Strain identifier

BacDive ID: 24057

Type strain: Yes

Species: Geodermatophilus normandii

Strain Designation: CF5/3

Strain history: MTCC 11412 <-- A. A. Gorbushina CF5/3.

NCBI tax ID(s): 1137989 (species)

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General

@ref: 20582

BacDive-ID: 24057

DSM-Number: 45417

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

description: Geodermatophilus normandii CF5/3 is an aerobe, spore-forming, mesophilic bacterium that was isolated from desert sand.

NCBI tax id

  • NCBI tax id: 1137989
  • Matching level: species

strain history

@refhistory
20582<- A. Gorbushina, Bundesanstalt für Materialforschung und -prüfung, Berlin; CF5/3
67770MTCC 11412 <-- A. A. Gorbushina CF5/3.

doi: 10.13145/bacdive24057.20230509.8.1

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

@ref: 20582

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Geodermatophilus

species: Geodermatophilus normandii

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

strain designation: CF5/3

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
31067positiveyes
69480positive100

colony morphology

  • @ref: 62905
  • incubation period: 2-3 days

pigmentation

  • @ref: 31067
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_45417_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45417_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45417_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45417_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_45417_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20582R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
20582GYM 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
20582positivegrowth28mesophilic
31067positivegrowth15-40
62905positivegrowth30-37mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 31067
  • ability: positive
  • type: growth
  • pH: 6.0-10.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31067aerobe
62905aerobe

spore formation

  • @ref: 31067
  • spore formation: yes

halophily

  • @ref: 31067
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

observation

@refobservation
31067aggregates in clumps
67770quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3106730089acetate+carbon source
3106735391aspartate+carbon source
3106717057cellobiose+carbon source
3106723652dextrin+carbon source
3106715740formate+carbon source
3106728757fructose+carbon source
3106728260galactose+carbon source
3106724265gluconate+carbon source
3106717234glucose+carbon source
3106732323glucuronamide+carbon source
3106729987glutamate+carbon source
3106717754glycerol+carbon source
3106717596inosine+carbon source
3106725115malate+carbon source
3106717306maltose+carbon source
3106737684mannose+carbon source
3106737657methyl D-glucoside+carbon source
3106751850methyl pyruvate+carbon source
3106717272propionate+carbon source
3106726546rhamnose+carbon source
3106717822serine+carbon source
3106717992sucrose+carbon source
3106727082trehalose+carbon source
3106753423tween 40+carbon source

enzymes

@refvalueactivityec
31067alkaline phosphatase+3.1.3.1
31067catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling date
20582desert sandSahara, Ouré Cassoni (15° 42' 44'' N 23° 3' 1'' E)ChadTCDAfrica15.712223.0503
62905Sand,desertnear Ouré CussoniChadTCDAfrica2007
67770Sand of the Sahara Desert in 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: HE654546
  • Sequence Identity:
  • Total samples: 6810
  • soil counts: 4562
  • aquatic counts: 408
  • animal counts: 721
  • plant counts: 1119

Safety information

risk assessment

  • @ref: 20582
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20582
  • description: Geodermatophilus normandii partial 16S rRNA gene, culture collection DSM:45417, type strain CF 5/3T
  • accession: HE654546
  • length: 1469
  • database: ena
  • NCBI tax ID: 1137989

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Geodermatophilus normandii strain DSM 454171137989.5wgspatric1137989
66792Geodermatophilus normandii DSM 454172585427554draftimg1137989
67770Geodermatophilus normandii DSM 45417GCA_003182485contigncbi1137989

GC content

@refGC-contentmethod
2058275.5high performance liquid chromatography (HPLC)
3106775.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes83no
motileyes76.437yes
flagellatedno92.286no
gram-positiveyes93.687no
anaerobicno99.006yes
aerobicyes95.006yes
halophileno91.157no
spore-formingno65.513yes
glucose-utilyes88.31yes
glucose-fermentno90.273no
thermophileno98.047no

External links

@ref: 20582

culture collection no.: DSM 45417, CCUG 62814, MTCC 11412, JCM 30064

straininfo link

  • @ref: 88028
  • straininfo: 398540

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23543496Geodermatophilus normandii sp. nov., isolated from Saharan desert sand.Montero-Calasanz MDC, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Gorbushina AA, Klenk HPInt J Syst Evol Microbiol10.1099/ijs.0.051201-02013Actinomycetales/*classification/genetics/isolation & purification, Africa, Northern, Bacterial Typing Techniques, Base Composition, Chad, DNA, Bacterial/genetics, Desert Climate, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Silicon Dioxide, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
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

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20582Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45417Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45417)
31067Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172739628776041
62905Curators of the CCUGhttps://www.ccug.se/strain?id=62814Culture Collection University of Gothenburg (CCUG) (CCUG 62814)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66793Mukherjee et al.GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life10.1038/nbt.388628604660 35: 676-683 2017
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
88028Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID398540.1