Strain identifier

BacDive ID: 14672

Type strain: Yes

Species: Staphylococcus microti

Strain Designation: 4005-LJ(m)

Strain history: <- D. Nováková, CCM; 4005-LJ(m) <- Z. Hubálek

NCBI tax ID(s): 569857 (species)

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General

@ref: 16122

BacDive-ID: 14672

DSM-Number: 22147

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

description: Staphylococcus microti 4005-LJ is an aerobe, mesophilic, Gram-positive animal pathogen that was isolated from liver of free-living common vole Microtus arvalis.

NCBI tax id

  • NCBI tax id: 569857
  • Matching level: species

strain history

  • @ref: 16122
  • history: <- D. Nováková, CCM; 4005-LJ(m) <- Z. Hubálek

doi: 10.13145/bacdive14672.20230509.8.1

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 microti
  • full scientific name: Staphylococcus microti Nováková et al. 2010

@ref: 16122

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus microti

full scientific name: Staphylococcus microti Nováková et al. 2010

strain designation: 4005-LJ(m)

type strain: yes

Morphology

cell morphology

  • @ref: 29352
  • gram stain: positive
  • cell shape: coccus-shaped

colony morphology

  • @ref: 16122
  • type of hemolysis: beta
  • hemolysis ability: 1

pigmentation

  • @ref: 29352
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16122COLUMBIA 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
16122TRYPTICASE 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
16122positivegrowth37mesophilic
29352positivegrowth15-45
60765positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 60765
  • oxygen tolerance: aerobe

halophily

  • @ref: 29352
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 10 %

observation

  • @ref: 29352
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2935228757fructose+carbon source
2935217234glucose+carbon source
2935217716lactose+carbon source
29352506227N-acetylglucosamine+carbon source
2935217992sucrose+carbon source
2935227082trehalose+carbon source
2935218222xylose+carbon source
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

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: yes

metabolite tests

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

enzymes

@refvalueactivityec
29352acid phosphatase+3.1.3.2
29352alkaline phosphatase+3.1.3.1
29352catalase+1.11.1.6
29352cytochrome oxidase+1.9.3.1
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
16122---+++--+++---++--+++++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling date
16122liver of free-living common vole Microtus arvalisMicrotus arvalisSouth Moravia, BreclavCzech RepublicCZEEurope
60765Common vole (Microtus arvalis) liver and kidneyDrnholecCzech RepublicCZEEurope2000-09-01

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Rodentia (Other)
#Host Body-Site#Organ#Liver

Safety information

risk assessment

  • @ref: 16122
  • pathogenicity animal: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16122
  • description: Staphylococcus microti strain CCM 4903 16S ribosomal RNA gene, partial sequence
  • accession: EU888120
  • length: 1477
  • database: ena
  • NCBI tax ID: 569857

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus microti DSM 22147GCA_000934465contigncbi569857
66792Staphylococcus microti DSM 22147GCA_002902635scaffoldncbi569857
66792Staphylococcus microti strain DSM 22147569857.6wgspatric569857
66792Staphylococcus microti strain DSM 22147569857.9wgspatric569857
66792Staphylococcus microti DSM 221472917456370draftimg569857
66792Staphylococcus microti DSM 221472627854114draftimg569857

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno94.979no
gram-positiveyes93.052no
anaerobicno98.635yes
aerobicyes86.832yes
halophileyes94.665yes
spore-formingno88.246no
glucose-utilyes86.696yes
thermophileno99.553yes
motileno91.699no
glucose-fermentyes83.297yes

External links

@ref: 16122

culture collection no.: DSM 22147, CCM 4903, CCUG 55861

straininfo link

  • @ref: 83798
  • straininfo: 139493

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19654347Staphylococcus microti sp. nov., isolated from the common vole (Microtus arvalis).Novakova D, Pantucek R, Hubalek Z, Falsen E, Busse HJ, Schumann P, Sedlacek IInt J Syst Evol Microbiol10.1099/ijs.0.011429-02009Animals, *Arvicolinae, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rodent Diseases/*microbiology, Staphylococcal Infections/microbiology/*veterinary, Staphylococcus/*classification/genetics/*isolation & purificationGenetics
Phylogeny19819995Staphylococcus rostri sp. nov., a haemolytic bacterium isolated from the noses of healthy pigs.Riesen A, Perreten VInt J Syst Evol Microbiol10.1099/ijs.0.012443-02009Animals, Bacterial Proteins/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Hemolysin Proteins/metabolism, Hemolysis, Molecular Sequence Data, Nose/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Staphylococcus/*classification/genetics/*isolation & purification/metabolism, Sus scrofa/*microbiology, SwitzerlandMetabolism
Genetics29773631Draft Genome Sequence of Staphylococcus microti DSM 22147, Isolated from the Common Vole.Hu X, Shang Y, Guo J, Zhang H, Liang Y, Sun J, Yue FGenome Announc10.1128/genomeA.00420-182018Phylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16122Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22147)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22147
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
29352Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2576428776041
60765Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55861)https://www.ccug.se/strain?id=55861
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
68375Automatically annotated from API ID32STA
83798Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID139493.1StrainInfo: A central database for resolving microbial strain identifiers