Strain identifier
BacDive ID: 24218
Type strain: 
Species: Rhizocola hellebori
Strain Designation: K12-0602
Strain history: <- A. Matsumoto, Kitasato Univ., Tokyo, Japan; K12-0602 <- Y. Kawaguchi
NCBI tax ID(s): 1392758 (species)
version 9.1 (current version)
General
@ref: 21345
BacDive-ID: 24218
DSM-Number: 45988
keywords: genome sequence, 16S sequence, Bacteria, spore-forming
description: Rhizocola hellebori K12-0602 is a spore-forming bacterium that was isolated from root of Helleborus orientalis .
NCBI tax id
- NCBI tax id: 1392758
- Matching level: species
strain history
- @ref: 21345
- history: <- A. Matsumoto, Kitasato Univ., Tokyo, Japan; K12-0602 <- Y. Kawaguchi
doi: 10.13145/bacdive24218.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micromonosporales
- family: Micromonosporaceae
- genus: Rhizocola
- species: Rhizocola hellebori
- full scientific name: Rhizocola hellebori Matsumoto et al. 2014
@ref: 21345
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micromonosporaceae
genus: Rhizocola
species: Rhizocola hellebori
full scientific name: Rhizocola hellebori Matsumoto et al. 2014
strain designation: K12-0602
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 90.344
multimedia
- @ref: 21345
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45988.jpg
- caption: Medium 554 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 92
Isolation, sampling and environmental information
isolation
- @ref: 21345
- sample type: root of Helleborus orientalis
- host species: Helleborus orientalis
- geographic location: Kanagawa Prefecture, Medicinal Plant Garden of Kitasato University
- country: Japan
- origin.country: JPN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_179086.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_4915;97_56061;98_74220;99_179086&stattab=map
- Last taxonomy: Rhizocola hellebori subclade
- 16S sequence: AB848707
- Sequence Identity:
- Total samples: 936
- soil counts: 852
- aquatic counts: 28
- animal counts: 16
- plant counts: 40
Safety information
risk assessment
- @ref: 21345
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21345
- description: Rhizocola hellebori gene for 16S ribosomal RNA, partial sequence
- accession: AB848707
- length: 1451
- database: nuccore
- NCBI tax ID: 1392758
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhizocola hellebori NBRC 109834 | GCA_016862955 | contig | ncbi | 1392758 |
| 66792 | Rhizocola hellebori strain NBRC 109834 | 1392758.3 | wgs | patric | 1392758 |
GC content
- @ref: 21345
- GC-content: 67
- 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 | 92 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 90.344 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.253 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 86 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 88.139 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 91.278 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86.5 | no |
External links
@ref: 21345
culture collection no.: DSM 45988, NBRC 109834
straininfo link
- @ref: 88161
- straininfo: 398233
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24893943 | Rhizocola hellebori gen. nov., sp. nov., an actinomycete of the family Micromonosporaceae containing 3,4-dihydroxydiaminopimelic acid in the cell-wall peptidoglycan. | Matsumoto A, Kawaguchi Y, Nakashima T, Iwatsuki M, Omura S, Takahashi Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.060293-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Helleborus/*microbiology, Japan, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 30444473 | Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum. | Sun Y, Jiang ZM, Zhao LL, Su J, Yu LY, Tian YQ, Zhang YQ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003114 | 2018 | Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, Polygonaceae/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry | 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 | |
| 21345 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45988 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45988) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 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 | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 88161 | 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-ID398233.1 |