Strain identifier

BacDive ID: 14665

Type strain: Yes

Species: Staphylococcus simiae

Strain history: <- CCM <- D. Koukalova, Olomouc 25

NCBI tax ID(s): 911238 (strain), 308354 (species)

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General

@ref: 7100

BacDive-ID: 14665

DSM-Number: 17636

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, coccus-shaped, animal pathogen

description: Staphylococcus simiae CCUG 51256 is an anaerobe, mesophilic, Gram-positive animal pathogen that was isolated from faeces, South American squirrel monkey.

NCBI tax id

NCBI tax idMatching level
911238strain
308354species

strain history

  • @ref: 7100
  • history: <- CCM <- D. Koukalova, Olomouc 25

doi: 10.13145/bacdive14665.20230509.8.1

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 simiae
  • full scientific name: Staphylococcus simiae Pant??ek et al. 2005

@ref: 7100

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus simiae

full scientific name: Staphylococcus simiae Pant??ek et al. 2005

type strain: yes

Morphology

cell morphology

  • @ref: 31449
  • gram stain: positive
  • cell length: 0.75 µm
  • cell width: 0.75 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 7100
  • type of hemolysis: beta
  • hemolysis ability: 1
  • incubation period: 1-2 days

pigmentation

  • @ref: 31449
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7100COLUMBIA 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
7100TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
7100positivegrowth37mesophilic
31449positivegrowth15-45
31449positiveoptimum30mesophilic
59117positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31449anaerobe
59117aerobe

spore formation

  • @ref: 31449
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31449NaClpositivegrowth12 %
31449NaClpositiveoptimum12 %

observation

  • @ref: 31449
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3144922599arabinose+carbon source
3144928757fructose+carbon source
3144928260galactose+carbon source
3144917234glucose+carbon source
3144917716lactose+carbon source
3144917306maltose+carbon source
3144929864mannitol+carbon source
3144917992sucrose+carbon source
3144927082trehalose+carbon source
3144917632nitrate+reduction
6837516199urea+hydrolysis
6837529016arginine+hydrolysis
6837518257ornithine-degradation
683754853esculin-hydrolysis
6837517634D-glucose+fermentation
6837515824D-fructose+fermentation
6837516024D-mannose-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

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
7100catalase+1.11.1.6
7100cytochrome-c oxidase-1.9.3.1
31449acid phosphatase+3.1.3.2
31449alkaline phosphatase+3.1.3.1
31449catalase+1.11.1.6
31449urease+3.5.1.5
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    59117C16:01.516
    59117C18:02.418
    59117C20:00.520
    59117C14:0 ISO0.813.618
    59117C15:0 ANTEISO53.514.711
    59117C15:0 ISO3.814.621
    59117C16:0 iso1.715.626
    59117C17:0 anteiso24.916.722
    59117C17:0 iso3.416.629
    59117C18:0 ISO0.617.632
    59117C18:1 ω9c1.117.769
    59117C18:2 ω6,9c/C18:0 ANTE2.517.724
    59117C19:0 ANTEISO2.818.729
    59117C19:0 ISO0.418.633
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
7100++--++-++++---+---+--+++--
7100++--++-++++---+---+-++++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
7100faeces, South American squirrel monkeyOlomouc, Zoological GardenCzech RepublicCZEEurope
59117Monkey feces,South American squirrelOlomouc,Zoological GardenCzech RepublicCZEEurope2004

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Primates
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_3;99_3&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AY727530
  • Sequence Identity:
  • Total samples: 23199
  • soil counts: 353
  • aquatic counts: 991
  • animal counts: 21663
  • plant counts: 192

Safety information

risk assessment

  • @ref: 7100
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7100
  • description: Staphylococcus simiae strain CCM 7213 16S ribosomal RNA gene, partial sequence
  • accession: AY727530
  • length: 1478
  • database: ena
  • NCBI tax ID: 911238

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus simiae CCUG 51256GCA_002902085scaffoldncbi308354
66792Staphylococcus simiae CCM 7213 = CCUG 51256GCA_000235645contigncbi911238
66792Staphylococcus simiae CCM 7213911238.3wgspatric911238
66792Staphylococcus simiae strain CCUG 51256308354.6wgspatric308354
66792Staphylococcus simiae Olomouc 25, CCM 72132513237273draftimg911238

GC content

  • @ref: 7100
  • GC-content: 33.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.232yes
flagellatedno92.438yes
gram-positiveyes91.647no
anaerobicno99.539no
halophileyes95.784yes
spore-formingno92.032no
thermophileno99.579yes
glucose-utilyes89.051yes
aerobicyes91.559no
glucose-fermentyes79.993no

External links

@ref: 7100

culture collection no.: CCUG 51256, DSM 17636, CCM 7213, CIP 108931, LMG 22723

straininfo link

  • @ref: 83791
  • straininfo: 132706

literature

  • topic: Phylogeny
  • Pubmed-ID: 16166694
  • title: Staphylococcus simiae sp. nov., isolated from South American squirrel monkeys.
  • authors: Pantucek R, Sedlacek I, Petras P, Koukalova D, Svec P, Stetina V, Vancanneyt M, Chrastinova L, Vokurkova J, Ruzickova V, Doskar J, Swings J, Hajek V
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63590-0
  • year: 2005
  • mesh: Animals, Bacterial Proteins/analysis, Bacterial Typing Techniques, Chaperonin 60/genetics, DNA, Bacterial/analysis, Gastrointestinal Tract/*microbiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Saimiri/*microbiology, Sequence Analysis, DNA, South America, Staphylococcus/*classification/genetics/isolation & purification/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7100Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17636)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17636
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31449Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2775228776041
59117Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51256)https://www.ccug.se/strain?id=51256
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68375Automatically annotated from API ID32STA
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
83791Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132706.1StrainInfo: A central database for resolving microbial strain identifiers