Strain identifier
BacDive ID: 2377
Type strain:
Species: Cellulomonas soli
Strain Designation: Kc1
Strain history: K. Hatayama Kc1.
NCBI tax ID(s): 931535 (species)
General
@ref: 17687
BacDive-ID: 2377
DSM-Number: 24484
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Cellulomonas soli Kc1 is an aerobe, spore-forming, mesophilic bacterium that was isolated from Soil.
NCBI tax id
- NCBI tax id: 931535
- Matching level: species
strain history
@ref | history |
---|---|
17687 | <- K. Hatayama, Sagami Chemical Research Institute, Kanagawa, Japan; Kc1 <- K. Esaki |
67770 | K. Hatayama Kc1. |
doi: 10.13145/bacdive2377.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Cellulomonadaceae
- genus: Cellulomonas
- species: Cellulomonas soli
- full scientific name: Cellulomonas soli Hatayama et al. 2013
@ref: 17687
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Cellulomonadaceae
genus: Cellulomonas
species: Cellulomonas soli
full scientific name: Cellulomonas soli Hatayama et al. 2013
strain designation: Kc1
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30542 | positive | 6 µm | 1.5 µm | rod-shaped | yes | |
69480 | positive | 100 |
pigmentation
- @ref: 30542
- production: yes
Culture and growth conditions
culture medium
- @ref: 17687
- name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
- growth: yes
- link: https://mediadive.dsmz.de/medium/92
- composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
17687 | positive | growth | 25 | mesophilic |
30542 | positive | growth | 15-37 | |
30542 | positive | optimum | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30542 | positive | growth | 06-11 | alkaliphile |
30542 | positive | optimum | 8.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30542
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 91 |
69480 | no | 99.519 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30542 | NaCl | positive | growth | 0-3 % |
30542 | NaCl | positive | optimum | 1.5 % |
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30542 | 22599 | arabinose | + | carbon source |
30542 | 17057 | cellobiose | + | carbon source |
30542 | 28757 | fructose | + | carbon source |
30542 | 28260 | galactose | + | carbon source |
30542 | 5291 | gelatin | + | carbon source |
30542 | 17234 | glucose | + | carbon source |
30542 | 17754 | glycerol | + | carbon source |
30542 | 28087 | glycogen | + | carbon source |
30542 | 17306 | maltose | + | carbon source |
30542 | 37684 | mannose | + | carbon source |
30542 | 16634 | raffinose | + | carbon source |
30542 | 17814 | salicin | + | carbon source |
30542 | 17992 | sucrose | + | carbon source |
30542 | 27082 | trehalose | + | carbon source |
30542 | 18222 | xylose | + | carbon source |
30542 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30542 | catalase | + | 1.11.1.6 |
30542 | gelatinase | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
17687 | Soil | Kanegawa, Kawasaki, botanical garden | Japan | JPN | Asia |
67770 | Wet soil from a botanical garden | Kawasaki, Kanagawa Pref. | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_28581.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_1685;98_4020;99_28581&stattab=map
- Last taxonomy: Cellulomonas
- 16S sequence: AB602498
- Sequence Identity:
- Total samples: 229
- soil counts: 147
- aquatic counts: 24
- animal counts: 39
- plant counts: 19
Safety information
risk assessment
- @ref: 17687
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17687
- description: Cellulomonas soli gene for 16S ribosomal RNA, partial sequence
- accession: AB602498
- length: 1446
- database: ena
- NCBI tax ID: 931535
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Cellulomonas soli NBRC 109434 | GCA_007992535 | contig | ncbi | 931535 |
66792 | Cellulomonas soli strain DSM 24484 | 931535.4 | wgs | patric | 931535 |
66792 | Cellulomonas soli strain NBRC 109434 | 931535.3 | wgs | patric | 931535 |
66792 | Cellulomonas soli DSM 24484 | 2831319000 | draft | img | 931535 |
67770 | Cellulomonas soli DSM 24484 | GCA_013409305 | contig | ncbi | 931535 |
GC content
@ref | GC-content | method |
---|---|---|
17687 | 73.6 | high performance liquid chromatography (HPLC) |
30542 | 73.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 91 | no |
motile | yes | 82.824 | no |
flagellated | no | 89.331 | no |
gram-positive | yes | 85.83 | yes |
anaerobic | no | 97.627 | no |
halophile | no | 93.027 | yes |
spore-forming | no | 88.49 | no |
glucose-util | yes | 86.398 | yes |
aerobic | yes | 80.161 | yes |
thermophile | no | 99.055 | yes |
glucose-ferment | no | 58.77 | no |
External links
@ref: 17687
culture collection no.: DSM 24484, JCM 17535, NBRC 109434
straininfo link
- @ref: 71932
- straininfo: 405946
literature
- topic: Phylogeny
- Pubmed-ID: 22328604
- title: Cellulomonas soli sp. nov. and Cellulomonas oligotrophica sp. nov., isolated from soil.
- authors: Hatayama K, Esaki K, Ide T
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.038364-0
- year: 2012
- mesh: Bacterial Typing Techniques, Base Composition, Cellulomonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
17687 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24484) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24484 | ||||
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 | ||||
30542 | 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 | 26873 | 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) | ||||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
71932 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405946.1 | StrainInfo: A central database for resolving microbial strain identifiers |