Strain identifier
BacDive ID: 134321
Type strain: 
Species: Streptacidiphilus rugosus
Strain Designation: AM16
Strain history: <- SB Kim, Chungnam Natl. Univ.
NCBI tax ID(s): 981369 (strain), 405783 (species)
version 9.1 (current version)
General
@ref: 64724
BacDive-ID: 134321
DSM-Number: 108660
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive
description: Streptacidiphilus rugosus AM16 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 405783 | species |
| 981369 | strain |
strain history
| @ref | history |
|---|---|
| 64724 | <- NBRC; NBRC 103186 <- S. B. Kim and S. H. Cho, School Biosci. Biotechnol., Chungnam Natl. Univ., Republic of Korea; AM16 |
| 67770 | KCTC 19279 <-- S. B. Kim AM16. |
| 67771 | <- SB Kim, Chungnam Natl. Univ. |
doi: 10.13145/bacdive134321.20240916.9.1
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 rugosus
- full scientific name: Streptacidiphilus rugosus Cho et al. 2008
@ref: 64724
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptacidiphilus
species: Streptacidiphilus rugosus
full scientific name: Streptacidiphilus rugosus Cho et al. 2008 emend. Nouioui et al. 2018
strain designation: AM16
type strain: yes
Morphology
cell morphology
- @ref: 67771
- gram stain: positive
pigmentation
- @ref: 32427
- production: no
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 64724 | 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 |
| 64724 | 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 |
| 64724 | 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 |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 64724 | positive | growth | 28 |
| 32427 | positive | growth | 28-35 |
| 67770 | positive | growth | 28 |
| 67771 | positive | growth | 30 |
culture pH
- @ref: 32427
- ability: positive
- type: growth
- pH: 03-08
- PH range: acidophile
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32427 | yes | |
| 69480 | yes | 91.234 |
observation
- @ref: 67770
- observation: quinones: MK-9(H8), MK-9(H6)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32427 | 29016 | arginine | + | carbon source |
| 32427 | 24265 | gluconate | + | carbon source |
| 32427 | 17754 | glycerol | + | carbon source |
| 32427 | 17268 | myo-inositol | + | carbon source |
| 32427 | 30911 | sorbitol | + | carbon source |
| 32427 | 17992 | sucrose | + | carbon source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | host species |
|---|---|---|---|---|---|---|
| 32427 | soil | |||||
| 64724 | soil of Pinus thunbergii | Anmyeon, Tae-an, Chungnam | Republic of Korea | KOR | Asia | |
| 67770 | Pinus-associated soil | Anmyeon, near the coastal areas of Tae-An, Chungnam | Republic of Korea | KOR | Asia | Pinus |
| 67771 | From `Pinus` soil | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_3302.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_1291;97_2062;98_2532;99_3302&stattab=map
- Last taxonomy: Streptacidiphilus
- 16S sequence: DQ904547
- Sequence Identity:
- Total samples: 852
- soil counts: 623
- aquatic counts: 86
- animal counts: 112
- plant counts: 31
Safety information
risk assessment
- @ref: 64724
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 64724
- description: Streptacidiphilus rugosus AM-16 16S ribosomal RNA gene, partial sequence
- accession: DQ904547
- length: 1383
- database: nuccore
- NCBI tax ID: 981369
Genome sequences
- @ref: 67770
- description: Streptacidiphilus rugosus AM-16
- accession: GCA_000744655
- assembly level: contig
- database: ncbi
- NCBI tax ID: 981369
GC content
- @ref: 67770
- GC-content: 71.8
- 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 | 89.547 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.778 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.879 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 91.234 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.5 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 89.6 | no |
External links
@ref: 64724
culture collection no.: NBRC 103186, KCTC 19279, DSM 108660, JCM 16225
straininfo link
- @ref: 91896
- straininfo: 398612
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18599696 | Streptacidiphilus anmyonensis sp. nov., Streptacidiphilus rugosus sp. nov. and Streptacidiphilus melanogenes sp. nov., acidophilic actinobacteria isolated from Pinus soils. | Cho SH, Han JH, Ko HY, Kim SB | Int J Syst Evol Microbiol | 10.1099/ijs.0.65480-0 | 2008 | Actinobacteria/*classification/genetics/growth & development/isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, *Pinus, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity | Genetics |
| Phylogeny | 29620496 | Streptacidiphilus monticola sp. nov., a novel actinomycete isolated from soil. | Song W, Duan L, Jin L, Zhao J, Jiang S, Sun T, Guo XW, Xiang W, Wang X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002751 | 2018 | Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed | 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 | |||
| 32427 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 28650 | 28776041 | |
| 64724 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-108660 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108660) | |||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 91896 | 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-ID398612.1 |