Strain identifier

BacDive ID: 5820

Type strain: Yes

Species: Geodermatophilus arenarius

Strain Designation: CF5/4

Strain history: MTCC 11413 <-- A. A. Gorbushina CF5/4.

NCBI tax ID(s): 1137990 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16550

BacDive-ID: 5820

DSM-Number: 45418

keywords: 16S sequence, Bacteria, aerobe, mesophilic

description: Geodermatophilus arenarius CF5/4 is an aerobe, mesophilic bacterium that was isolated from desert sand.

NCBI tax id

  • NCBI tax id: 1137990
  • Matching level: species

strain history

@refhistory
16550<- A. Gorbushina, Bundesanstalt für Materialforschung und -prüfung, Berlin; CF5/4
67770MTCC 11413 <-- A. A. Gorbushina CF5/4.

doi: 10.13145/bacdive5820.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Geodermatophilales
  • family: Geodermatophilaceae
  • genus: Geodermatophilus
  • species: Geodermatophilus arenarius
  • full scientific name: Geodermatophilus arenarius Montero-Calasanz et al. 2013

@ref: 16550

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Geodermatophilus

species: Geodermatophilus arenarius

full scientific name: Geodermatophilus arenarius Montero-Calasanz et al. 2013

strain designation: CF5/4

type strain: yes

Morphology

colony morphology

  • @ref: 62896
  • incubation period: 1-2 days

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_45418_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45418_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45418_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45418_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45418_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16550GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
16550TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
16550R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16550positivegrowth28mesophilic
62896positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 62896
  • oxygen tolerance: aerobe

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    62896C15:02.315
    62896C16:01.716
    62896C17:01.217
    62896C13:0 3OH/C15:1 i I/H1.414.469
    62896C14:0 ISO1.213.618
    62896C15:0 ANTEISO1.714.711
    62896C15:0 ISO27.114.621
    62896C15:1 ω6c114.856
    62896C16:0 iso26.615.626
    62896C16:1 ISO H10.715.461
    62896C16:1 ω3c1.715.933
    62896C16:1 ω7c2.515.819
    62896C17:0 anteiso2.316.722
    62896C17:0 iso2.916.629
    62896C17:1 ω8c7.516.792
    62896C17:1 ω9c ISO4.916.416
    62896C18:1 ω9c1.117.769
    62896Unidentified2.414.927
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16550desert sandSaharan, Ouré CassoniChadTCDAfrica
62896arid desert soilOuré CassoniChadTCDAfrica2007
67770Sand of the Sahara Desert near Ouré CassoniChadTCDAfrica

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Sandy
#Condition#Xerophilic

taxonmaps

  • @ref: 69479
  • File name: preview.99_156662.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_3177;98_103257;99_156662&stattab=map
  • Last taxonomy: Geodermatophilus arenarius subclade
  • 16S sequence: HE654547
  • Sequence Identity:
  • Total samples: 613
  • soil counts: 487
  • aquatic counts: 44
  • animal counts: 50
  • plant counts: 32

Safety information

risk assessment

  • @ref: 16550
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16550
  • description: Geodermatophilus arenarius partial 16S rRNA gene, type strain CF 5/4T
  • accession: HE654547
  • length: 1511
  • database: ena
  • NCBI tax ID: 1137990

GC content

  • @ref: 16550
  • GC-content: 75.9
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 16550

culture collection no.: DSM 45418, CCUG 62763, MTCC 11413, JCM 30063

straininfo link

  • @ref: 75302
  • straininfo: 405995

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23081798Geodermatophilus arenarius sp. nov., a xerophilic actinomycete isolated from Saharan desert sand in Chad.Montero-Calasanz MC, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Gorbushina AA, Klenk HPExtremophiles10.1007/s00792-012-0486-42012Actinomycetales/*classification/cytology/genetics/*isolation & purification, Africa, Northern, Bacterial Typing Techniques, Base Composition, Chad, Desert Climate, Geologic Sediments/chemistry/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Silicon DioxideEnzymology
Phylogeny23159748Geodermatophilus telluris sp. nov., an actinomycete isolated from Saharan desert sand.Montero-Calasanz MDC, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Klenk HP, Gorbushina AAInt J Syst Evol Microbiol10.1099/ijs.0.046888-02012Actinomycetales/*classification/genetics/isolation & purification, Africa, Northern, Bacterial Typing Techniques, Base Composition, Chad, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16550Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45418)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45418
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
62896Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 62763)https://www.ccug.se/strain?id=62763
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
75302Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405995.1StrainInfo: A central database for resolving microbial strain identifiers