methyl alpha-D-glucopyranoside-assimilation
6789859640N-acetylglucosamine-assimilation
6789865327D-xylose+builds acid from
6789817634D-glucose+builds acid from
6789817306maltose+builds acid from
6789827082trehalose+builds acid from
6789815824D-fructose+builds acid from
6789817992sucrose+builds acid from
6789828053melibiose+builds acid from
6789816024D-mannose+builds acid from
6789817716lactose+builds acid from
6789816899D-mannitol+builds acid from
6789816634raffinose+builds acid from
6789817151xylitol+builds acid from

antibiotic resistance

  • @ref: 67898
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is sensitive: yes
  • sensitivity conc.: 1.6 µg/mL

enzymes

@refvalueactivityec
67898catalase+1.11.1.6
67898alkaline phosphatase+3.1.3.1
67898cytochrome oxidase-1.9.3.1
67898DNase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
65889bovine milkQuebecCanadaCANNorth America
67898milk of the right fore quarter of an eighth lactation cow at 35 days-in-milk housedtie-stall herd in QuébecCanadaCANNorth America

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Fluids#Milk

taxonmaps

  • @ref: 69479
  • File name: preview.99_1206.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_955;99_1206&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: MK121623
  • Sequence Identity:
  • Total samples: 22504
  • soil counts: 1443
  • aquatic counts: 1299
  • animal counts: 19130
  • plant counts: 632

Sequence information

16S sequences

  • @ref: 65889
  • description: Staphylococcus sp. SDB 2975 16S ribosomal RNA gene, partial sequence
  • accession: MK121623
  • length: 1540
  • database: ena
  • NCBI tax ID: 2044912

GC content

  • @ref: 67898
  • GC-content: 36.6
  • method: genome sequence analysis

External links

@ref: 65889

culture collection no.: DSM 105892, SDB 2975, CECT 9737

literature

  • topic: Phylogeny
  • Pubmed-ID: 31135334
  • title: Staphylococcus debuckii sp. nov., a coagulase-negative species from bovine milk.
  • authors: Naushad S, Kanevets U, Nobrega D, Carson D, Dufour S, Roy JP, Lewis PJ, Barkema HW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003457
  • year: 2019
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Milk/*microbiology, Nucleic Acid Hybridization, *Phylogeny, Quebec, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Staphylococcus/*classification/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
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
65889Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105892Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105892)
67898Sohail Naushad, Uliana Kanevets, Diego Nobrega, Domonique Carson, Simon Dufour, Jean-Philippe Roy, P. Jeffrey Lewis, Herman W. BarkemaStaphylococcus debuckii sp. nov., a coagulase-negative species from bovine milk10.1099/ijsem.0.003457IJSEM 69: 2239-2249 2019
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