Strain identifier

BacDive ID: 14506

Type strain: Yes

Species: Staphylococcus capitis subsp. capitis

Strain Designation: LK 499

Strain history: CIP <- 1981, J. Pillet, Inst. Pasteur, Garches, France <- ATCC <- W.E. Kloos: strain LK 499

NCBI tax ID(s): 29388 (species), 72758 (subspecies)

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General

@ref: 8717

BacDive-ID: 14506

DSM-Number: 20326

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

description: Staphylococcus capitis subsp. capitis LK 499 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from human skin.

NCBI tax id

NCBI tax idMatching level
29388species
72758subspecies

strain history

@refhistory
8717<- K.H. Schleifer <- W.E. Kloos, LK 499
117150CIP <- 1981, J. Pillet, Inst. Pasteur, Garches, France <- ATCC <- W.E. Kloos: strain LK 499

doi: 10.13145/bacdive14506.20250331.9.3

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 capitis subsp. capitis
  • full scientific name: Staphylococcus capitis subsp. capitis (Kloos and Schleifer 1975) Bannerman and Kloos 1991

@ref: 8717

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus capitis subsp. capitis

full scientific name: Staphylococcus capitis subsp. capitis (Kloos and Schleifer 1975) Bannerman and Kloos 1991

strain designation: LK 499

type strain: yes

Morphology

cell morphology

  • @ref: 117150
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@reftype of hemolysishemolysis ability
8717beta1
117150

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8717COLUMBIA 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
8717TRYPTICASE 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
37721MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
117150CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
117150CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
8717positivegrowth37
37721positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
117150obligate aerobe
125439microaerophile93.2

spore formation

@refspore formationconfidence
117150no
125439no91.3

murein

  • @ref: 8717
  • murein short key: A11.03
  • type: A3alpha L-Lys-Gly2-4-L-Ser1-2-Gly

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837522599arabinose-fermentation
6837559640N-acetylglucosamine-fermentation
6837517632nitrate+reduction
6837517057cellobiose-fermentation
6837516988D-ribose-fermentation
6837516634raffinose-fermentation
6837527082trehalose-fermentation
6837517306maltose-fermentation
6837516024D-mannose+fermentation
6837515824D-fructose+fermentation
683754853esculin-hydrolysis
6837517634D-glucose+fermentation
6837518257ornithine-degradation
11715017632nitrate+reduction
11715016301nitrite-reduction
6837532528turanose-fermentation
6837517716lactose-fermentation
6837516199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinyes
11715035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
8717catalase+1.11.1.6
8717cytochrome-c oxidase-1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
117150oxidase-
117150alcohol dehydrogenase+1.1.1.1
117150catalase+1.11.1.6
117150lysine decarboxylase-4.1.1.18
117150ornithine decarboxylase-4.1.1.17
117150urease-3.5.1.5
68375beta-galactosidase-3.2.1.23
68375beta-glucosidase-3.2.1.21
68375beta-glucuronidase-3.2.1.31
68375alkaline phosphatase-3.1.3.1
68375L-arginine arylamidase-
68375ornithine decarboxylase-4.1.1.17
68375urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117150--++------++--------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
8717-+--+++---+---++-----+----
8717-+--+++---+---++----++----
8717-+--+++---+---++----++----
8717----+++---+/----++----------
8717----+++---+/----++----+/-+----
8717-+--+++---+---++---+++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8717human skin
44977Human skin
117150Human, Healthy skinUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Organ#Skin, Nail, Hair

taxonmaps

  • @ref: 69479
  • File name: preview.99_86.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_3;99_86&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: L37599
  • Sequence Identity:
  • Total samples: 8633
  • soil counts: 44
  • aquatic counts: 284
  • animal counts: 8287
  • plant counts: 18

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
8717yes, in single cases1Risk group (German classification)
1171501Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus capitis partial 16S rRNA gene, type strain ATCC 27840TFN5547131288nuccore29388
20218Staphylococcus capitis 16S ribosomal RNA (16S rRNA) geneL375991469nuccore29388
20218S.capitis (capitis) gene for 16S ribosomal RNAZ26940771nuccore29388
20218Staphylococcus capitis subsp. capitis strain DSM 20326 16S ribosomal RNA gene, partial sequenceAY688038464nuccore72758
8717Staphylococcus capitis subsp. capitis gene for 16S rRNA, partial sequence, strain: JCM 2420AB6261271473nuccore72758
124043Staphylococcus capitis ATCC 27840 gene for 16S rRNA, partial sequence.LC752426588nuccore29388

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus capitis NCTC11045GCA_901482635contigncbi29388
66792Staphylococcus capitis CCM 2734GCA_014635765contigncbi29388
66792Staphylococcus capitis subsp. capitis NCTC 11045GCA_002902325scaffoldncbi72758
66792Staphylococcus capitis strain CCM 273429388.267wgspatric29388
66792Staphylococcus capitis strain NCTC1104529388.172wgspatric29388
66792Staphylococcus capitis subsp. capitis strain NCTC 1104572758.11wgspatric72758
66792Staphylococcus capitis subsp. capitis DSM 20326GCA_025272975completencbi72758
66792Staphylococcus capitis subsp. capitis strain DSM 2032672758.23completepatric72758

GC content

  • @ref: 8717
  • GC-content: 35.5

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes87.536no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no99.465no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes65.592yes
125438spore-formingspore-formingAbility to form endo- or exosporesno74.559no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.692no
125438motile2+flagellatedAbility to perform flagellated movementno79.554no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno91.3
125439BacteriaNetmotilityAbility to perform movementno66.3
125439BacteriaNetgram_stainReaction to gram-stainingpositive72.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile93.2

External links

@ref: 8717

culture collection no.: DSM 20326, ATCC 27840, CCM 2734, CCUG 7326, NCTC 11045, CIP 81.53, JCM 2420, GIFU 9121

straininfo link

  • @ref: 83643
  • straininfo: 7695

literature

  • topic: Metabolism
  • Pubmed-ID: 7935060
  • title: Immunological recognition of fibronectin-binding proteins of Staphylococcus aureus and Staphylococcus capitis, strain LK 499.
  • authors: Sakata N, Rozalska B, Wadstrom T
  • journal: Microbiol Immunol
  • DOI: 10.1111/j.1348-0421.1994.tb01791.x
  • year: 1994
  • mesh: *Adhesins, Bacterial, Animals, Antibodies, Bacterial/*immunology, Antibodies, Monoclonal/immunology, Bacterial Outer Membrane Proteins/*immunology/metabolism, *Bacterial Proteins, *Carrier Proteins, Cross Reactions/immunology, Fibronectins/metabolism, Humans, Mice, Protein Binding, Rabbits, Recombinant Fusion Proteins/immunology, Staphylococcus aureus/classification/*immunology
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8717Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20326)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20326
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
37721Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11216
44977Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 7326)https://www.ccug.se/strain?id=7326
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
83643Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7695.1StrainInfo: A central database for resolving microbial strain identifiers
117150Curators of the CIPCollection of Institut Pasteur (CIP 81.53)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.53
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1