Strain identifier
BacDive ID: 24058
Type strain: 
Species: Geodermatophilus africanus
Strain Designation: CF11/1
Strain history: <- A. Gorbushina, Bundesanstalt für Materialforschung und -prüfung, Berlin; CF11/1
NCBI tax ID(s): 1137993 (species)
version 8.1 (current version)
General
@ref: 20583
BacDive-ID: 24058
DSM-Number: 45422
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Geodermatophilus africanus CF11/1 is an aerobe, spore-forming, mesophilic bacterium that was isolated from desert sand.
NCBI tax id
- NCBI tax id: 1137993
- Matching level: species
strain history
- @ref: 20583
- history: <- A. Gorbushina, Bundesanstalt für Materialforschung und -prüfung, Berlin; CF11/1
doi: 10.13145/bacdive24058.20230509.8.1
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 africanus
- full scientific name: Geodermatophilus africanus Montero-Calasanz et al. 2013
@ref: 20583
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Geodermatophilaceae
genus: Geodermatophilus
species: Geodermatophilus africanus
full scientific name: Geodermatophilus africanus Montero-Calasanz et al. 2013 emend. Montero-Calasanz et al. 2017
strain designation: CF11/1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
- @ref: 62918
- incubation period: 1 day
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_45422_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_45422_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_45422_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_45422_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 20583 | R2A MEDIUM (DSMZ Medium 830) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf | |
| 20583 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20583 | positive | growth | 28 | mesophilic |
| 62918 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 62918
- oxygen tolerance: aerobe
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 99
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | sampling date |
|---|---|---|---|---|---|---|---|---|
| 20583 | desert sand | Sahara, near Ourba (N15.23.905, E22.42.297) | Chad | TCD | Africa | 15.3984 | 22.7049 | |
| 62918 | Sand,desert | near Oudé Cassoni | Chad | TCD | Africa | 2007 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Desert |
| #Environmental | #Terrestrial | #Sandy |
| #Condition | #Xerophilic |
taxonmaps
- @ref: 69479
- File name: preview.99_156663.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_3177;98_3990;99_156663&stattab=map
- Last taxonomy: Geodermatophilus africanus
- 16S sequence: HE654550
- Sequence Identity:
- Total samples: 1615
- soil counts: 1252
- aquatic counts: 72
- animal counts: 212
- plant counts: 79
Safety information
risk assessment
- @ref: 20583
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20583
- description: Geodermatophilus africanus partial 16S rRNA gene, strain DSM 45422, isolate CF 11/1
- accession: HE654550
- length: 1511
- database: ena
- NCBI tax ID: 1137993
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geodermatophilus africanus DSM 45422 | GCA_900107105 | scaffold | ncbi | 1137993 |
| 66792 | Geodermatophilus africanus strain DSM 45422 | 1137993.4 | wgs | patric | 1137993 |
| 66792 | Geodermatophilus africanus DSM 45422 | 2599185203 | draft | img | 1137993 |
GC content
- @ref: 20583
- GC-content: 74.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 99 | no |
| motile | yes | 72.044 | no |
| glucose-ferment | no | 89.694 | no |
| flagellated | no | 92.532 | no |
| gram-positive | yes | 92.352 | no |
| anaerobic | no | 98.49 | yes |
| aerobic | yes | 90.422 | yes |
| halophile | no | 90.979 | no |
| spore-forming | no | 65.463 | no |
| thermophile | no | 98.506 | yes |
| glucose-util | yes | 87.764 | no |
External links
@ref: 20583
culture collection no.: DSM 45422, CCUG 62969, MTCC 11556
straininfo link
- @ref: 88029
- straininfo: 404149
literature
- topic: Phylogeny
- Pubmed-ID: 23723018
- title: Geodermatophilus africanus sp. nov., a halotolerant actinomycete isolated from Saharan desert sand.
- authors: Montero-Calasanz Mdel C, Goker M, Potter G, Rohde M, Sproer C, Schumann P, Gorbushina AA, Klenk HP
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-013-9939-8
- year: 2013
- mesh: Actinomycetales/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Chad, DNA, Bacterial/genetics, Desert Climate, Fatty Acids/analysis, RNA, Ribosomal, 16S/genetics, Silicon Dioxide/*analysis, *Soil Microbiology
- topic2: Enzymology
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
| 20583 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45422 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45422) | |||
| 62918 | Curators of the CCUG | https://www.ccug.se/strain?id=62969 | Culture Collection University of Gothenburg (CCUG) (CCUG 62969) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66793 | Mukherjee et al. | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 10.1038/nbt.3886 | 35: 676-683 2017 | 28604660 | |
| 69479 | João 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 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 88029 | Reimer, 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 identifiers | 10.60712/SI-ID404149.1 |