Strain identifier
BacDive ID: 5249
Type strain: 
Species: Gibbsiella quercinecans
Strain history: S. Denman; For. Res., UK; FRB 97.
NCBI tax ID(s): 929813 (species)
version 8.1 (current version)
General
@ref: 18122
BacDive-ID: 5249
DSM-Number: 25889
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, plant pathogen
description: Gibbsiella quercinecans DSM 25889 is a mesophilic plant pathogen that was isolated from inner bark of Quercus petraea displaying Acute Oak Decline.
NCBI tax id
- NCBI tax id: 929813
- Matching level: species
strain history
| @ref | history |
|---|---|
| 18122 | <- LMG <- S. E. Denman and S. Kirk, Centre for Forestry and Climatic Change, Surrey, United Kingdom |
| 67770 | S. Denman; For. Res., UK; FRB 97. |
doi: 10.13145/bacdive5249.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Enterobacteriaceae
- genus: Gibbsiella
- species: Gibbsiella quercinecans
- full scientific name: Gibbsiella quercinecans Brady et al. 2011
synonyms
- @ref: 20215
- synonym: Gibbsiella acetica
@ref: 18122
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Enterobacteriaceae
genus: Gibbsiella
species: Gibbsiella quercinecans
full scientific name: Gibbsiella quercinecans Brady et al. 2011
type strain: yes
Morphology
multimedia
- @ref: 18122
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25889.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 18122
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 18122 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 18122 | inner bark of Quercus petraea displaying Acute Oak Decline | Quercus petraea | Hoddesdon Park | United Kingdom | GBR | Europe |
| 67770 | Quercus petraea in Hoddesdon Park Wood | Quercus petraea | Hertfordshire | United Kingdom | GBR | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Tree |
| #Host Body-Site | #Plant | #Bark |
taxonmaps
- @ref: 69479
- File name: preview.99_19157.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_2268;97_11785;98_14480;99_19157&stattab=map
- Last taxonomy: Gibbsiella
- 16S sequence: GU562337
- Sequence Identity:
- Total samples: 171
- soil counts: 15
- aquatic counts: 56
- animal counts: 90
- plant counts: 10
Safety information
risk assessment
- @ref: 18122
- pathogenicity plant: yes
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18122
- description: Gibbsiella quercinecans strain FRB 97 16S ribosomal RNA gene, partial sequence
- accession: GU562337
- length: 1396
- database: ena
- NCBI tax ID: 929813
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gibbsiella quercinecans strain DSM 25889 | 929813.12 | wgs | patric | 929813 |
| 66792 | Gibbsiella quercinecans DSM 25889 | 2791354871 | draft | img | 929813 |
| 67770 | Gibbsiella quercinecans FRB97 | GCA_002291425 | complete | ncbi | 929813 |
| 67770 | Gibbsiella quercinecans DSM 25889 | GCA_004342245 | scaffold | ncbi | 929813 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 67.049 | no |
| flagellated | no | 91.577 | no |
| gram-positive | no | 97.464 | no |
| anaerobic | no | 98.664 | no |
| halophile | no | 90.508 | no |
| spore-forming | no | 95.312 | no |
| thermophile | no | 99.367 | no |
| glucose-util | yes | 94.759 | no |
| aerobic | yes | 65.773 | no |
| glucose-ferment | yes | 89.123 | no |
External links
@ref: 18122
culture collection no.: DSM 25889, LMG 25500, NCPPB 4470, FRB 97, JCM 30407
straininfo link
- @ref: 74739
- straininfo: 365336
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21115313 | Description of Gibbsiella quercinecans gen. nov., sp. nov., associated with Acute Oak Decline. | Brady C, Denman S, Kirk S, Venter S, Rodriguez-Palenzuela P, Coutinho T | Syst Appl Microbiol | 10.1016/j.syapm.2010.08.006 | 2010 | Bacterial Proteins/genetics, DNA Gyrase/genetics, Enterobacteriaceae/*classification/genetics, Genes, Bacterial/genetics, Molecular Sequence Data, Phylogeny, Plant Diseases/microbiology, Quercus/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Spain, United Kingdom | Genetics |
| Phylogeny | 23264501 | Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella. | Kim PS, Shin NR, Kim JY, Yun JH, Hyun DW, Bae JW | Int J Syst Evol Microbiol | 10.1099/ijs.0.045880-0 | 2012 | Animals, Bacterial Typing Techniques, Base Composition, Butterflies/*microbiology, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/genetics/isolation & purification, Fatty Acids/analysis, Intestines/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 18122 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25889) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25889 | |||
| 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 | |||
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 74739 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID365336.1 | StrainInfo: A central database for resolving microbial strain identifiers |