Strain identifier

BacDive ID: 3927

Type strain: No

Species: Kytococcus sedentarius

Strain Designation: DM 51

Strain history: <- K.H. Schleifer <- W.E. Kloos, DM 51

NCBI tax ID(s): 1276 (species)

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General

@ref: 8595

BacDive-ID: 3927

DSM-Number: 20317

keywords: genome sequence, Bacteria, aerobe, mesophilic, human pathogen

description: Kytococcus sedentarius DM 51 is an aerobe, mesophilic human pathogen that was isolated from human skin.

NCBI tax id

  • NCBI tax id: 1276
  • Matching level: species

strain history

  • @ref: 8595
  • history: <- K.H. Schleifer <- W.E. Kloos, DM 51

doi: 10.13145/bacdive3927.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Kytococcaceae
  • genus: Kytococcus
  • species: Kytococcus sedentarius
  • full scientific name: Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995

  • synonyms

    • @ref: 20215
    • synonym: Micrococcus sedentarius

@ref: 8595

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kytococcaceae

genus: Kytococcus

species: Kytococcus sedentarius

full scientific name: Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 emend. Nouioui et al. 2018

strain designation: DM 51

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.587
69480100positive

Culture and growth conditions

culture medium

  • @ref: 8595
  • name: CORYNEBACTERIUM AGAR (DSMZ Medium 53)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/53
  • composition: Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
8595positivegrowth30mesophilic
51334positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 51334
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

murein

  • @ref: 8595
  • murein short key: A11.43
  • type: A4alpha L-Lys-D-Glu2

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation
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
6837817634D-glucose-builds acid from
6837815824D-fructose-builds acid from
6837816024D-mannose-builds acid from
6837817306maltose-builds acid from
6837817716lactose-builds acid from
6837827082trehalose-builds acid from
6837816899D-mannitol-builds acid from
6837817151xylitol-builds acid from
6837828053melibiose-builds acid from
6837817632nitrate-reduction
6837816634raffinose-builds acid from
6837865327D-xylose-builds acid from
6837817992sucrose-builds acid from
68378320061methyl alpha-D-glucopyranoside-builds acid from
6837859640N-acetylglucosamine-builds acid from
6837829016arginine-hydrolysis
6837816199urea-hydrolysis

antibiotic resistance

@refmetaboliteis antibioticis sensitiveChEBIsensitivity conc.
68378lysostaphinyesyes
68375novobiocinyesyes283681.8 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837815688acetoinyes
6837515688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6837815688acetoin+
6837515688acetoin-

enzymes

@refvalueactivityec
68378urease-3.5.1.5
68378arginine dihydrolase-3.5.3.6
68378alkaline phosphatase-3.1.3.1
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
68379catalase+1.11.1.6
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    51334C15:01.515
    51334C17:02.217
    51334C15:0 ANTEISO2.114.711
    51334C15:0 ISO9.414.621
    51334C15:1 ω6c2.214.856
    51334C16:0 10-methyl26.216.433
    51334C16:0 iso3.915.626
    51334C16:1 ω7c2.315.819
    51334C17:0 anteiso19.616.722
    51334C17:0 iso16.416.629
    51334C17:1 anteiso A5.516.541
    51334C17:1 ω6c1.616.862
    51334C17:1 ω8c5.816.792
    51334C18:2 ω6,9c/C18:0 ANTE1.317.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
51334---+--+---+---------+

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
51334--------------------------

API STA

@refGLUFRUMNEMALLACTREMANXLTMELNITPALVPRAFXYLSACMDGNAGADHURELSTR
51334-----------+--------

Isolation, sampling and environmental information

isolation

@refsample type
8595human skin
51334Human skin

isolation source categories

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

Safety information

risk assessment

  • @ref: 8595
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

  • @ref: 66792
  • description: Kytococcus sedentarius strain FDAARGOS_1200
  • accession: 1276.17
  • assembly level: complete
  • database: patric
  • NCBI tax ID: 1276

GC content

  • @ref: 8595
  • GC-content: 67.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.278no
gram-positiveyes94.124no
anaerobicno99.066yes
aerobicyes90.694yes
halophileyes52.037no
spore-formingno92.05no
glucose-utilyes87.808no
flagellatedno97.739no
thermophileno95.791no
glucose-fermentno88.841yes

External links

@ref: 8595

culture collection no.: DSM 20317, CCM 2699, CCUG 33031, LMG 14230

straininfo link

  • @ref: 73437
  • straininfo: 9320

Reference

@idauthorscataloguedoi/urltitle
8595Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20317)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20317
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
51334Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33031)https://www.ccug.se/strain?id=33031
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
68378Automatically annotated from API STA
68379Automatically annotated from API Coryne
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
73437Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9320.1StrainInfo: A central database for resolving microbial strain identifiers