Strain identifier
BacDive ID: 132197
Type strain: 
Species: Actinomadura rayongensis
Strain Designation: RY35-68
Strain history: S. Tanasupawat; Chulalongkorn Univ., Thailand; RY35-68.
NCBI tax ID(s): 1429076 (species)
version 9.3 (current version)
General
@ref: 23986
BacDive-ID: 132197
DSM-Number: 102126
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Actinomadura rayongensis RY35-68 is a mesophilic bacterium that was isolated from Peat swamp forest soil.
NCBI tax id
- NCBI tax id: 1429076
- Matching level: species
strain history
| @ref | history |
|---|---|
| 23986 | <- JCM; JCM 19830 <- S. Tanasupawat; RY35-68 |
| 67770 | S. Tanasupawat; Chulalongkorn Univ., Thailand; RY35-68. |
doi: 10.13145/bacdive132197.20250331.9.3
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 rayongensis
- full scientific name: Actinomadura rayongensis Phongsopitanun et al. 2015
@ref: 23986
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Thermomonosporaceae
genus: Actinomadura
species: Actinomadura rayongensis
full scientific name: Actinomadura rayongensis Phongsopitanun et al. 2015
strain designation: RY35-68
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence | motility |
|---|---|---|---|
| 125439 | positive | 99.8 | |
| 125439 | 90 | no |
multimedia
- @ref: 23986
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_102126.jpg
- caption: Medium 553 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 23986 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | 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 |
| 23986 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 23986 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 97.8
spore formation
- @ref: 125439
- spore formation: yes
- confidence: 94.7
observation
- @ref: 67770
- observation: quinones: MK-9(H6), MK-9(H8), MK-9(H4)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 23986 | Peat swamp forest soil | Rayong Province | Thailand | THA | Asia |
| 67770 | Peat swamp forest soil | Rayong Province | Thailand | THA | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Forest |
| #Environmental | #Terrestrial | #Soil |
| #Environmental | #Terrestrial | #Wetland (Swamp) |
| #Condition | #Acidic |
taxonmaps
- @ref: 69479
- File name: preview.99_17616.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_2558;97_10845;98_13314;99_17616&stattab=map
- Last taxonomy: Actinomadura rayongensis
- 16S sequence: AB889544
- Sequence Identity:
- Total samples: 412
- soil counts: 317
- aquatic counts: 15
- animal counts: 38
- plant counts: 42
Safety information
risk assessment
- @ref: 23986
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 23986
- description: Actinomadura rayongensis gene for 16S ribosomal RNA, partial sequence
- accession: AB889544
- length: 1418
- database: nuccore
- NCBI tax ID: 1429076
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Actinomadura rayongensis DSM 102126 | GCA_009831215 | scaffold | ncbi | 1429076 |
| 66792 | Actinomadura rayongensis strain DSM 102126 | 1429076.3 | wgs | patric | 1429076 |
GC content
- @ref: 23986
- GC-content: 73.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 87.174 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.087 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.241 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 88.105 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 86 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | yes | 94.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 90 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | positive | 99.8 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97.8 |
External links
@ref: 23986
culture collection no.: DSM 102126, JCM 19830, PCU 332, TISTR 2211
straininfo link
- @ref: 90551
- straininfo: 406651
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25525125 | Actinomadura rayongensis sp. nov., isolated from peat swamp forest soil. | Phongsopitanun W, Tanasupawat S, Suwanborirux K, Ohkuma M, Kudo T | Int J Syst Evol Microbiol | 10.1099/ijs.0.000033 | 2014 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry, *Wetlands | Genetics |
| Phylogeny | 32845828 | Actinomadura rubteroloni sp. nov. and Actinomadura macrotermitis sp. nov., isolated from the gut of the fungus growing-termite Macrotermes natalensis. | Benndorf R, Martin K, Kufner M, de Beer ZW, Vollmers J, Kaster AK, Beemelmanns C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004403 | 2020 | Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gastrointestinal Microbiome, Isoptera/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, South Africa, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 23986 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-102126 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102126) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 90551 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID406651.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |