Strain identifier

BacDive ID: 14651

Type strain: No

Species: Staphylococcus equorum subsp. linens

Strain Designation: ID 01-1208, RP29

Strain history: CIP <- 2002, R. Place, Zürich, Switzerland: strain RP29

NCBI tax ID(s): 201829 (subspecies)

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General

@ref: 5709

BacDive-ID: 14651

DSM-Number: 15097

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive

description: Staphylococcus equorum subsp. linens ID 01-1208 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from rind of surface ripened cheese.

NCBI tax id

  • NCBI tax id: 201829
  • Matching level: subspecies

strain history

@refhistory
5709<- R. Place, ETH; RP29 <- R. Place
364142002, R. Place, Zürich, Switzerland: strain RP29
119125CIP <- 2002, R. Place, Zürich, Switzerland: strain RP29

doi: 10.13145/bacdive14651.20230509.8.1

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 equorum subsp. linens
  • full scientific name: Staphylococcus equorum subsp. linens Place et al. 2003

@ref: 5709

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus equorum

full scientific name: Staphylococcus equorum Schleifer et al. 1985 emend. Jeong et al. 2013

strain designation: ID 01-1208, RP29

type strain: no

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
119125positivecoccus-shapedno

colony morphology

  • @ref: 119125

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5709COLUMBIA 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
5709TRYPTICASE 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
36414MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119125CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5709positivegrowth30mesophilic
36414positivegrowth30mesophilic
58446positivegrowth30mesophilic
119125positivegrowth22-37
119125nogrowth10psychrophilic
119125nogrowth41thermophilic
119125nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58446aerobe
119125obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.859

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
119125606565hippurate+hydrolysis
11912517632nitrate+reduction
11912516301nitrite-reduction
6837516199urea+hydrolysis
6837529016arginine-hydrolysis
6837518257ornithine-degradation
683754853esculin-hydrolysis
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 sensitive: yes
  • sensitivity conc.: 1.8 µg

metabolite production

  • @ref: 119125
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 119125
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68375pyrrolidonyl arylamidase-3.4.19.3
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
119125oxidase-
119125beta-galactosidase-3.2.1.23
119125alcohol dehydrogenase-1.1.1.1
119125gelatinase-
119125amylase-
119125DNase-
119125caseinase-3.4.21.50
119125catalase+1.11.1.6
119125coagulase-
119125tween esterase-
119125gamma-glutamyltransferase-2.3.2.2
119125lecithinase-
119125lipase-
119125lysine decarboxylase-4.1.1.18
119125ornithine decarboxylase-4.1.1.17
119125phenylalanine ammonia-lyase-4.3.1.24
119125protease-
119125urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119125-+++------++--++----

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
5709+---++--------+-----------
5709+---+/-+--------++/---+------+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119125+++++----++--+-----+-++---+-+--+---++-------------------+--+-------------+-+----------+---++-------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
5709rind of surface ripened cheeseSwitzerlandCHEEurope
58446Rind of surface ripened cheeseSwitzerlandCHEEurope2001
119125Food, Rind of surface ripened cheeseSwitzerlandCHEEurope2001

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_743.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_3;99_743&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AF527483
  • Sequence Identity:
  • Total samples: 4759
  • soil counts: 295
  • aquatic counts: 209
  • animal counts: 4104
  • plant counts: 151

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57091Risk group (German classification)
1191251Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus equorum subsp. linens strain DSM 15097 16S ribosomal RNA gene, partial sequenceAY688056464ena201829
5709Staphylococcus equorum subsp. linens 16S ribosomal RNA gene, partial sequenceAF5274831535ena201829

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus equorum subsp. linens DSM 15097GCA_002901955scaffoldncbi201829
66792Staphylococcus equorum strain FDAARGOS_1150246432.120completepatric246432
66792Staphylococcus equorum subsp. linens strain DSM 15097201829.6wgspatric201829

GC content

  • @ref: 5709
  • GC-content: 35.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno88.461no
gram-positiveyes90.931no
anaerobicno99.264yes
aerobicyes92.535yes
halophileyes96.549no
spore-formingno90.107no
glucose-utilyes89.542no
flagellatedno91.716no
thermophileno99.776yes
glucose-fermentyes83.088no

External links

@ref: 5709

culture collection no.: CCUG 49024, DSM 15097, CIP 107656, CCM 7278

straininfo link

  • @ref: 83778
  • straininfo: 113579

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12747407Staphylococcus equorum subsp. linens, subsp. nov., a starter culture component for surface ripened semi-hard cheeses.Place RB, Hiestand D, Gallmann HR, Teuber MSyst Appl Microbiol10.1078/0723202033223372812003Amino Acid Sequence, Base Composition, Biochemical Phenomena, Cheese/*microbiology, Culture Media, Fermentation/physiology, *Food Microbiology, *Food-Processing Industry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/analysis, Sequence Alignment, Sequence Analysis, DNA, *Staphylococcus/classification/genetics/isolation & purification/ultrastructureCultivation
Phylogeny24057981A proposal to unify two subspecies of Staphylococcus equorum: Staphylococcus equorum subsp. equorum and Staphylococcus equorum subsp. linens.Jeong DW, Kim HR, Han S, Jeon CO, Lee JHAntonie Van Leeuwenhoek10.1007/s10482-013-0025-z2013Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Food Microbiology, Genotype, Molecular Sequence Data, Molecular Typing, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Staphylococcus/*classification/genetics/*isolation & purification/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5709Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15097)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15097
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
36414Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5115
58446Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49024)https://www.ccug.se/strain?id=49024
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
68382Automatically annotated from API zym
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83778Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID113579.1StrainInfo: A central database for resolving microbial strain identifiers
119125Curators of the CIPCollection of Institut Pasteur (CIP 107656)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107656