Strain identifier
BacDive ID: 24846
Type strain: 
Species: Geodermatophilus poikilotrophus
Strain Designation: G18
Strain history: <- M. Eppard, isolate G18, ("Geodermatophilus obscurus ssp. dictyosporus")
NCBI tax ID(s): 1333667 (species)
version 8.1 (current version)
General
@ref: 20579
BacDive-ID: 24846
DSM-Number: 44209
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Geodermatophilus poikilotrophus G18 is an aerobe, spore-forming, mesophilic bacterium that was isolated from dolomitic marble outcrops.
NCBI tax id
- NCBI tax id: 1333667
- Matching level: species
strain history
- @ref: 20579
- history: <- M. Eppard, isolate G18, ("Geodermatophilus obscurus ssp. dictyosporus")
doi: 10.13145/bacdive24846.20230509.8.1
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 poikilotrophus
- full scientific name: Geodermatophilus poikilotrophus corrig. Montero-Calasanz et al. 2015
synonyms
- @ref: 20215
- synonym: Geodermatophilus poikilotrophi
@ref: 20579
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Geodermatophilaceae
genus: Geodermatophilus
species: Geodermatophilus poikilotrophus
full scientific name: Geodermatophilus poikilotrophus Montero-Calasanz et al. 2015 emend. Montero-Calasanz et al. 2017
strain designation: G18
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
- @ref: 62931
- incubation period: 7-10 days
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_44209_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_44209_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_44209_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_44209_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_44209_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 20579
- name: GEO-MEDIUM (DSMZ Medium 714)
- growth: yes
- link: https://mediadive.dsmz.de/medium/714
- composition: Name: GEO-MEDIUM (DSMZ Medium 714) Composition: Agar 15.0 g/l CaCO3 1.0 g/l Starch 1.0 g/l Glucose 1.0 g/l Yeast extract 1.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 62931 | positive | growth | 30 | mesophilic |
| 20579 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 62931
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 92 |
| 69480 | no | 95.173 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 20579 | dolomitic marble outcrops | Samara | Namibia | NAM | Africa | |
| 62931 | Dolomitic marble | Samara | Namibia | NAM | Africa | 1993 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Geologic
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: HF970583
- Sequence Identity:
- Total samples: 1374
- soil counts: 974
- aquatic counts: 84
- animal counts: 84
- plant counts: 232
Safety information
risk assessment
- @ref: 20579
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20579
- description: Geodermatophilus poikilotrophus partial 16S rRNA gene, type strain DSM 44209T
- accession: HF970583
- length: 1514
- database: ena
- NCBI tax ID: 1333667
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geodermatophilus poikilotrophus DSM 44209 | GCA_900111455 | scaffold | ncbi | 1333667 |
| 66792 | Geodermatophilus poikilotrophus strain DSM 44209 | 1333667.3 | wgs | patric | 1333667 |
| 66792 | Geodermatophilus poikilotrophi DSM 44209 | 2636416082 | draft | img | 1333667 |
GC content
- @ref: 20579
- GC-content: 74.4
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 92 | no |
| motile | yes | 76.875 | no |
| flagellated | no | 91.865 | no |
| gram-positive | yes | 93.075 | no |
| anaerobic | no | 98.239 | yes |
| aerobic | yes | 90.076 | yes |
| halophile | no | 84.974 | no |
| spore-forming | no | 73.344 | no |
| glucose-ferment | no | 90.346 | no |
| thermophile | no | 95.493 | no |
| glucose-util | yes | 87.506 | no |
External links
@ref: 20579
culture collection no.: DSM 44209, CCUG 63018
straininfo link
- @ref: 88662
- straininfo: 405259
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25114928 | Geodermatophilus poikilotrophi sp. nov.: a multitolerant actinomycete isolated from dolomitic marble. | del Carmen Montero-Calasanz M, Hofner B, Goker M, Rohde M, Sproer C, Hezbri K, Gtari M, Schumann P, Klenk HP | Biomed Res Int | 10.1155/2014/914767 | 2014 | *Actinomycetales/classification/drug effects/isolation & purification/physiology, *Calcium Carbonate, Cell Shape, Chemotaxis/physiology, Environmental Microbiology, *Magnesium, Metals, Heavy/pharmacology, Microbial Sensitivity Tests, Namibia, Phenotype | Phenotype |
| Phylogeny | 27381197 | Geodermatophilus pulveris sp. nov., a gamma-radiation-resistant actinobacterium isolated from the Sahara desert. | Hezbri K, Ghodhbane-Gtari F, Montero-Calasanz MDC, Nouioui I, Rohde M, Sproer C, Schumann P, Klenk HP, Gtari M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001272 | 2016 | 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 | 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 | |||
| 20579 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44209 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44209) | |||
| 62931 | Curators of the CCUG | https://www.ccug.se/strain?id=63018 | Culture Collection University of Gothenburg (CCUG) (CCUG 63018) | |||
| 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 | |||
| 88662 | 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-ID405259.1 |