Strain identifier
BacDive ID: 14879
Type strain: 
Species: Streptacidiphilus oryzae
Strain Designation: TH49
Strain history: <- JCM <- L. Wang TH49
NCBI tax ID(s): 348818 (species)
version 9.1 (current version)
General
@ref: 12340
BacDive-ID: 14879
DSM-Number: 45098
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive, rod-shaped
description: Streptacidiphilus oryzae TH49 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from rice field soil sample.
NCBI tax id
- NCBI tax id: 348818
- Matching level: species
strain history
| @ref | history |
|---|---|
| 12340 | <- JCM <- L. Wang; TH49 |
| 67770 | L. Wang TH49. |
| 67771 | <- JCM <- L. Wang TH49 |
doi: 10.13145/bacdive14879.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Kitasatosporales
- family: Streptomycetaceae
- genus: Streptacidiphilus
- species: Streptacidiphilus oryzae
- full scientific name: Streptacidiphilus oryzae Wang et al. 2006
synonyms
- @ref: 20215
- synonym: Phaeacidiphilus oryzae
@ref: 12340
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptacidiphilus
species: Streptacidiphilus oryzae
full scientific name: Streptacidiphilus oryzae Wang et al. 2006 emend. Nouioui et al. 2018
strain designation: TH49
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility |
|---|---|---|---|---|---|
| 31741 | positive | 1 µm | 0.7 µm | rod-shaped | no |
| 67771 | positive |
pigmentation
- @ref: 31741
- production: yes
multimedia
- @ref: 12340
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45098.jpg
- caption: Medium 987 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 12340 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water |
| 12340 | 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 |
| 12340 | 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 |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 12340 | positive | growth | 28 |
| 31741 | positive | growth | 28-37 |
| 31741 | positive | optimum | 30 |
| 67770 | positive | growth | 28 |
| 67771 | positive | growth | 28 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31741 | positive | growth | 3-6.5 | acidophile |
| 31741 | positive | optimum | 05-06 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 31741 | aerobe |
| 67771 | aerobe |
spore formation
- @ref: 31741
- spore formation: yes
observation
| @ref | observation |
|---|---|
| 31741 | aggregates in chains |
| 67770 | quinones: MK-9(H6), MK-9(H8) |
| 67771 | quinones: MK-9(H6), MK-9(H8) |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31741 | 16449 | alanine | + | carbon source |
| 31741 | 22599 | arabinose | + | carbon source |
| 31741 | 18403 | L-arabitol | + | carbon source |
| 31741 | 17057 | cellobiose | + | carbon source |
| 31741 | 28757 | fructose | + | carbon source |
| 31741 | 28260 | galactose | + | carbon source |
| 31741 | 17234 | glucose | + | carbon source |
| 31741 | 28087 | glycogen | + | carbon source |
| 31741 | 27570 | histidine | + | carbon source |
| 31741 | 17716 | lactose | + | carbon source |
| 31741 | 29864 | mannitol | + | carbon source |
| 31741 | 37684 | mannose | + | carbon source |
| 31741 | 28044 | phenylalanine | + | carbon source |
| 31741 | 15361 | pyruvate | + | carbon source |
| 31741 | 16634 | raffinose | + | carbon source |
| 31741 | 26546 | rhamnose | + | carbon source |
| 31741 | 17814 | salicin | + | carbon source |
| 31741 | 26986 | threonine | + | carbon source |
| 31741 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 12340 | rice field soil sample | Nontaburi Province | Thailand | THA | Asia |
| 67770 | Rice-field soil | Nontaburi Province | Thailand | THA | Asia |
| 67771 | From Rice-field soil | Nontaburi Province | Thailand | THA | 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_27.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_22;97_23;98_26;99_27&stattab=map
- Last taxonomy: Streptacidiphilus oryzae subclade
- 16S sequence: DQ208700
- Sequence Identity:
- Total samples: 739
- soil counts: 524
- aquatic counts: 84
- animal counts: 77
- plant counts: 54
Safety information
risk assessment
- @ref: 12340
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 12340
- description: Streptacidiphilus oryzae strain TH49 16S ribosomal RNA gene, partial sequence
- accession: DQ208700
- length: 1446
- database: nuccore
- NCBI tax ID: 348818
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptacidiphilus oryzae TH49 | 1449353.3 | wgs | patric | 1449353 |
| 66792 | Streptacidiphilus oryzae TH49 | 2574179794 | draft | img | 1449353 |
| 67770 | Phaeacidiphilus oryzae TH49 | GCA_000744815 | contig | ncbi | 1449353 |
GC content
- @ref: 67770
- GC-content: 73.4
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 89.776 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.283 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 86.778 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.034 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 82.5 | no |
External links
@ref: 12340
culture collection no.: DSM 45098, CGMCC 4.2012, CIP 109342, JCM 13271, KCTC 19220, BCRC 16837
straininfo link
- @ref: 83988
- straininfo: 297340
literature
- topic: Phylogeny
- Pubmed-ID: 16738101
- title: Streptacidiphilus oryzae sp. nov., an actinomycete isolated from rice-field soil in Thailand.
- authors: Wang L, Huang Y, Liu Z, Goodfellow M, Rodriguez C
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64165-0
- year: 2006
- mesh: Actinobacteria/*classification/genetics/growth & development/*isolation & purification, Culture Media, Molecular Sequence Data, Oryza, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Taiwan
- topic2: Cultivation
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 12340 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45098) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45098 | |||
| 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 | |||
| 31741 | 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 | 28016 | 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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) | |||
| 83988 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297340.1 | StrainInfo: A central database for resolving microbial strain identifiers |