Strain identifier
BacDive ID: 133703
Type strain: 
Species: Amycolatopsis granulosa
Strain Designation: GY307
Strain history: <- G. Y. A. Tan, Univ. of Malaya, Kuala Lumpur, Malaysia; GY307
NCBI tax ID(s): 185684 (species)
version 8.1 (current version)
General
@ref: 18034
BacDive-ID: 133703
DSM-Number: 45669
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Amycolatopsis granulosa GY307 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 185684
- Matching level: species
strain history
- @ref: 18034
- history: <- G. Y. A. Tan, Univ. of Malaya, Kuala Lumpur, Malaysia; GY307
doi: 10.13145/bacdive133703.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Amycolatopsis
- species: Amycolatopsis granulosa
- full scientific name: Amycolatopsis granulosa Zucchi et al. 2012
@ref: 18034
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Amycolatopsis
species: Amycolatopsis granulosa
full scientific name: Amycolatopsis granulosa Zucchi et al. 2012
strain designation: GY307
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30219 | positive | 1.1 µm | 0.45 µm | rod-shaped | no | |
| 69480 | no | 96.023 | ||||
| 69480 | positive | 100 |
pigmentation
- @ref: 30219
- production: yes
multimedia
- @ref: 18034
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45669.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 18034
- 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 | growth | type | temperature | range |
|---|---|---|---|---|
| 18034 | positive | growth | 28 | mesophilic |
| 30219 | positive | growth | 20-50 |
culture pH
- @ref: 30219
- ability: positive
- type: growth
- pH: 05-07
Physiology and metabolism
oxygen tolerance
- @ref: 30219
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30219 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 100 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30219 | 28757 | fructose | + | carbon source |
| 30219 | 37684 | mannose | + | carbon source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 30219 | soil | ||||
| 18034 | arid soil | Marla | Australia | AUS | Australia and Oceania |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_53224.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_935;97_1087;98_1297;99_53224&stattab=map
- Last taxonomy: Amycolatopsis
- 16S sequence: AF466101
- Sequence Identity:
- Total samples: 78
- soil counts: 63
- aquatic counts: 2
- animal counts: 6
- plant counts: 7
Safety information
risk assessment
- @ref: 18034
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18034
- description: Amycolatopsis granulosa 16S ribosomal RNA gene, partial sequence
- accession: AF466101
- length: 1421
- database: ena
- NCBI tax ID: 185684
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Amycolatopsis granulosa DSM 45669 | GCA_011758745 | contig | ncbi | 185684 |
| 66792 | Amycolatopsis granulosa strain DSM 45669 | 185684.3 | wgs | patric | 185684 |
| 66792 | Amycolatopsis granulosa DSM 45669 | 2821246215 | draft | img | 185684 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 92.41 | yes |
| gram-positive | yes | 91.996 | no |
| anaerobic | no | 99.285 | no |
| aerobic | yes | 90.21 | no |
| halophile | no | 82.116 | no |
| spore-forming | yes | 90.041 | yes |
| glucose-util | yes | 90.834 | no |
| flagellated | no | 98.479 | yes |
| thermophile | no | 86.197 | no |
| glucose-ferment | no | 92.679 | no |
External links
@ref: 18034
culture collection no.: NCIMB 14709, NRRL B-24844, DSM 45669
straininfo link
- @ref: 91567
- straininfo: 402420
literature
- topic: Phylogeny
- Pubmed-ID: 21764982
- title: Amycolatopsis granulosa sp. nov., Amycolatopsis ruanii sp. nov. and Amycolatopsis thermalba sp. nov., thermophilic actinomycetes isolated from arid soils.
- authors: Zucchi TD, Tan GYA, Bonda ANV, Frank S, Kshetrimayum JD, Goodfellow M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.031039-0
- year: 2011
- mesh: Actinomycetales/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 18034 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45669) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45669 | |||
| 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 | |||
| 30219 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26562 | 28776041 | |
| 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) | |||
| 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 | |||
| 91567 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402420.1 | StrainInfo: A central database for resolving microbial strain identifiers |