Strain identifier
BacDive ID: 16968
Type strain: 
Species: Actinomadura viridilutea
Strain history: A. Shimazu <-- IFO 14480 <-- VKM <-- INMI 187.
NCBI tax ID(s): 58112 (species)
version 8.1 (current version)
General
@ref: 11744
BacDive-ID: 16968
DSM-Number: 44433
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, thermophilic
description: Actinomadura viridilutea DSM 44433 is a spore-forming, thermophilic bacterium that builds an aerial mycelium and was isolated from light-gray desert soil.
NCBI tax id
- NCBI tax id: 58112
- Matching level: species
strain history
| @ref | history |
|---|---|
| 11744 | <- IFO <- VKM <- INMI |
| 67770 | A. Shimazu <-- IFO 14480 <-- VKM <-- INMI 187. |
doi: 10.13145/bacdive16968.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Thermomonosporaceae
- genus: Actinomadura
- species: Actinomadura viridilutea
- full scientific name: Actinomadura viridilutea (Agre and Guzeva 1975) Zhang et al. 2001
synonyms
@ref synonym 20215 Excellospora rubrobrunea 20215 Excellospora viridilutea 20215 Actinomadura rubrobrunea 20215 Micropolyspora rubrobrunea
@ref: 11744
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Thermomonosporaceae
genus: Actinomadura
species: Actinomadura viridilutea
full scientific name: Actinomadura viridilutea (Agre and Guzeva 1975) Zhang et al. 2001 emend. Nouioui et al. 2018
type strain: yes
Morphology
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 20059 | Beige (1001) | 10-14 days | ISP 2 |
| 20059 | Beige (1001) | 10-14 days | ISP 3 |
| 20059 | Beige (1001) | 10-14 days | ISP 4 |
| 20059 | Beige (1001) | 10-14 days | ISP 5 |
| 20059 | Beige (1001) | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | medium name | complex name | complex color |
|---|---|---|---|---|
| 20059 | no | ISP 2 | ||
| 20059 | no | ISP 3 | ||
| 20059 | yes | ISP 4 | Aerial Mycelium | Turquoise blue (5018) |
| 20059 | no | ISP 5 | ||
| 20059 | no | ISP 6 | ||
| 20059 | no | ISP 7 |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 11744 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water |
| 20059 | ISP 2 | yes | Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes | |
| 20059 | ISP 3 | yes | Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms: | |
| 20059 | ISP 4 | yes | Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml | |
| 20059 | ISP 5 | yes | Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes | |
| 20059 | ISP 7 | yes | Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes | |
| 11744 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 11744 | positive | growth | 45 | thermophilic |
| 20059 | positive | optimum | 45 | thermophilic |
| 67770 | positive | growth | 50 | thermophilic |
Physiology and metabolism
spore formation
- @ref: 20059
- spore description: Formation of spore chains, spore surface smooth
- spore formation: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country |
|---|---|---|---|
| 11744 | light-gray desert soil | ||
| 67770 | Light-gray desert soil | Russia | RUS |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Desert |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_7506.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_3503;97_4295;98_5498;99_7506&stattab=map
- Last taxonomy: Actinomadura
- 16S sequence: D86943
- Sequence Identity:
- Total samples: 542
- soil counts: 285
- aquatic counts: 96
- animal counts: 116
- plant counts: 45
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 11744 | 1 | Risk group (German classification) |
| 20059 | 1 | German classification |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Actinomadura viridilutea gene for 16S ribosomal RNA, partial sequence | D86943 | 1475 | ena | 58112 |
| 20218 | Excellospora viridilutea 16S-23S ribosomal RNA intergenic spacer region, partial sequence | AF134110 | 418 | ena | 58112 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Actinomadura viridilutea strain DSM 44433 | 58112.4 | wgs | patric | 58112 |
| 66792 | Actinomadura viridilutea DSM 44433 | 2728369515 | draft | img | 58112 |
| 67770 | Actinomadura viridilutea DSM 44433 | GCA_003001795 | scaffold | ncbi | 58112 |
GC content
- @ref: 67770
- GC-content: 72.8
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| gram-positive | yes | 87.075 | no |
| anaerobic | no | 98.422 | no |
| halophile | no | 87.233 | no |
| spore-forming | yes | 91.75 | yes |
| glucose-util | yes | 91.053 | no |
| thermophile | yes | 64.62 | yes |
| flagellated | no | 98.185 | no |
| aerobic | yes | 86.892 | no |
| motile | no | 92.333 | no |
| glucose-ferment | no | 90.402 | no |
External links
@ref: 11744
culture collection no.: DSM 44433, IFO 14480, IMET 9742, INMI 187, JCM 3398, JCM 7346, ATCC 33925, BCRC 13638, KCTC 9185, NBRC 100039, NBRC 14480
straininfo link
- @ref: 85972
- straininfo: 92965
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 11744 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44433) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44433 | |||
| 20059 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44433.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
| 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 | |
| 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) | |||
| 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 | |||
| 85972 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92965.1 | StrainInfo: A central database for resolving microbial strain identifiers |