Strain identifier
BacDive ID: 140364
Type strain: 
Species: Gilliamella bombicola
Strain Designation: R-53248
Strain history: <- P. Vandamme, LMU Ghent, Belgium; R-53248
NCBI tax ID(s): 1798182 (species)
version 8.1 (current version)
General
@ref: 42971
BacDive-ID: 140364
DSM-Number: 104085
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Gilliamella bombicola R-53248 is a mesophilic, Gram-negative bacterium that was isolated from bumblebee gut.
NCBI tax id
- NCBI tax id: 1798182
- Matching level: species
strain history
- @ref: 42971
- history: <- P. Vandamme, LMU Ghent, Belgium; R-53248
doi: 10.13145/bacdive140364.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Orbales
- family: Orbaceae
- genus: Gilliamella
- species: Gilliamella bombicola
- full scientific name: Gilliamella bombicola Praet et al. 2017
@ref: 42971
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Orbales
family: Orbaceae
genus: Gilliamella
species: Gilliamella bombicola
full scientific name: Gilliamella bombicola Praet et al. 2017
strain designation: R-53248
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.964
Culture and growth conditions
culture medium
- @ref: 42971
- 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: 42971
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.996 |
Isolation, sampling and environmental information
isolation
- @ref: 42971
- sample type: bumblebee gut
- geographic location: Botanical Garden Ledeganck, Ghent (51.0368°N/3.7221°E)
- country: Belgium
- origin.country: BEL
- continent: Europe
- latitude: 51.0368
- longitude: 3.7221
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Arthropoda | #Insecta |
| #Host Body-Site | #Gastrointestinal tract | #Stomach |
taxonmaps
- @ref: 69479
- File name: preview.99_6702.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_84;96_200;97_217;98_821;99_6702&stattab=map
- Last taxonomy: Gilliamella
- 16S sequence: LT631739
- Sequence Identity:
- Total samples: 556
- soil counts: 2
- aquatic counts: 7
- animal counts: 541
- plant counts: 6
Safety information
risk assessment
- @ref: 42971
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 42971
- description: Gilliamella sp. R-53248 partial 16S rRNA gene, strain LMG 28359, isolate R-53248
- accession: LT631739
- length: 1467
- database: ena
- NCBI tax ID: 1798182
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gilliamella bombicola R-53248 | GCA_900094945 | scaffold | ncbi | 1798182 |
| 66792 | Gilliamella bombicola R-53248 | 2617270739 | draft | img | 1798182 |
GC content
- @ref: 42971
- GC-content: 35.9
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 66.648 | no |
| flagellated | no | 82.469 | no |
| gram-positive | no | 97.933 | no |
| anaerobic | no | 92.779 | no |
| aerobic | no | 93.886 | no |
| halophile | no | 66.829 | no |
| spore-forming | no | 97.751 | no |
| glucose-ferment | yes | 66.865 | no |
| thermophile | no | 99.34 | yes |
| glucose-util | yes | 72.162 | no |
External links
@ref: 42971
culture collection no.: DSM 104085, LMG 28359
straininfo link
- @ref: 96662
- straininfo: 401660
literature
- topic: Phylogeny
- Pubmed-ID: 28442157
- title: Gilliamella intestini sp. nov., Gilliamella bombicola sp. nov., Gilliamella bombi sp. nov. and Gilliamella mensalis sp. nov.: Four novel Gilliamella species isolated from the bumblebee gut.
- authors: Praet J, Cnockaert M, Meeus I, Smagghe G, Vandamme P
- journal: Syst Appl Microbiol
- DOI: 10.1016/j.syapm.2017.03.003
- year: 2017
- mesh: Animals, Bacterial Typing Techniques, Base Composition, Base Sequence, Bees, DNA, Bacterial/genetics, Fatty Acids/analysis, *Gammaproteobacteria/classification/genetics/isolation & purification, Gastrointestinal Tract/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | catalogue | journal | 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 | |||
| 42971 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104085 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104085) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 96662 | 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-ID401660.1 |