Strain identifier
BacDive ID: 133768
Type strain:
Species: Pedobacter ginsengiterrae
Strain history: D.-C. Yang DCY49.
NCBI tax ID(s): 871696 (species)
version 8.1 (current version)
General
@ref: 30449
BacDive-ID: 133768
keywords: 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped
description: Pedobacter ginsengiterrae KCTC 23317 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 871696
- Matching level: species
strain history
- @ref: 67770
- history: D.-C. Yang DCY49.
doi: 10.13145/bacdive133768.20230509.8.1
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 ginsengiterrae
- full scientific name: Pedobacter ginsengiterrae Hoang et al. 2013
@ref: 30449
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter ginsengiterrae
type strain: yes
Morphology
cell morphology
- @ref: 30449
- gram stain: negative
- cell length: 2 µm
- cell width: 0.7 µm
- cell shape: rod-shaped
- motility: yes
- flagellum arrangement: gliding
pigmentation
- @ref: 30449
- production: yes
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
30449 | positive | growth | 04-34 | |
30449 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30449 | positive | growth | 4.5-10 | alkaliphile |
30449 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 30449
- oxygen tolerance: aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30449 | NaCl | positive | growth | 0-3 % |
30449 | NaCl | positive | optimum | 0.5 % |
observation
@ref | observation |
---|---|
30449 | aggregates in clumps |
67770 | quinones: MK-7 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30449 | 22599 | arabinose | + | carbon source |
30449 | 17057 | cellobiose | + | carbon source |
30449 | 28260 | galactose | + | carbon source |
30449 | 17234 | glucose | + | carbon source |
30449 | 28087 | glycogen | + | carbon source |
30449 | 17716 | lactose | + | carbon source |
30449 | 17306 | maltose | + | carbon source |
30449 | 37684 | mannose | + | carbon source |
30449 | 28053 | melibiose | + | carbon source |
30449 | 506227 | N-acetylglucosamine | + | carbon source |
30449 | 16634 | raffinose | + | carbon source |
30449 | 26546 | rhamnose | + | carbon source |
30449 | 17814 | salicin | + | carbon source |
30449 | 17992 | sucrose | + | carbon source |
30449 | 27082 | trehalose | + | carbon source |
30449 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30449 | acid phosphatase | + | 3.1.3.2 |
30449 | alkaline phosphatase | + | 3.1.3.1 |
30449 | catalase | + | 1.11.1.6 |
30449 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
30449 | soil | |||
67770 | Soil of a ginseng field in a mountainous region of Chungbuk Province | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_14225.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1456;97_3275;98_4120;99_14225&stattab=map
- Last taxonomy: Pedobacter
- 16S sequence: HM776704
- Sequence Identity:
- Total samples: 7612
- soil counts: 2160
- aquatic counts: 1652
- animal counts: 1898
- plant counts: 1902
Sequence information
16S sequences
- @ref: 30449
- description: Pedobacter ginsengiterrae strain DCY49 16S ribosomal RNA gene, partial sequence
- accession: HM776704
- length: 1410
- database: nuccore
- NCBI tax ID: 871696
GC content
@ref | GC-content | method |
---|---|---|
30449 | 40.5 | |
67770 | 40.5 | high performance liquid chromatography (HPLC) |
External links
@ref: 30449
culture collection no.: KCTC 23317, JCM 17338, DCY 49
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 22771687 | Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field. | Hoang VA, Kim YJ, Nguyen NL, Min JW, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.036376-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis | Genetics |
Phylogeny | 24573158 | Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. | Kook M, Park Y, Yi TH | Int J Syst Evol Microbiol | 10.1099/ijs.0.058024-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pinus/microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
Phylogeny | 35819898 | Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovenbreen, Arctic. | Huang J, Peng X, Qin K, Liu Y, Niu J, Liu J, Dong J, Zhang Y, Peng F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005448 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover, *Pedobacter, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology | Transcriptome |
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 | ||
30449 | 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 | 26784 | 28776041 |
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |