Strain identifier
BacDive ID: 23215
Type strain: 
Species: Amycolatopsis umgeniensis
Strain Designation: UM16
Strain history: DSM 45272 <-- P. R. Meyers; Univ. of Cape Town; UM16.
NCBI tax ID(s): 336628 (species)
version 8.1 (current version)
General
@ref: 19273
BacDive-ID: 23215
DSM-Number: 45272
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Amycolatopsis umgeniensis UM16 is a spore-forming, mesophilic bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 336628
- Matching level: species
strain history
| @ref | history |
|---|---|
| 19273 | <- P. R. Meyers, Univ. of Cape Town; UM16 |
| 67770 | DSM 45272 <-- P. R. Meyers; Univ. of Cape Town; UM16. |
doi: 10.13145/bacdive23215.20230509.8.1
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 umgeniensis
- full scientific name: Amycolatopsis umgeniensis Everest et al. 2013
@ref: 19273
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Amycolatopsis
species: Amycolatopsis umgeniensis
full scientific name: Amycolatopsis umgeniensis Everest et al. 2013
strain designation: UM16
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 92.762 | |
| 69480 | 100 | positive |
multimedia
- @ref: 19273
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45272.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 19273
- 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 |
|---|---|---|---|---|
| 19273 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 91 |
| 69480 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 19273 | soil | KwaZulu Natal province, banks of Umgeni River (29° 28' 23'' S, 30° 28' 6'' E) | South Africa | ZAF | Africa | -29.4731 | 30.4683 |
| 67770 | Soil from the banks of the Umgeni River | KwaZulu Natal Province | South Africa | ZAF | Africa |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_2224.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_1734;99_2224&stattab=map
- Last taxonomy: Amycolatopsis
- 16S sequence: DQ110876
- Sequence Identity:
- Total samples: 106
- soil counts: 92
- aquatic counts: 3
- animal counts: 11
Safety information
risk assessment
- @ref: 19273
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19273
- description: Amycolatopsis umgeniensis strain UM16 16S ribosomal RNA gene, partial sequence
- accession: DQ110876
- length: 1446
- database: ena
- NCBI tax ID: 336628
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Amycolatopsis umgeniensis DSM 45272 | GCA_014205155 | contig | ncbi | 336628 |
| 66792 | Amycolatopsis umgeniensis strain DSM 45272 | 336628.3 | wgs | patric | 336628 |
| 66792 | Amycolatopsis umgeniensis DSM 45272 | 2870829307 | draft | img | 336628 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 91 | no |
| gram-positive | yes | 86.637 | no |
| anaerobic | no | 99.483 | no |
| halophile | no | 89.355 | no |
| spore-forming | yes | 91.12 | no |
| glucose-util | yes | 88.569 | no |
| motile | no | 93.411 | no |
| flagellated | no | 97.199 | no |
| thermophile | no | 98.428 | yes |
| aerobic | yes | 93.962 | no |
| glucose-ferment | no | 93.475 | no |
External links
@ref: 19273
culture collection no.: DSM 45272, JCM 31205, NRRL B-24724
straininfo link
- @ref: 87443
- straininfo: 406514
literature
- topic: Phylogeny
- Pubmed-ID: 23180373
- title: Amycolatopsis umgeniensis sp. nov., isolated from soil from the banks of the Umgeni River in South Africa.
- authors: Everest GJ, le Roes-Hill M, Omorogie C, Cheung SK, Cook AE, Goodwin CM, Meyers PR
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-012-9851-7
- year: 2012
- mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Cluster Analysis, DNA Gyrase/genetics, DNA Restriction Enzymes/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, South Africa
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 19273 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45272) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45272 | |
| 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 | |
| 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) | |
| 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) | |
| 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 | |
| 87443 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID406514.1 | StrainInfo: A central database for resolving microbial strain identifiers |