Strain identifier
BacDive ID: 13277
Type strain: 
Species: Amycolatopsis viridis
Strain Designation: GY 115
Variant: Isotype of BacDive ID 13278
Strain history: <- G. Y. A. Tan; GY 115
NCBI tax ID(s): 185678 (species)
version 8.1 (current version)
General
@ref: 18033
BacDive-ID: 13277
DSM-Number: 45668
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, coccus-shaped
description: Amycolatopsis viridis GY 115 is an aerobe, spore-forming, mesophilic bacterium that was isolated from arid composite soil sample.
NCBI tax id
- NCBI tax id: 185678
- Matching level: species
strain history
- @ref: 18033
- history: <- G. Y. A. Tan; GY 115
doi: 10.13145/bacdive13277.20230509.8.1
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 viridis
- full scientific name: Amycolatopsis viridis Zucchi et al. 2012
@ref: 18033
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Amycolatopsis
species: Amycolatopsis viridis
full scientific name: Amycolatopsis viridis Zucchi et al. 2012
strain designation: GY 115
variant: Isotype of BacDive ID 13278
type strain: no
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 30091 | positive | coccus-shaped | no | |
| 69480 | no | 96.9 | ||
| 69480 | positive | 100 |
pigmentation
- @ref: 30091
- production: no
Culture and growth conditions
culture medium
- @ref: 18033
- 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 |
|---|---|---|---|---|
| 18033 | positive | growth | 28 | mesophilic |
| 30091 | positive | growth | 10-50 |
culture pH
- @ref: 30091
- ability: positive
- type: growth
- pH: 5.0-10.0
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 30091
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 99.999 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30091 | 22599 | arabinose | + | carbon source |
| 30091 | 28260 | galactose | + | carbon source |
| 30091 | 17716 | lactose | + | carbon source |
| 30091 | 27082 | trehalose | + | carbon source |
enzymes
- @ref: 30091
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 18033
- sample type: arid composite soil sample
- country: Australia
- origin.country: AUS
- continent: Australia and Oceania
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Climate | #Hot | #Arid |
Safety information
risk assessment
- @ref: 18033
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18033
- description: Amycolatopsis viridis 16S ribosomal RNA gene, partial sequence
- accession: AF466095
- length: 1391
- database: ena
- NCBI tax ID: 185678
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Amycolatopsis viridis DSM 45668 | GCA_011758765 | contig | ncbi | 185678 |
| 66792 | Amycolatopsis viridis strain DSM 45668 | 185678.3 | wgs | patric | 185678 |
| 66792 | Amycolatopsis viridis DSM 45668 | 2821236178 | draft | img | 185678 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 92.244 | no |
| gram-positive | yes | 92.288 | yes |
| anaerobic | no | 99.123 | no |
| aerobic | yes | 90.849 | yes |
| halophile | no | 82.278 | no |
| spore-forming | yes | 85.558 | no |
| glucose-util | yes | 89.526 | no |
| flagellated | no | 98.291 | yes |
| thermophile | no | 86.285 | no |
| glucose-ferment | no | 92.892 | no |
External links
@ref: 18033
culture collection no.: DSM 45668, NCIMB 14700, NRRL B-24837
literature
- topic: Phylogeny
- Pubmed-ID: 21378137
- title: Amycolatopsis thermophila sp. nov. and Amycolatopsis viridis sp. nov., thermophilic actinomycetes isolated from arid soil.
- authors: Zucchi TD, Tan GYA, Goodfellow M
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.029256-0
- year: 2011
- mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Australia, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 18033 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45668) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45668 | |||
| 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 | |||
| 30091 | 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 | 26448 | 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) | |||
| 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 |