Strain identifier
BacDive ID: 2935
Type strain: 
Species: Comamonas granuli
Strain Designation: Ko03
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 1223521 (strain), 290309 (species)
version 9.3 (current version)
General
@ref: 7544
BacDive-ID: 2935
DSM-Number: 18411
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Comamonas granuli Ko03 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from granular sludge in industrial wastewater treatment plant.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 290309 | species |
| 1223521 | strain |
strain history
| @ref | history |
|---|---|
| 7544 | <- S.-T. Lee, KAIST, Republic of Korea <- W.-T. Im, KAIST |
| 67771 | <- ST Lee, KAIST |
doi: 10.13145/bacdive2935.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Comamonas
- species: Comamonas granuli
- full scientific name: Comamonas granuli Kim et al. 2011
@ref: 7544
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Comamonas
species: Comamonas granuli
full scientific name: Comamonas granuli Kim et al. 2011
strain designation: Ko03
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | negative | |
| 125438 | negative | 97.985 |
| 125439 | negative | 99.5 |
Culture and growth conditions
culture medium
- @ref: 7544
- name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 7544 | positive | growth | 28 |
| 67771 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 67771 | aerobe | |
| 125439 | obligate aerobe | 94.8 |
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99
observation
- @ref: 67771
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 7544 | granular sludge in industrial wastewater treatment plant | Kongju | Republic of Korea | KOR | Asia |
| 67771 | From granule sludge | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Waste | #Industrial wastewater |
| #Engineered | #Waste | #Activated sludge |
| #Engineered | #Waste | #Water treatment plant |
taxonmaps
- @ref: 69479
- File name: preview.99_4997.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_2446;97_2981;98_3735;99_4997&stattab=map
- Last taxonomy: Comamonas granuli subclade
- 16S sequence: AB681516
- Sequence Identity:
- Total samples: 5260
- soil counts: 627
- aquatic counts: 3461
- animal counts: 861
- plant counts: 311
Safety information
risk assessment
- @ref: 7544
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Comamonas granuli gene for 16S rRNA, partial sequence, strain: NBRC 101663 | AB681516 | 1454 | nuccore | 1223521 |
| 7544 | Comamonas granuli gene for 16S rRNA, partial sequence, strain: Ko03 | AB187586 | 1443 | nuccore | 1223521 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Comamonas granuli NBRC 101663 | GCA_000739995 | contig | ncbi | 1223521 |
| 66792 | Comamonas granuli NBRC 101663 | 1223521.5 | wgs | patric | 1223521 |
| 66792 | Comamonas granuli NBRC 101663 | 2600255078 | draft | img | 1223521 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7544 | 68.4 | high performance liquid chromatography (HPLC) |
| 67771 | 68.4 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 94.8 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.5 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 85.1 | |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99 | |
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.985 | yes |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 90.666 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.751 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 70.756 | yes |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 92.57 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 87.277 | no |
External links
@ref: 7544
culture collection no.: DSM 18411, KCTC 12199, NBRC 101663
straininfo link
- @ref: 72457
- straininfo: 138341
literature
- topic: Phylogeny
- Pubmed-ID: 18758728
- title: Comamonas granuli sp. nov., isolated from granules used in a wastewater treatment plant.
- authors: Kim KH, Ten LN, Liu QM, Im WT, Lee ST
- journal: J Microbiol
- DOI: 10.1007/s12275-008-0019-0
- year: 2008
- mesh: Base Composition, Bioreactors/microbiology, Comamonas/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, *Industrial Waste, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 7544 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18411) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18411 | |||
| 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) | |||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 72457 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID138341.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |||
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |