Strain identifier
BacDive ID: 5818
Type strain: 
Species: Geodermatophilus amargosae
Strain Designation: G12, G96
Strain history: <- IFO <- KCC <- G.M. Luedemann G-12
NCBI tax ID(s): 1296565 (species)
version 8.1 (current version)
General
@ref: 12459
BacDive-ID: 5818
DSM-Number: 46136
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Geodermatophilus amargosae G12 is an aerobe, spore-forming, mesophilic bacterium that was isolated from desert soil.
NCBI tax id
- NCBI tax id: 1296565
- Matching level: species
strain history
| @ref | history |
|---|---|
| 12459 | <- IMET <- M. Goodfellow; G96 <- G.M. Luedemann; G12 |
| 67770 | KCC A-0153 <-- G. M. Luedemann G-12. |
| 67771 | <- IFO <- KCC <- G.M. Luedemann G-12 |
doi: 10.13145/bacdive5818.20230509.8.1
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 amargosae
- full scientific name: Geodermatophilus amargosae Montero-Calasanz et al. 2014
synonyms
- @ref: 20215
- synonym: Geodermatophilus obscurus subsp. amargosae
@ref: 12459
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Geodermatophilaceae
genus: Geodermatophilus
species: Geodermatophilus amargosae
full scientific name: Geodermatophilus amargosae Montero-Calasanz et al. 2014 emend. Montero-Calasanz et al. 2017
strain designation: G12, G96
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | positive | |
| 69480 | positive | 100 |
colony morphology
- @ref: 62920
- incubation period: 6-10 days
multimedia
| @ref | multimedia content | caption | intellectual property rights |
|---|---|---|---|
| 66793 | EM_DSM_46136_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_46136_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_46136_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_46136_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_46136_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
| 66793 | EM_DSM_46136_6.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 12459
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 12459 | positive | growth | 28 | mesophilic |
| 62920 | positive | growth | 30 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 62920 | aerobe |
| 67771 | aerobe |
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 95
compound production
- @ref: 20216
- compound: Actinorhodin
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 |
|---|---|---|---|---|---|---|
| 12459 | desert soil | Nevada, Amargosa Desert | USA | USA | North America | |
| 62920 | Soil,desert | USA | USA | North America | 1976 | |
| 67770 | Soil, Amargosa Desert | NV | USA | USA | North America | |
| 67771 | From soil | Amargosa desert | USA | USA | North America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Desert |
| #Environmental | #Terrestrial | #Soil |
| #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: HF679056
- Sequence Identity:
- Total samples: 6810
- soil counts: 4562
- aquatic counts: 408
- animal counts: 721
- plant counts: 1119
Safety information
risk assessment
- @ref: 12459
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 12459
- description: Geodermatophilus amargosae partial 16S rRNA gene, strain DSM 46136, isolate G96
- accession: HF679056
- length: 1513
- database: ena
- NCBI tax ID: 1296565
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Geodermatophilus amargosae strain DSM 46136 | 1296565.3 | wgs | patric | 1296565 |
| 66792 | Geodermatophilus amargosae DSM 46136 | 2599185195 | draft | img | 1296565 |
| 67770 | Geodermatophilus amargosae DSM 46136 | GCA_900116515 | scaffold | ncbi | 1296565 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 12459 | 73.0 | high performance liquid chromatography (HPLC) |
| 67770 | 73 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 95 | no |
| motile | yes | 76.848 | no |
| gram-positive | yes | 92.99 | yes |
| anaerobic | no | 98.893 | yes |
| aerobic | yes | 91.324 | yes |
| halophile | no | 87.035 | no |
| spore-forming | no | 67.072 | no |
| thermophile | no | 98.297 | yes |
| glucose-util | yes | 90.315 | no |
| flagellated | no | 92.024 | no |
| glucose-ferment | no | 88.746 | no |
External links
@ref: 12459
culture collection no.: DSM 46136, ATCC 25081, CBS 236.69, CCUG 62971, IFO 13316, IMET 9240, JCM 3153, KCC A-0153, MTCC 11559, NBRC 13316, KCTC 9360, NRRL B-3578, NRRL WC-3937, KCC A-0152
straininfo link
- @ref: 75300
- straininfo: 125967
literature
- topic: Phylogeny
- Pubmed-ID: 24202736
- title: Description of Geodermatophilus amargosae sp. nov., to accommodate the not validly named Geodermatophilus obscurus subsp. amargosae (Luedemann, 1968).
- authors: Montero-Calasanz Mdel C, Goker M, Rohde M, Sproer C, Schumann P, Mayilraj S, Goodfellow M, Klenk HP
- journal: Curr Microbiol
- DOI: 10.1007/s00284-013-0479-2
- year: 2013
- mesh: Actinomycetales/chemistry/*classification/genetics/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Scanning, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 12459 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46136) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-46136 | |||
| 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 | |||
| 20216 | Curators of the HKI | http://www.leibniz-hki.de/de/ | Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) | |||
| 62920 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 62971) | https://www.ccug.se/strain?id=62971 | |||
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 75300 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID125967.1 | StrainInfo: A central database for resolving microbial strain identifiers |