Strain identifier

BacDive ID: 14655

Type strain: Yes

Species: Staphylococcus casei

Strain Designation: SB72

Strain history: CIP <- 2002, R. Place, Zürich, Switzerland: strain SB72 <- S. Burri

NCBI tax ID(s): 201828 (species)

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General

@ref: 5708

BacDive-ID: 14655

DSM-Number: 15096

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

description: Staphylococcus casei SB72 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from surface ripened cheese.

NCBI tax id

  • NCBI tax id: 201828
  • Matching level: species

strain history

@refhistory
5708<- R.B. Place <- S. Burri; SB72
123369CIP <- 2002, R. Place, Zürich, Switzerland: strain SB72 <- S. Burri

doi: 10.13145/bacdive14655.20230509.8.1

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 casei
  • full scientific name: Staphylococcus casei (Place et al. 2003) Madhaiyan et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Staphylococcus succinus subsp. casei

@ref: 5708

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus casei

full scientific name: Staphylococcus casei (Place et al. 2003) Madhaiyan et al. 2020

strain designation: SB72

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
123369positivecoccus-shapedno

colony morphology

  • @ref: 123369

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5708COLUMBIA 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
5708TRYPTICASE 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
39915MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123369CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5708positivegrowth37mesophilic
39915positivegrowth30mesophilic
57813positivegrowth30-37mesophilic
123369positivegrowth10-41
123369nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57813aerobe
123369facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.551

murein

  • @ref: 5708
  • murein short key: A11.03
  • type: A3alpha L-Lys-Gly2-4-L-Ser1-2-Gly

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123369hippurate+hydrolysis606565
123369nitrate+reduction17632
123369nitrite-reduction16301
68375urea+hydrolysis16199
68375arginine-hydrolysis29016
68375ornithine-degradation18257
68375esculin+hydrolysis4853
68375D-glucose+fermentation17634
68375D-fructose+fermentation15824
68375D-mannose-fermentation16024
68375maltose+fermentation17306
68375trehalose+fermentation27082
68375D-mannitol+fermentation16899
68375raffinose-fermentation16634
68375D-ribose-fermentation16988
68375cellobiose-fermentation17057
68375nitrate+reduction17632
68375sucrose+fermentation17992
68375N-acetylglucosamine+fermentation59640
68375turanose-fermentation32528
68375arabinose+fermentation22599

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is resistant: yes
  • resistance conc.: 1.8 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinyes
12336935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
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
123369oxidase-
123369beta-galactosidase+3.2.1.23
123369alcohol dehydrogenase-1.1.1.1
123369gelatinase+/-
123369amylase-
123369DNase+
123369caseinase-3.4.21.50
123369catalase+1.11.1.6
123369coagulase-
123369tween esterase-
123369gamma-glutamyltransferase-2.3.2.2
123369lecithinase-
123369lipase-
123369lysine decarboxylase-4.1.1.18
123369ornithine decarboxylase-4.1.1.17
123369phenylalanine ammonia-lyase-4.3.1.24
123369urease+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
123369-++-------++--+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123369-----+/-----++-----+/----+/---++/--+/---++------+/-----------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
5708+--+++-++/-++---+++-+-+++-++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123369+++++-+++++++--++++++++--+-----+-++++-+----------+---++-+--++--------------+--+-----------++--+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
5708surface ripened cheeseSwitzerlandCHEEurope
57813Rind of surface ripened cheeseSwitzerlandCHEEurope1997
123369Food, Rind of surface ripened cheeseSwitzerlandCHEEurope1997

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_63.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_3;99_63&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AJ320272
  • Sequence Identity:
  • Total samples: 26921
  • soil counts: 930
  • aquatic counts: 1554
  • animal counts: 23674
  • plant counts: 763

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
57081Risk group (German classification)
1233692Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus succinus subsp. casei strain DSM 15096 16S ribosomal RNA gene, partial sequenceAY688102464ena201828
5708Staphylococcus succinus subsp. casei 16S rRNA gene, strain SB72AJ3202721535ena201828

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus casei DSM 15096GCA_002902445scaffoldncbi201828
66792Staphylococcus succinus subsp. casei strain DSM 15096201828.3wgspatric201828
66792Staphylococcus succinus casei DSM 150962917474615draftimg201828

GC content

  • @ref: 5708
  • GC-content: 34.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno56no
flagellatedno88.394no
gram-positiveyes90.298no
anaerobicno99.37yes
aerobicyes93.246yes
halophileyes94.321no
spore-formingno88.566no
glucose-utilyes90.927no
thermophileno99.851no
motileno88.202no
glucose-fermentyes84.335yes

External links

@ref: 5708

culture collection no.: DSM 15096, CIP 107658, CCUG 47674, CCM 7194

straininfo link

  • @ref: 83781
  • straininfo: 100966

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5708Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15096)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15096
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
39915Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5118
57813Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 47674)https://www.ccug.se/strain?id=47674
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)
68371Automatically annotated from API 50CH acid
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)
83781Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100966.1StrainInfo: A central database for resolving microbial strain identifiers
123369Curators of the CIPCollection of Institut Pasteur (CIP 107658)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107658