Strain identifier

BacDive ID: 23032

Type strain: Yes

Species: Geodermatophilus saharensis

Strain Designation: CF5/5

Strain history: MTCC 11416 <-- A. A. Gorbushina CF5/5.

NCBI tax ID(s): 1137994 (species)

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General

@ref: 19313

BacDive-ID: 23032

DSM-Number: 45423

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

description: Geodermatophilus saharensis CF5/5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from desert sand.

NCBI tax id

  • NCBI tax id: 1137994
  • Matching level: species

strain history

@refhistory
19313<- A. Gorbushina, Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany; CF5/5
67770MTCC 11416 <-- A. A. Gorbushina CF5/5.

doi: 10.13145/bacdive23032.20230509.8.1

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

@ref: 19313

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Geodermatophilus

species: Geodermatophilus saharensis

full scientific name: Geodermatophilus saharensis Montero-Calasanz et al. 2013 emend. Montero-Calasanz et al. 2017

strain designation: CF5/5

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

  • @ref: 62904
  • incubation period: 2-3 days

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_45423_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45423_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45423_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45423_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45423_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19313R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
19313GYM 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

culture temp

@refgrowthtypetemperaturerange
19313positivegrowth28mesophilic
62904positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 62904
  • oxygen tolerance: aerobe

observation

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

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
19313desert sandSahara, Ouré CassoniChadTCDAfrica
62904Sand,desertnear Ouré 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_42219.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_2459;98_3041;99_42219&stattab=map
  • Last taxonomy: Geodermatophilus
  • 16S sequence: HE654551
  • Sequence Identity:
  • Total samples: 6810
  • soil counts: 4562
  • aquatic counts: 408
  • animal counts: 721
  • plant counts: 1119

Safety information

risk assessment

  • @ref: 19313
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19313
  • description: Geodermatophilus saharensis partial 16S rRNA gene, type strain CF5/5T
  • accession: HE654551
  • length: 1510
  • database: ena
  • NCBI tax ID: 1137994

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geodermatophilus saharensis strain DSM 454231137994.3wgspatric1137994
66792Geodermatophilus saharensis DSM 454232622736631draftimg1137994
67770Geodermatophilus saharensis DSM 45423GCA_900188205scaffoldncbi1137994

GC content

  • @ref: 19313
  • GC-content: 75.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes66no
motileyes71.577no
flagellatedno92.853no
gram-positiveyes92.671no
anaerobicno99.271yes
aerobicyes90.88yes
halophileno92.843no
spore-formingno61.154no
glucose-utilyes89.162no
thermophileno96.636no
glucose-fermentno89.58no

External links

@ref: 19313

culture collection no.: DSM 45423, CCUG 62813, MTCC 11416, JCM 30065

straininfo link

  • @ref: 87272
  • straininfo: 398627

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23269498Geodermatophilus saharensis sp. nov., isolated from sand of the Saharan desert in Chad.Montero-Calasanz MC, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Gorbushina AA, Klenk HPArch Microbiol10.1007/s00203-012-0860-82012Actinomycetales/chemistry/*classification/genetics/isolation & purification/ultrastructure, Cell Wall/chemistry, Chad, DNA, Bacterial/chemistry/genetics, Microscopy, Electron, Scanning, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Silicon Dioxide, *Soil Microbiology, Species SpecificityGenetics
Phylogeny28289918Geodermatophilus daqingensis sp. nov., isolated from petroleum-contaminated soil.Wang Y, Zhang L, Zhang X, Huang J, Zhao Y, Zhao Y, Liu J, Huang C, Wang J, Hu Y, Ren G, Xu XAntonie Van Leeuwenhoek10.1007/s10482-017-0853-32017Actinobacteria/*isolation & purification/metabolism, Bacterial Typing Techniques, China, DNA, Bacterial, Fatty Acids, *Petroleum, Phospholipids, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Soil, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
19313Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45423)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45423
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
62904Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 62813)https://www.ccug.se/strain?id=62813
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)
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
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)
87272Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398627.1StrainInfo: A central database for resolving microbial strain identifiers