Strain identifier
BacDive ID: 17635
Type strain: 
Species: Actinospica robiniae
Strain Designation: GE134769
Strain history: DSM 44927 <-- L. Cavaletti GE134769.
NCBI tax ID(s): 479430 (strain), 304901 (species)
version 8.1 (current version)
General
@ref: 12200
BacDive-ID: 17635
DSM-Number: 44927
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped
description: Actinospica robiniae GE134769 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 304901 | species |
| 479430 | strain |
strain history
| @ref | history |
|---|---|
| 12200 | <- L. Cavaletti; GE134769 |
| 67770 | DSM 44927 <-- L. Cavaletti GE134769. |
doi: 10.13145/bacdive17635.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Catenulisporales
- family: Actinospicaceae
- genus: Actinospica
- species: Actinospica robiniae
- full scientific name: Actinospica robiniae Cavaletti et al. 2006
@ref: 12200
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Actinospicaceae
genus: Actinospica
species: Actinospica robiniae
full scientific name: Actinospica robiniae Cavaletti et al. 2006
strain designation: GE134769
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 31589 | positive | 1-1.2 µm | 0.6 µm | rod-shaped | no | |
| 69480 | no | 95.667 | ||||
| 69480 | positive | 100 |
pigmentation
- @ref: 31589
- production: yes
Culture and growth conditions
culture medium
- @ref: 12200
- name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)
- growth: yes
- link: https://mediadive.dsmz.de/medium/84
- composition: 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 | range |
|---|---|---|---|---|
| 12200 | positive | growth | 28 | mesophilic |
| 31589 | positive | growth | 17-33 | |
| 31589 | positive | optimum | 22-28 | |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 31589 | positive | growth | 4.8-6.2 |
| 31589 | positive | optimum | 5.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 31589
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 31589 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 99.729 |
observation
| @ref | observation |
|---|---|
| 31589 | aggregates in chains |
| 67770 | quinones: MK-9(H4), MK-9(H6), MK-9(H8) |
metabolite utilization
- @ref: 43413
- Chebi-ID: 62968
- metabolite: cellulose
- utilization activity: +
- kind of utilization tested: degradation
metabolite production
- @ref: 31589
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
- @ref: 31589
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 12200 | forest soil | Lombardia, Gerenzano | Italy | ITA | Europe |
| 67770 | Soil in a wooded area | Gerenzano | Italy | ITA | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Forest |
| #Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_149.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15873;96_110;97_117;98_130;99_149&stattab=map
- Last taxonomy: Actinospica robiniae
- 16S sequence: AJ865863
- Sequence Identity:
- Total samples: 6420
- soil counts: 4561
- aquatic counts: 342
- animal counts: 820
- plant counts: 697
Safety information
risk assessment
- @ref: 12200
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 12200
- description: Actinospica robiniae partial 16S rRNA gene, type strain GE134769T
- accession: AJ865863
- length: 1444
- database: ena
- NCBI tax ID: 479430
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Actinospica robiniae DSM 44927 | 479430.3 | wgs | patric | 479430 |
| 66792 | Actinospica robiniae DSM 44927 | 2510065062 | draft | img | 479430 |
| 67770 | Actinospica robiniae DSM 44927 | GCA_000504285 | scaffold | ncbi | 479430 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 12200 | 70.8 | |
| 67770 | 70.8 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| gram-positive | yes | 88.035 | yes |
| anaerobic | no | 99.046 | yes |
| halophile | no | 95.923 | no |
| spore-forming | yes | 93.881 | no |
| glucose-util | yes | 86.258 | no |
| aerobic | yes | 90.907 | no |
| thermophile | no | 98.34 | yes |
| motile | no | 94.269 | yes |
| flagellated | no | 98.114 | yes |
| glucose-ferment | no | 85.092 | no |
External links
@ref: 12200
culture collection no.: DSM 44927, JCM 14908, NRRL B-24432, BCRC 16839, NBRC 102112
straininfo link
- @ref: 86627
- straininfo: 343938
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16902002 | Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales. | Cavaletti L, Monciardini P, Schumann P, Rohde M, Bamonte R, Busti E, Sosio M, Donadio S | Int J Syst Evol Microbiol | 10.1099/ijs.0.63859-0 | 2006 | Actinomycetales/chemistry/*classification/genetics/ultrastructure, Amino Acids, Diamino/analysis, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/chemistry, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Monosaccharides/analysis, Peptidoglycan/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Species Specificity, Trees, Vitamin K 2/analysis | Genetics |
| Phylogeny | 26026797 | Actinospica durhamensis sp. nov., isolated from a spruce forest soil. | Golinska P, Zucchi TD, Silva L, Dahm H, Goodfellow M | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0496-1 | 2015 | Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Forests, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Picea, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 12200 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44927) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44927 | ||||
| 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 | ||||
| 31589 | 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 | 27878 | 28776041 | ||
| 43413 | Iain Anderson, Birte Abt, Athanasios Lykidis, Hans-Peter Klenk, Nikos Kyrpides, Natalia Ivanova | 10.1371/journal.pone.0039331 | Genomics of Aerobic Cellulose Utilization Systems in Actinobacteria | 22723998 | PLoS ONE 7: - 2012 | ||
| 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/ | |||||
| 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) | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
| 86627 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID343938.1 | StrainInfo: A central database for resolving microbial strain identifiers |