Strain identifier
BacDive ID: 14115
Type strain: 
Species: Pedobacter glucosidilyticus
Strain Designation: 1-2
Strain history: <- KCTC <- X. Luo, CCTCC
NCBI tax ID(s): 540906 (strain), 1122941 (species)
version 9.1 (current version)
General
@ref: 17263
BacDive-ID: 14115
DSM-Number: 23534
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, rod-shaped
description: Pedobacter glucosidilyticus 1-2 is a Gram-negative, rod-shaped bacterium that was isolated from soil.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 540906 | strain |
| 1122941 | species |
strain history
- @ref: 17263
- history: <- KCTC <- X. Luo, CCTCC
doi: 10.13145/bacdive14115.20240916.9.1
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 glucosidilyticus
- full scientific name: Pedobacter glucosidilyticus Luo et al. 2010
@ref: 17263
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter glucosidilyticus
full scientific name: Pedobacter glucosidilyticus Luo et al. 2010 emend. Zhou et al. 2012 emend. Hahnke et al. 2016
strain designation: 1-2
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29180 | negative | 3.1 µm | 0.65 µm | rod-shaped | no | |
| 69480 | negative | 95.371 |
pigmentation
- @ref: 29180
- production: yes
Culture and growth conditions
culture medium
- @ref: 17263
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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 |
|---|---|---|---|
| 17263 | positive | growth | 28 |
| 29180 | positive | growth | 15-37 |
| 29180 | positive | optimum | 30 |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 29180 | positive | growth | 5.5-9 | alkaliphile |
| 29180 | positive | optimum | 7.5 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29180 | no | |
| 69481 | no | 100 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29180 | NaCl | positive | growth | 0-3 % |
| 29180 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29180 | 17057 | cellobiose | + | carbon source |
| 29180 | 23652 | dextrin | + | carbon source |
| 29180 | 28757 | fructose | + | carbon source |
| 29180 | 28260 | galactose | + | carbon source |
| 29180 | 17234 | glucose | + | carbon source |
| 29180 | 17716 | lactose | + | carbon source |
| 29180 | 17306 | maltose | + | carbon source |
| 29180 | 37684 | mannose | + | carbon source |
| 29180 | 506227 | N-acetylglucosamine | + | carbon source |
| 29180 | 51850 | methyl pyruvate | + | carbon source |
| 29180 | 17992 | sucrose | + | carbon source |
| 29180 | 27082 | trehalose | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29180 | catalase | + | 1.11.1.6 |
| 29180 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 17263
- sample type: soil
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_112018.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_3026;97_3717;98_4712;99_112018&stattab=map
- Last taxonomy: Pedobacter
- 16S sequence: EU585748
- Sequence Identity:
- Total samples: 3445
- soil counts: 865
- aquatic counts: 1779
- animal counts: 535
- plant counts: 266
Safety information
risk assessment
- @ref: 17263
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17263
- description: Pedobacter sp. 1-2 16S ribosomal RNA gene, partial sequence
- accession: EU585748
- length: 1386
- database: nuccore
- NCBI tax ID: 540906
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pedobacter glucosidilyticus DSM 23534 | GCA_000425145 | scaffold | ncbi | 540906 |
| 66792 | Pedobacter glucosidilyticus DSM 23534 | 540906.3 | wgs | patric | 540906 |
| 66792 | Pedobacter glucosidilyticus DSM 23534 | 2523533576 | draft | img | 540906 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 29180 | 37.2-37.6 | |
| 17263 | 34.4 | sequence analysis |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 95.371 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.452 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 83.848 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.129 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.162 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86 | yes |
External links
@ref: 17263
culture collection no.: DSM 23534, CCTCC AB 206110, KCTC 22348
straininfo link
- @ref: 83282
- straininfo: 397012
literature
- topic: Phylogeny
- Pubmed-ID: 19648325
- title: Pedobacter glucosidilyticus sp. nov., isolated from dry riverbed soil.
- authors: Luo X, Wang Z, Dai J, Zhang L, Li J, Tang Y, Wang Y, Fang C
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.008060-0
- year: 2009
- mesh: Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 17263 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23534) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23534 | ||||
| 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 | ||||
| 29180 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25604 | 28776041 | ||
| 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) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | ||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
| 83282 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397012.1 | StrainInfo: A central database for resolving microbial strain identifiers |