Strain identifier
BacDive ID: 133436
Type strain: 
Species: Daejeonella composti
Strain Designation: TR6-06T, TR6-06
Strain history: <- ST Lee, KAIST
NCBI tax ID(s): 398052 (species)
version 8.1 (current version)
General
@ref: 28979
BacDive-ID: 133436
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Daejeonella composti TR6-06T is an aerobe, mesophilic, Gram-negative bacterium that was isolated from compost.
NCBI tax id
- NCBI tax id: 398052
- Matching level: species
strain history
- @ref: 67771
- history: <- ST Lee, KAIST
doi: 10.13145/bacdive133436.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Daejeonella
- species: Daejeonella composti
- full scientific name: Daejeonella composti (Lee et al. 2009) García-López et al. 2020
synonyms
- @ref: 20215
- synonym: Pedobacter composti
@ref: 28979
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter composti
strain designation: TR6-06T, TR6-06
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility |
|---|---|---|---|---|---|
| 28979 | negative | 1.4 µm | 0.25 µm | rod-shaped | no |
| 67771 | rod-shaped | no | |||
| 67771 | negative |
pigmentation
- @ref: 28979
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 28979 | positive | growth | 25-37 | mesophilic |
| 28979 | positive | optimum | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 28979 | positive | growth | 05-08 |
| 28979 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 28979 | aerobe |
| 67771 | aerobe |
spore formation
- @ref: 28979
- spore formation: no
halophily
- @ref: 28979
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-1 %
observation
- @ref: 67771
- observation: quinones: MK-7
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 28979 | 22599 | arabinose | + | carbon source |
| 28979 | 17234 | glucose | + | carbon source |
| 28979 | 17306 | maltose | + | carbon source |
| 28979 | 37684 | mannose | + | carbon source |
| 28979 | 506227 | N-acetylglucosamine | + | carbon source |
| 28979 | 17814 | salicin | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 28979 | acid phosphatase | + | 3.1.3.2 |
| 28979 | alkaline phosphatase | + | 3.1.3.1 |
| 28979 | catalase | + | 1.11.1.6 |
| 28979 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 28979 | compost | ||||
| 67771 | From compost | Daejeon | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Biodegradation
- Cat3: #Composting
taxonmaps
- @ref: 69479
- File name: preview.99_19998.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1777;97_2127;98_15116;99_19998&stattab=map
- Last taxonomy: Daejeonella composti subclade
- 16S sequence: AB267720
- Sequence Identity:
- Total samples: 2693
- soil counts: 702
- aquatic counts: 1787
- animal counts: 86
- plant counts: 118
Sequence information
16S sequences
- @ref: 28979
- description: Pedobacter composti gene for 16S rRNA, partial sequence, strain: TR6-06
- accession: AB267720
- length: 1430
- database: nuccore
- NCBI tax ID: 398052
GC content
- @ref: 28979
- GC-content: 41.9
External links
@ref: 28979
culture collection no.: KCTC 12638, LMG 23490
straininfo link
- @ref: 91440
- straininfo: 290309
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed |
|---|---|---|---|---|---|
| 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 | ||
| 28979 | 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 | 25413 | 28776041 |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | ||
| 91440 | 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-ID290309.1 |