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Strain identifier

BacDive ID: 14562

Type strain: Yes

Species: Staphylococcus lugdunensis

Strain Designation: N860297

Strain history: <- J. Fleurette; <- Centre National des Staphylocoques, Lyon, France; N860297

NCBI tax ID(s): 28035 (species)

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General

@ref: 1827

BacDive-ID: 14562

DSM-Number: 4804

keywords: 16S sequence, Bacteria, microaerophile, mesophilic

description: Staphylococcus lugdunensis N860297 is a microaerophile, mesophilic bacterium that was isolated from axillary lymph node.

NCBI tax id

  • NCBI tax id: 28035
  • Matching level: species

strain history: <- J. Fleurette; <- Centre National des Staphylocoques, Lyon, France; N860297

doi: 10.13145/bacdive14562.20221219.7.1

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 lugdunensis
  • full scientific name: Staphylococcus lugdunensis Freney et al. 1988

@ref: 1827

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus lugdunensis

full scientific name: Staphylococcus lugdunensis Freney et al. 1988

strain designation: N860297

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 93.813

colony morphology

  • @ref: 1827
  • type of hemolysis: gamma

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1827COLUMBIA 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
1827TRYPTICASE 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
40750MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)

culture temp

@refgrowthtypetemperaturerange
1827positivegrowth37mesophilic
40750positivegrowth37mesophilic
48175positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 48175
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 97.405

halophily

  • @ref: 69480
  • halophily level: halophilic
  • confidence: 99.293

murein

  • @ref: 1827
  • murein short key: A11.02
  • type: A3alpha L-Lys-Gly5-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837522599arabinose-fermentation
6837559640N-acetylglucosamine+fermentation
6837517992sucrose+fermentation
6837517632nitrate+reduction
6837517057cellobiose-fermentation
6837516988D-ribose-fermentation
6837516634raffinose-fermentation
6837516899D-mannitol-fermentation
6837527082trehalose+fermentation
6837517716lactose+fermentation
6837517306maltose+fermentation
6837515824D-fructose+fermentation
6837517634D-glucose+fermentation
683754853esculin-hydrolysis
6837518257ornithine+degradation
6837529016arginine-hydrolysis

metabolite production

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

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

enzymes

@refvalueactivityec
1827catalase+1.11.1.6
1827cytochrome-c oxidase-1.9.3.1
68375beta-glucuronidase-3.2.1.31
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

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
1827--+-++-+++----++---+-++---
1827--+-++++++----++--+/-+++++/---
1827+/--+-++++++----++---+/-+++---
1827--+-++++++----++---+/-++++--
1827+-+-++++++----++---++/-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1827axillary lymph node
48175Human axillary lymph nodeLyonFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Human
#Host Body-Site#Limb#Arm

taxonmaps

  • @ref: 69479
  • File name: preview.99_590.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_3;99_590&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AB009941
  • Sequence Identity:
  • Total samples: 3146
  • soil counts: 18
  • aquatic counts: 54
  • animal counts: 3062
  • plant counts: 12

Safety information

risk assessment

  • @ref: 1827
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus lugdunensis strain DSM 4804 16S ribosomal RNA gene, partial sequenceAY688074464ena28035
20218S.lugdunensis gene for 16S ribosomal RNAZ26899771ena28035
1827Staphylococcus lugdunensis rrn gene for 16S ribosomal RNAAB0099411492ena28035

GC content

  • @ref: 1827
  • GC-content: 32.0

External links

@ref: 1827

culture collection no.: CCUG 25348, DSM 4804, ATCC 43809

straininfo link

@refpassport
20218http://www.straininfo.net/strains/31381
20218http://www.straininfo.net/strains/31380

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity10467667False-positive beta-lactamase results with Staphylococcus lugdunensis in the Vitek AutoMicrobic system.Zbinden R, von Graevenitz A, Rossi J, Kumin E, Berger-Bachi B, Hachler H, Nadal DZentralbl Bakteriol10.1016/s0934-8840(99)80076-01999Diffusion, False Positive Reactions, Humans, Microbial Sensitivity Tests, Penicillin Resistance, Quality Control, Staphylococcus/drug effects/*enzymology, beta-Lactamases/*metabolismEnzymology
32038604Role of the LytSR Two-Component Regulatory System in Staphylococcus lugdunensis Biofilm Formation and Pathogenesis.Dahyot S, Oxaran V, Niepceron M, Dupart E, Legris S, Destruel L, Didi J, Clamens T, Lesouhaitier O, Zerdoumi Y, Flaman JM, Pestel-Caron MFront Microbiol10.3389/fmicb.2020.000392020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1827Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4804)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4804
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
40750Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15462
48175Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 25348)https://www.ccug.se/strain?id=25348
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
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)