Strain identifier
BacDive ID: 16911
Type strain: 
Species: Actinocorallia herbida
Strain history: IFO 15485 <-- Takeda Chem. Ind., Ltd.; AL-50780.
NCBI tax ID(s): 58109 (species)
version 9.1 (current version)
General
@ref: 11626
BacDive-ID: 16911
DSM-Number: 44254
keywords: genome sequence, 16S sequence, Bacteria, spore-forming
description: Actinocorallia herbida DSM 44254 is a spore-forming bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 58109
- Matching level: species
strain history
| @ref | history |
|---|---|
| 11626 | <- IFO <- S. Iinuma, Takeda Chem. Ind., AL-50780 |
| 67770 | IFO 15485 <-- Takeda Chem. Ind., Ltd.; AL-50780. |
doi: 10.13145/bacdive16911.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Thermomonosporaceae
- genus: Actinocorallia
- species: Actinocorallia herbida
- full scientific name: Actinocorallia herbida Iinuma et al. 1994
@ref: 11626
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Thermomonosporaceae
genus: Actinocorallia
species: Actinocorallia herbida
full scientific name: Actinocorallia herbida Iinuma et al. 1994
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 11626 | 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 |
| 11626 | CORYNEBACTERIUM AGAR (DSMZ Medium 53) | yes | https://mediadive.dsmz.de/medium/53 | Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 11626 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 100
compound production
- @ref: 11626
- compound: azaserine-like antibiotic
observation
| @ref | observation |
|---|---|
| 67770 | Production of Azaserine-like antibiotic |
| 67770 | quinones: MK-9(H4), MK-9(H6) |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 11626 | soil | Bangkok | Thailand | THA | Asia |
| 67770 | Soil | Bangkok | Thailand | THA | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_18416.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_9402;97_11308;98_13907;99_18416&stattab=map
- Last taxonomy: Actinocorallia herbida
- 16S sequence: LC066303
- Sequence Identity:
- Total samples: 241
- soil counts: 21
- aquatic counts: 1
- animal counts: 3
- plant counts: 216
Safety information
risk assessment
- @ref: 11626
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Actinocorallia herbida 16S-23S ribosomal RNA intergenic spacer region, partial sequence | AF134109 | 403 | nuccore | 58109 |
| 20218 | Actinocorallia herbida gene for 16S ribosomal RNA, partial sequence | D85473 | 1465 | nuccore | 58109 |
| 67770 | Actinocorallia herbida gene for 16S ribosomal RNA, partial sequence, strain: JCM 9647 | LC066303 | 1452 | nuccore | 58109 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Actinocorallia herbida strain DSM 44254 | 58109.3 | wgs | patric | 58109 |
| 66792 | Actinocorallia herbida DSM 44254 | 2784132147 | draft | img | 58109 |
| 67770 | Actinocorallia herbida DSM 44254 | GCA_003751225 | contig | ncbi | 58109 |
GC content
- @ref: 11626
- GC-content: 73
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 87.155 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.902 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 82.968 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.803 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 95.1 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86 | no |
External links
@ref: 11626
culture collection no.: DSM 44254, ATCC 51528, IFO 15485, JCM 9647, NBRC 15485, NCIMB 13337, VKM Ac-1994, IMSNU 21271
straininfo link
- @ref: 85916
- straininfo: 93001
literature
- topic: Phylogeny
- Pubmed-ID: 12139476
- title: Cell wall teichoic acids of actinomycetes of three genera of the order actinomycetales.
- authors: Streshinskaya GM, Shashkov AS, Usov AI, Evtushenko LI, Naumova IB
- journal: Biochemistry (Mosc)
- DOI: 10.1023/a:1016348724308
- year: 2002
- mesh: Actinomycetales/*chemistry/*classification, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Teichoic Acids/*analysis
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 11626 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44254) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44254 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 85916 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID93001.1 | StrainInfo: A central database for resolving microbial strain identifiers |