Strain identifier

BacDive ID: 14677

Type strain: Yes

Species: Staphylococcus agnetis

Strain Designation: 6 VT, 6-4

Strain history: <- S. Taponen, University of Helsinki, Faculty of Veterinary Medicine; 6-4

NCBI tax ID(s): 985762 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 17328

BacDive-ID: 14677

DSM-Number: 23656

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

description: Staphylococcus agnetis 6 VT is a facultative anaerobe, mesophilic, Gram-positive animal pathogen that was isolated from bovine mastitic milk.

NCBI tax id

  • NCBI tax id: 985762
  • Matching level: species

strain history

  • @ref: 17328
  • history: <- S. Taponen, University of Helsinki, Faculty of Veterinary Medicine; 6-4

doi: 10.13145/bacdive14677.20230509.8.1

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 agnetis
  • full scientific name: Staphylococcus agnetis Taponen et al. 2012

@ref: 17328

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus agnetis

full scientific name: Staphylococcus agnetis Taponen et al. 2012

strain designation: 6 VT, 6-4

type strain: yes

Morphology

cell morphology

  • @ref: 30020
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 17328
  • type of hemolysis: gamma
  • incubation period: 1-2 days

pigmentation

  • @ref: 30020
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17328COLUMBIA 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
17328TRYPTICASE 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
17328positivegrowth37mesophilic
30020positiveoptimum15-45
62115positivegrowth37mesophilic

culture pH

  • @ref: 30020
  • ability: positive
  • type: optimum
  • pH: 6-10
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30020facultative anaerobe
62115aerobe

spore formation

  • @ref: 30020
  • spore formation: no

halophily

  • @ref: 30020
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 2-19 %

observation

  • @ref: 30020
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3002028757fructose+carbon source
3002028260galactose+carbon source
3002017234glucose+carbon source
3002017716lactose+carbon source
3002037684mannose+carbon source
3002028053melibiose+carbon source
3002033942ribose+carbon source
3002017992sucrose+carbon source
3002027082trehalose+carbon source
3002017632nitrate+reduction
6837516199urea-hydrolysis
6837529016arginine+hydrolysis
6837518257ornithine-degradation
683754853esculin-hydrolysis
6837517634D-glucose+fermentation
6837515824D-fructose+fermentation
6837516024D-mannose+fermentation
6837517306maltose-fermentation
6837517716lactose+fermentation
6837527082trehalose-fermentation
6837516634raffinose-fermentation
6837517632nitrate+reduction
6837517992sucrose+fermentation
6837559640N-acetylglucosamine+fermentation

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is sensitive: yes
  • sensitivity 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
17328catalase+1.11.1.6
17328cytochrome-c oxidase-1.9.3.1
30020catalase+1.11.1.6
68375beta-glucuronidase+3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
68375L-arginine arylamidase-
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
17328-+--+++-+-----+------++--+
17328-+--+++-+-+-+++-+-+/---+++/-++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
17328bovine mastitic milkFinlandFINEurope
62115Bovine mastitisFinlandFINEuropeSouth

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2789.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_888;99_2789&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: HM484980
  • Sequence Identity:
  • Total samples: 74
  • soil counts: 1
  • aquatic counts: 1
  • animal counts: 72

Safety information

risk assessment

  • @ref: 17328
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17328
  • description: Staphylococcus agnetis strain 6-4 16S ribosomal RNA gene, partial sequence
  • accession: HM484980
  • length: 1409
  • database: ena
  • NCBI tax ID: 985762

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus agnetis DSM 23656GCA_002901865scaffoldncbi985762
66792Staphylococcus agnetis strain DSM 23656985762.14wgspatric985762

GC content

@refGC-contentmethod
1732837.2high performance liquid chromatography (HPLC)
3002037.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno93.704yes
gram-positiveyes89.545yes
anaerobicno98.95yes
aerobicyes90.602no
halophileyes90.087no
spore-formingno89.086yes
glucose-utilyes86.672no
thermophileno99.624yes
motileno90.975yes
glucose-fermentyes81.935yes

External links

@ref: 17328

culture collection no.: DSM 23656, CCUG 59809

straininfo link

  • @ref: 83803
  • straininfo: 397173

literature

  • topic: Phylogeny
  • Pubmed-ID: 21335502
  • title: Staphylococcus agnetis sp. nov., a coagulase-variable species from bovine subclinical and mild clinical mastitis.
  • authors: Taponen S, Supre K, Piessens V, Van Coillie E, De Vliegher S, Koort JMK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.028365-0
  • year: 2011
  • mesh: Amplified Fragment Length Polymorphism Analysis, Animals, Asymptomatic Diseases, Bacterial Typing Techniques, Cattle, Cluster Analysis, Coagulase/*metabolism, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, Fatty Acids/analysis, Mastitis, Bovine/*microbiology, Milk/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptide Elongation Factor Tu/genetics, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Staphylococcal Infections/microbiology/*veterinary, Staphylococcus/*classification/genetics/*isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17328Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23656)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23656
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
30020Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2638428776041
62115Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 59809)https://www.ccug.se/strain?id=59809
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
83803Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397173.1StrainInfo: A central database for resolving microbial strain identifiers