Strain identifier
BacDive ID: 133429
Type strain: 
Species: Paenibacillus contaminans
Strain Designation: CKOBP-6
NCBI tax ID(s): 450362 (species)
version 8.1 (current version)
General
@ref: 28915
BacDive-ID: 133429
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-variable, motile, rod-shaped
description: Paenibacillus contaminans CKOBP-6 is a facultative anaerobe, spore-forming, Gram-variable bacterium that was isolated from contaminated lab plate.
NCBI tax id
- NCBI tax id: 450362
- Matching level: species
doi: 10.13145/bacdive133429.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Paenibacillaceae
- genus: Paenibacillus
- species: Paenibacillus contaminans
- full scientific name: Paenibacillus contaminans Chou et al. 2009
@ref: 28915
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Caryophanales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus contaminans
strain designation: CKOBP-6
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 28915 | variable | 2.5 µm | 0.9 µm | rod-shaped | yes | |
| 69480 | yes | 96.119 | ||||
| 69480 | positive | 100 |
pigmentation
- @ref: 28915
- production: no
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 28915 | positive | growth | 10-37 | |
| 28915 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 28915 | positive | growth | 6.5-8.0 |
| 28915 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 28915
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 28915 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 100 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 28915 | NaCl | positive | growth | 0-2 % |
| 28915 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28915 | 22599 | arabinose | + | carbon source |
| 28915 | 17057 | cellobiose | + | carbon source |
| 28915 | 16947 | citrate | + | carbon source |
| 28915 | 17234 | glucose | + | carbon source |
| 28915 | 17754 | glycerol | + | carbon source |
| 28915 | 17306 | maltose | + | carbon source |
| 28915 | 28053 | melibiose | + | carbon source |
| 28915 | 506227 | N-acetylglucosamine | + | carbon source |
| 28915 | 26546 | rhamnose | + | carbon source |
| 28915 | 17992 | sucrose | + | carbon source |
| 28915 | 27082 | trehalose | + | carbon source |
| 28915 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28915 | catalase | + | 1.11.1.6 |
| 28915 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 28915
- sample type: contaminated lab plate
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | |
| #Engineered | #Laboratory | #Lab enrichment |
taxonmaps
- @ref: 69479
- File name: preview.99_3062.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_1602;97_1912;98_2352;99_3062&stattab=map
- Last taxonomy: Paenibacillus contaminans subclade
- 16S sequence: EF626690
- Sequence Identity:
- Total samples: 8762
- soil counts: 6458
- aquatic counts: 816
- animal counts: 723
- plant counts: 765
Sequence information
16S sequences
- @ref: 28915
- description: Paenibacillus contaminans strain CKOBP-6 16S ribosomal RNA gene, partial sequence
- accession: EF626690
- length: 1472
- database: nuccore
- NCBI tax ID: 450362
Genome sequences
- @ref: 66792
- description: Paenibacillus contaminans CKOBP-6
- accession: GCA_003285015
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 450362
GC content
- @ref: 28915
- GC-content: 51.2
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 87.848 | yes |
| flagellated | yes | 66.513 | no |
| gram-positive | yes | 82.598 | no |
| anaerobic | no | 98.845 | yes |
| aerobic | yes | 79.577 | yes |
| halophile | no | 96.375 | no |
| spore-forming | yes | 96.184 | yes |
| glucose-util | yes | 89.006 | yes |
| thermophile | no | 98.62 | yes |
| glucose-ferment | no | 90.66 | no |
External links
@ref: 28915
culture collection no.: BCRC 17728, LMG 24216
straininfo link
- @ref: 91434
- straininfo: 309045
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19126735 | Paenibacillus contaminans sp. nov., isolated from a contaminated laboratory plate. | Chou JH, Lee JH, Lin MC, Chang PS, Arun AB, Young CC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.001495-0 | 2009 | Bacteria, Aerobic/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Culture Media, DNA, Bacterial/analysis, *Equipment Contamination, Genes, rRNA, Genotype, *Laboratories, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Spores, Bacterial/physiology | Cultivation |
| Phylogeny | 24425736 | Paenibacillus doosanensis sp. nov., isolated from soil. | Kim JH, Kang H, Kim W | Int J Syst Evol Microbiol | 10.1099/ijs.0.050716-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 24871973 | Paenibacillus cucumis sp. nov. isolated from greenhouse soil. | Ahn JH, Kim BC, Kim BY, Kim SJ, Song J, Kwon SW, Weon HY | J Microbiol | 10.1007/s12275-014-4071-7 | 2014 | Cucumis, Paenibacillus/*genetics/*isolation & purification, RNA, Ribosomal, 16S/genetics, *Soil Microbiology | Enzymology |
| Phylogeny | 26558840 | Paenibacillus cavernae sp. nov., isolated from soil of a natural cave. | Dong Lee S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000762 | 2015 | ||
| Phylogeny | 28920828 | Paenibacillus arcticus sp. nov., isolated from Arctic soil. | Cha IT, Cho ES, Yoo Y, Seok YJ, Park I, Lim HS, Park JM, Roh SW, Nam YD, Choi HJ, Lee YK, Seo MJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002299 | 2017 | Arctic Regions, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Paenibacillus/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 33666545 | Paenibacillus cymbidii sp. nov., isolated from Cymbidium goeringii roots. | Sun L, Wang P, Zhao D, Wang J, Wu Q, Liu L, Lyu Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004731 | 2021 |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|
| 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 | |||
| 28915 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 25354 | 28776041 | |
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | |
| 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 | |||
| 91434 | 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-ID309045.1 |