Strain identifier
BacDive ID: 2376
Type strain:
Species: Cellulomonas oligotrophica
Strain Designation: Kc5
Strain history: K. Hatayama Kc5.
NCBI tax ID(s): 931536 (species)
General
@ref: 17686
BacDive-ID: 2376
DSM-Number: 24482
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, motile, rod-shaped
description: Cellulomonas oligotrophica Kc5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil at an urban area.
NCBI tax id
- NCBI tax id: 931536
- Matching level: species
strain history
@ref | history |
---|---|
17686 | <- K. Hatayama, Sagami Chemical Research Institute, Kanagawa, Japan; Kc5 <- K. Esaki |
67770 | K. Hatayama Kc5. |
doi: 10.13145/bacdive2376.20230509.8.1
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 oligotrophica
- full scientific name: Cellulomonas oligotrophica Hatayama et al. 2013
@ref: 17686
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Cellulomonadaceae
genus: Cellulomonas
species: Cellulomonas oligotrophica
full scientific name: Cellulomonas oligotrophica Hatayama et al. 2013
strain designation: Kc5
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30542 | positive | 6 µm | 2 µm | rod-shaped | yes | |
69480 | positive | 100 |
pigmentation
- @ref: 30542
- production: yes
Culture and growth conditions
culture medium
- @ref: 17686
- 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 |
---|---|---|---|---|
17686 | positive | growth | 28 | mesophilic |
30542 | positive | growth | 25 | mesophilic |
30542 | positive | optimum | 15-37 | |
67770 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30542 | positive | growth | 06-11 | alkaliphile |
30542 | positive | optimum | 9 |
Physiology and metabolism
oxygen tolerance
- @ref: 30542
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
30542 | no | |
69480 | no | 99.882 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30542 | NaCl | positive | growth | 0-6 % |
30542 | NaCl | positive | optimum | 3 % |
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9(H2)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30542 | 30089 | acetate | + | carbon source |
30542 | 22599 | arabinose | + | carbon source |
30542 | 17057 | cellobiose | + | carbon source |
30542 | 28757 | fructose | + | carbon source |
30542 | 28260 | galactose | + | carbon source |
30542 | 17234 | glucose | + | carbon source |
30542 | 17754 | glycerol | + | carbon source |
30542 | 28087 | glycogen | + | carbon source |
30542 | 17306 | maltose | + | carbon source |
30542 | 29864 | mannitol | + | carbon source |
30542 | 37684 | mannose | + | carbon source |
30542 | 28053 | melibiose | + | carbon source |
30542 | 17814 | salicin | + | carbon source |
30542 | 30911 | sorbitol | + | 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 |
---|---|---|---|---|---|
17686 | soil at an urban area | Kanagawa, Kawasaki | Japan | JPN | Asia |
67770 | Moist soil from an urban area | Kawasaki, Kanagawa Pref. | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_28313.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_1685;98_2637;99_28313&stattab=map
- Last taxonomy: Cellulomonas oligotrophica
- 16S sequence: AB602499
- Sequence Identity:
- Total samples: 33
- soil counts: 15
- aquatic counts: 14
- animal counts: 4
Safety information
risk assessment
- @ref: 17686
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17686
- description: Cellulomonas oligotrophica gene for 16S ribosomal RNA, partial sequence
- accession: AB602499
- length: 1443
- database: ena
- NCBI tax ID: 931536
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Cellulomonas oligotrophica NBRC 109435 | GCA_016862735 | contig | ncbi | 931536 |
66792 | Cellulomonas oligotrophica strain DSM 24482 | 931536.4 | wgs | patric | 931536 |
66792 | Cellulomonas oligotrophica strain JCM 17534 | 931536.3 | wgs | patric | 931536 |
66792 | Cellulomonas oligotrophica strain NBRC 109435 | 931536.5 | wgs | patric | 931536 |
66792 | Cellulomonas oligotrophica DSM 24482 | 2844845222 | draft | img | 931536 |
67770 | Cellulomonas oligotrophica DSM 24482 | GCA_013409875 | contig | ncbi | 931536 |
67770 | Cellulomonas oligotrophica JCM 17534 | GCA_006386485 | scaffold | ncbi | 931536 |
GC content
@ref | GC-content | method |
---|---|---|
17686 | 75.8 | high performance liquid chromatography (HPLC) |
30542 | 75.8 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 88 | no |
motile | yes | 85.744 | yes |
flagellated | no | 90.655 | no |
gram-positive | yes | 93.308 | yes |
anaerobic | no | 98.894 | no |
halophile | no | 91.713 | no |
spore-forming | no | 80.413 | yes |
glucose-util | yes | 87.936 | yes |
aerobic | yes | 89.242 | yes |
thermophile | no | 99.402 | no |
glucose-ferment | no | 64.654 | no |
External links
@ref: 17686
culture collection no.: DSM 24482, JCM 17534, NBRC 109435
straininfo link
- @ref: 71931
- straininfo: 399478
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22328604 | Cellulomonas soli sp. nov. and Cellulomonas oligotrophica sp. nov., isolated from soil. | Hatayama K, Esaki K, Ide T | Int J Syst Evol Microbiol | 10.1099/ijs.0.038364-0 | 2012 | 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 | Genetics |
Phylogeny | 31661043 | Cellulomonas telluris sp. nov., an endoglucanase-producing actinobacterium isolated from Badain Jaran desert sand. | Shi YL, Sun Y, Ruan ZY, Su J, Yu LY, Zhang YQ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003806 | 2020 | Bacterial Typing Techniques, Base Composition, *Cellulase, Cellulomonas/*classification/enzymology/isolation & purification, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sand/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Enzymology |
Phylogeny | 32038002 | Cellulomonas shaoxiangyii sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau. | Tian Z, Lu S, Jin D, Yang J, Pu J, Lai XH, Ren ZH, Wu XM, Li J, Wang S, Xu J | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003939 | 2020 | Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cellulomonas/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Nucleic Acid Hybridization, Ornithine/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
17686 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24482) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24482 | |||
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) | |||
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) | |||
71931 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399478.1 | StrainInfo: A central database for resolving microbial strain identifiers |