Strain identifier
BacDive ID: 5816
Type strain: 
Species: Geodermatophilus dictyosporus
Strain Designation: G-5
Strain history: KCC A-0154 <-- G. M. Luedemann G-5.
NCBI tax ID(s): 1523247 (species)
version 8.1 (current version)
General
@ref: 10829
BacDive-ID: 5816
DSM-Number: 43161
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive
description: Geodermatophilus dictyosporus G-5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 1523247
- Matching level: species
strain history
| @ref | history |
|---|---|
| 10829 | <- KCC <- G.M. Luedemann, G-5 |
| 67770 | KCC A-0154 <-- G. M. Luedemann G-5. |
doi: 10.13145/bacdive5816.20230509.8.1
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 dictyosporus
- full scientific name: Geodermatophilus dictyosporus Montero-Calasanz et al. 2015
synonyms
- @ref: 20215
- synonym: Geodermatophilus obscurus subsp. dictyosporus
@ref: 10829
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Geodermatophilaceae
genus: Geodermatophilus
species: Geodermatophilus dictyosporus
full scientific name: Geodermatophilus dictyosporus Montero-Calasanz et al. 2015 emend. Montero-Calasanz et al. 2017
strain designation: G-5
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
- @ref: 62919
- incubation period: 6-10 days
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_43161_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_43161_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_43161_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_43161_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_43161_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 10829 | 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 |
| 10829 | CZAPEK PEPTONE AGAR (DSMZ Medium 83) | yes | https://mediadive.dsmz.de/medium/83 | Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 10829 | positive | growth | 28 | mesophilic |
| 62919 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 62919
- oxygen tolerance: aerobe
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 10829 | soil | California, Westgard Pass | USA | USA | North America | |
| 62919 | Soil,desert | California,Westgard Pass | USA | USA | North America | 1989 |
| 67770 | Soil | Westgard Pass, CA | USA | USA | North America |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_4012.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_2039;97_2459;98_3041;99_4012&stattab=map
- Last taxonomy: Geodermatophilus
- 16S sequence: X92355
- Sequence Identity:
- Total samples: 870
- soil counts: 565
- aquatic counts: 58
- animal counts: 210
- plant counts: 37
Safety information
risk assessment
- @ref: 10829
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Geodermatophilus obscurus subsp. dictyosporus 16S ribosomal RNA (strain DSM43161) | X92355 | 1469 | ena | 1523247 |
| 10829 | Geodermatophilus dictyosporus partial 16S rRNA gene, type strain G-5T | HF970584 | 1517 | ena | 1523247 |
| 67770 | Geodermatophilus obscurus dictyosporus 16S ribosomal RNA (16S rRNA) gene | L40621 | 1411 | ena | 1523247 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geodermatophilus obscurus strain DSM 43161 | 1861.3 | wgs | patric | 1861 |
| 66792 | Geodermatophilus dictyosporus DSM 43161 | 2599185183 | draft | img | 1861 |
| 67770 | Geodermatophilus obscurus DSM 43161 | GCA_900115395 | scaffold | ncbi | 1861 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 10829 | 75.3 | high performance liquid chromatography (HPLC) |
| 67770 | 74.4 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 58 | no |
| motile | yes | 80.85 | no |
| gram-positive | yes | 90.647 | no |
| anaerobic | no | 99.072 | no |
| aerobic | yes | 91.858 | yes |
| halophile | no | 86.438 | no |
| spore-forming | no | 62.646 | no |
| glucose-util | yes | 88.042 | no |
| flagellated | no | 91.966 | no |
| thermophile | no | 99.21 | no |
| glucose-ferment | no | 86.776 | no |
External links
@ref: 10829
culture collection no.: DSM 43161, ATCC 25080, CBS 234.69, CCUG 62970, IFO 13317, KCC A-0154, MTCC 11558, NBRC 13317, NBRC 1331, JCM 3154, IMET 9241, IMSNU 22090, KCTC 9074, NRRL B-3579, RIA 945, VKM Ac-659
straininfo link
- @ref: 75298
- straininfo: 265321
literature
- topic: Phylogeny
- Pubmed-ID: 25399311
- title: Description of gamma radiation-resistant Geodermatophilus dictyosporus sp. nov. to accommodate the not validly named Geodermatophilus obscurus subsp. dictyosporus (Luedemann, 1968).
- authors: Montero-Calasanz Mdel C, Hezbri K, Goker M, Sghaier H, Rohde M, Sproer C, Schumann P, Klenk HP
- journal: Extremophiles
- DOI: 10.1007/s00792-014-0708-z
- year: 2014
- mesh: Actinomycetales/*classification/*genetics/radiation effects, Bacterial Typing Techniques, Base Composition, California, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gamma Rays, Genomics, Hydrogen-Ion Concentration, Peptidoglycan/chemistry, Phenotype, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 10829 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43161) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43161 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 62919 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 62970) | https://www.ccug.se/strain?id=62970 | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 75298 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265321.1 | StrainInfo: A central database for resolving microbial strain identifiers |