Strain identifier
BacDive ID: 24184
Type strain: 
Species: Agromyces iriomotensis
Strain Designation: IY07-20
Strain history: <- M. Hamada, NBRC <- Y. Ishida
NCBI tax ID(s): 717856 (species)
version 8.1 (current version)
General
@ref: 20272
BacDive-ID: 24184
DSM-Number: 26155
keywords: 16S sequence, Bacteria, mesophilic
description: Agromyces iriomotensis IY07-20 is a mesophilic bacterium that was isolated from soil from a pineapple field.
NCBI tax id
- NCBI tax id: 717856
- Matching level: species
strain history
- @ref: 20272
- history: <- M. Hamada, NBRC <- Y. Ishida
doi: 10.13145/bacdive24184.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Agromyces
- species: Agromyces iriomotensis
- full scientific name: Agromyces iriomotensis Hamada et al. 2014
@ref: 20272
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Agromyces
species: Agromyces iriomotensis
full scientific name: Agromyces iriomotensis Hamada et al. 2014
strain designation: IY07-20
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 20272 | 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 |
| 20272 | PP-MEDIUM (DSMZ Medium 513) | yes | https://mediadive.dsmz.de/medium/513 | Name: PP-MEDIUM (DSMZ Medium 513) Composition: Agar 15.0 g/l Polypeptone 10.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Distilled water |
culture temp
- @ref: 20272
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 20272
- sample type: soil from a pineapple field
- geographic location: Okinawa, Iriomote Island
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | #Field |
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
taxonmaps
- @ref: 69479
- File name: preview.99_58498.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_3714;98_4708;99_58498&stattab=map
- Last taxonomy: Agromyces
- 16S sequence: AB546308
- Sequence Identity:
- Total samples: 290
- soil counts: 259
- aquatic counts: 10
- animal counts: 18
- plant counts: 3
Safety information
risk assessment
- @ref: 20272
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20272
- description: Agromyces iriomotensis gene for 16S ribosomal RNA, partial sequence
- accession: AB546308
- length: 1482
- database: ena
- NCBI tax ID: 717856
GC content
- @ref: 20272
- GC-content: 72.9
- method: high performance liquid chromatography (HPLC)
External links
@ref: 20272
culture collection no.: DSM 26155, NBRC 106452
straininfo link
- @ref: 88137
- straininfo: 406544
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24243967 | Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil. | Hamada M, Shibata C, Ishida Y, Tamura T, Yamamura H, Hayakawa M, Suzuki KI | Int J Syst Evol Microbiol | 10.1099/ijs.0.057349-0 | 2013 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry | Genetics |
| Phylogeny | 32790601 | Agromyces humi sp. nov., actinobacterium isolated from farm soil. | Lee JC, Whang KS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004376 | 2020 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Farms, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spinacia oleracea, Vitamin K 2/chemistry | Transcriptome |
| Phylogeny | 34559623 | Agromyces mariniharenae sp. nov., a novel indole-acetic acid producing actinobacterium isolated from marine sand. | Zhang Y, Zhao J, Hu J, Han C, Yu B, Wu Y, Xiao J, Wang X, Xiang W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005026 | 2021 | Acetates, Actinobacteria, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Indoles, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, *Sand, Sequence Analysis, DNA, Vitamin K 2 | 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 | |
| 20272 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26155 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26155) | |
| 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/ | |
| 88137 | 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-ID406544.1 |