Strain identifier
BacDive ID: 132629
Type strain: 
Species: Geodermatophilus pulveris
Strain history: <- M. Gtari, Tunisia; BMG 825 <- K. Hezbri, Tunisia
NCBI tax ID(s): 1564159 (species)
version 8.1 (current version)
General
@ref: 24418
BacDive-ID: 132629
DSM-Number: 46839
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Geodermatophilus pulveris DSM 46839 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from desert limestone dust from grooves in limestone cliffs.
NCBI tax id
- NCBI tax id: 1564159
- Matching level: species
strain history
- @ref: 24418
- history: <- M. Gtari, Tunisia; BMG 825 <- K. Hezbri, Tunisia
doi: 10.13145/bacdive132629.20230509.8.1
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 pulveris
- full scientific name: Geodermatophilus pulveris Hezbri et al. 2016
@ref: 24418
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Geodermatophilaceae
genus: Geodermatophilus
species: Geodermatophilus pulveris
full scientific name: Geodermatophilus pulveris Hezbri et al. 2016 emend. Montero-Calasanz et al. 2017
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 24418 | https://www.dsmz.de/microorganisms/photos/DSM_46839.jpg | Medium 65 28°C | © Leibniz-Institut DSMZ |
| 66793 | EM_DSM_46839_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_46839_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_46839_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_46839_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_46839_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 24418
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: 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: 24418
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 93
Isolation, sampling and environmental information
isolation
- @ref: 24418
- sample type: desert limestone dust from grooves in limestone cliffs
- geographic location: Sahara desert, Grand Erg Oriental
- country: Tunisia
- origin.country: TUN
- continent: Africa
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Desert |
| #Environmental | #Terrestrial | #Dust |
taxonmaps
- @ref: 69479
- File name: preview.99_102131.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_3177;98_3990;99_102131&stattab=map
- Last taxonomy: Geodermatophilus
- 16S sequence: LN626270
- Sequence Identity:
- Total samples: 1374
- soil counts: 974
- aquatic counts: 84
- animal counts: 84
- plant counts: 232
Safety information
risk assessment
- @ref: 24418
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24418
- description: Geodermatophilus sp. BMG 825 partial 16S rRNA gene, strain BMG 825
- accession: LN626270
- length: 1370
- database: ena
- NCBI tax ID: 1564159
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geodermatophilus pulveris DSM 46839 | GCA_900188375 | contig | ncbi | 1564159 |
| 66792 | Geodermatophilus pulveris strain DSM 46839 | 1564159.3 | wgs | patric | 1564159 |
| 66792 | Geodermatophilus pulveris DSM 46839 | 2700988693 | draft | img | 1564159 |
GC content
- @ref: 24418
- GC-content: 75.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 93 | no |
| motile | yes | 76.825 | no |
| gram-positive | yes | 94.809 | no |
| anaerobic | no | 98.207 | no |
| aerobic | yes | 87.603 | no |
| halophile | no | 82.38 | no |
| spore-forming | no | 66.194 | no |
| thermophile | no | 96.476 | yes |
| glucose-util | yes | 86.363 | no |
| flagellated | no | 89.821 | no |
| glucose-ferment | no | 88.822 | no |
External links
@ref: 24418
culture collection no.: DSM 46839, CECT 9003, BMG 825
straininfo link
- @ref: 90943
- straininfo: 398412
literature
- topic: Phylogeny
- Pubmed-ID: 27381197
- title: Geodermatophilus pulveris sp. nov., a gamma-radiation-resistant actinobacterium isolated from the Sahara desert.
- authors: Hezbri K, Ghodhbane-Gtari F, Montero-Calasanz MDC, Nouioui I, Rohde M, Sproer C, Schumann P, Klenk HP, Gtari M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001272
- year: 2016
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Calcium Carbonate, Cell Wall/chemistry, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Gamma Rays, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tunisia, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Transcriptome
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 | |||
| 24418 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-46839 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46839) | |||
| 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 | |||
| 90943 | 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-ID398412.1 |