Strain identifier
BacDive ID: 133662
Type strain: 
Species: Pedobacter boryungensis
Strain Designation: BR-9
Strain history: <- JH Yoon, KRIBB
NCBI tax ID(s): 869962 (species)
version 8.1 (current version)
General
@ref: 30005
BacDive-ID: 133662
keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Pedobacter boryungensis BR-9 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 869962
- Matching level: species
strain history
- @ref: 67771
- history: <- JH Yoon, KRIBB
doi: 10.13145/bacdive133662.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pedobacter
- species: Pedobacter boryungensis
- full scientific name: Pedobacter boryungensis Jung et al. 2012
@ref: 30005
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter boryungensis
strain designation: BR-9
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility |
|---|---|---|---|---|---|
| 30005 | negative | 2.0-5.0 µm | 0.2-0.5 µm | rod-shaped | no |
| 67771 | rod-shaped | no | |||
| 67771 | negative |
colony morphology
- @ref: 62186
- incubation period: 1 day
pigmentation
- @ref: 30005
- production: yes
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 30005 | positive | growth | 04-35 | |
| 30005 | positive | optimum | 30 | mesophilic |
| 62186 | positive | growth | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 30005
- ability: positive
- type: optimum
- pH: 6.0-7.0
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 30005 | aerobe |
| 62186 | aerobe |
| 67771 | aerobe |
spore formation
| @ref | spore formation |
|---|---|
| 30005 | no |
| 67771 | no |
halophily
- @ref: 30005
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <1 %
observation
- @ref: 67771
- observation: quinones: MK-7
enzymes
- @ref: 30005
- value: cytochrome oxidase
- activity: +
- ec: 1.9.3.1
Isolation, sampling and environmental information
isolation
| @ref | sample type | sampling date | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 30005 | soil | |||||
| 62186 | Soil | 2008 | Boryung | Republic of Korea | KOR | Asia |
| 67771 | From soil | Boryung | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Sequence information
16S sequences
- @ref: 30005
- description: Pedobacter boryungensis strain BR-9 16S ribosomal RNA gene, partial sequence
- accession: HM640986
- length: 1443
- database: nuccore
- NCBI tax ID: 869962
GC content
| @ref | GC-content | method |
|---|---|---|
| 30005 | 38.5 | |
| 67771 | 38.5 | high performance liquid chromatography (HPLC) |
External links
@ref: 30005
culture collection no.: KCTC 23344, CCUG 60024
straininfo link
- @ref: 91549
- straininfo: 410897
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21257683 | Pedobacter boryungensis sp. nov., isolated from soil. | Jung YT, Lee SY, Choi WC, Oh TK, Yoon JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.028183-0 | 2011 | Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Vitamin K 2/analysis | Genetics |
| Phylogeny | 25613852 | Pedobacter lotistagni sp. nov. isolated from lotus pond water. | Singh H, Du J, Ngo HT, Kim KY, Yi TH | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0387-5 | 2015 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Locomotion, Lotus/growth & development, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/*isolation & purification/physiology, Phospholipids/analysis, Phylogeny, Ponds/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Genetics |
| Phylogeny | 25634950 | Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter. | Du J, Singh H, Ngo HTT, Won KH, Kim KY, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijs.0.000087 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Trees/*microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 33502299 | Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana. | Qi SS, Cnockaert M, Carlier A, Vandamme P | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004667 | 2021 |
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed | catalogue |
|---|---|---|---|---|---|---|
| 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 | |||
| 30005 | 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 | 26369 | 28776041 | |
| 62186 | Curators of the CCUG | https://www.ccug.se/strain?id=60024 | Culture Collection University of Gothenburg (CCUG) (CCUG 60024) | |||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 91549 | 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-ID410897.1 |