Strain identifier
BacDive ID: 130136
Type strain: 
Species: Bombella intestini
Strain Designation: R-52487
Strain history: <- P. Vandamme, Univ. Ghent, Belgium; R-52487 <- L. Li
NCBI tax ID(s): 1539051 (species)
version 8.1 (current version)
General
@ref: 22131
BacDive-ID: 130136
DSM-Number: 28636
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Bombella intestini R-52487 is a mesophilic, Gram-negative bacterium that was isolated from crop of a bumblebee Bombus lapidarius.
NCBI tax id
- NCBI tax id: 1539051
- Matching level: species
strain history
- @ref: 22131
- history: <- P. Vandamme, Univ. Ghent, Belgium; R-52487 <- L. Li
doi: 10.13145/bacdive130136.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Acetobacteraceae
- genus: Bombella
- species: Bombella intestini
- full scientific name: Bombella intestini Li et al. 2015
@ref: 22131
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Acetobacteraceae
genus: Bombella
species: Bombella intestini
full scientific name: Bombella intestini Li et al. 2015
strain designation: R-52487
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.999
Culture and growth conditions
culture medium
- @ref: 22131
- name: GY-MEDIUM (DSMZ Medium 1543)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1543
- composition: Name: GY - MEDIUM (DSMZ Medium 1543) Composition: Glucose 50.0 g/l Agar 15.0 g/l Yeast extract 10.0 g/l Distilled water
culture temp
- @ref: 22131
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.998 |
Isolation, sampling and environmental information
isolation
- @ref: 22131
- sample type: crop of a bumblebee Bombus lapidarius
- host species: Bombus lapidarius
- geographic location: Ghent
- country: Belgium
- origin.country: BEL
- continent: Europe
isolation source categories
- Cat1: #Host
- Cat2: #Arthropoda
- Cat3: #Insecta
taxonmaps
- @ref: 69479
- File name: preview.99_2943.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_1552;97_1851;98_2273;99_2943&stattab=map
- Last taxonomy: Acetobacteraceae
- 16S sequence: KJ584313
- Sequence Identity:
- Total samples: 2563
- soil counts: 705
- aquatic counts: 372
- animal counts: 1381
- plant counts: 105
Safety information
risk assessment
- @ref: 22131
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22131
- description: Bombella intestini strain R-52487 16S ribosomal RNA gene, partial sequence
- accession: KJ584313
- length: 1450
- database: ena
- NCBI tax ID: 1539051
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Bombella intestini R-52487 | GCA_002003665 | contig | ncbi | 1539051 |
| 66792 | Bombella intestini strain R-52487 | 1539051.3 | wgs | patric | 1539051 |
| 66792 | Bombella intestini R-52487 | 2791354941 | draft | img | 1539051 |
GC content
- @ref: 22131
- GC-content: 54.9
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 68.17 | no |
| gram-positive | no | 98.431 | no |
| anaerobic | no | 98.577 | no |
| aerobic | yes | 52.141 | no |
| halophile | no | 81.112 | no |
| spore-forming | no | 96.303 | no |
| thermophile | no | 90.569 | yes |
| glucose-util | yes | 71.943 | no |
| flagellated | no | 84.174 | no |
| glucose-ferment | no | 80.7 | no |
External links
@ref: 22131
culture collection no.: DSM 28636, LMG 28161
straininfo link
- @ref: 88690
- straininfo: 404319
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25336723 | Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop. | Li L, Praet J, Borremans W, Nunes OC, Manaia CM, Cleenwerck I, Meeus I, Smagghe G, De Vuyst L, Vandamme P | Int J Syst Evol Microbiol | 10.1099/ijs.0.068049-0 | 2014 | Acetic Acid, Acetobacteraceae/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Bees/*microbiology, Belgium, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Genetics |
| Metabolism | 27851750 | Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius. | Li L, Illeghems K, Van Kerrebroeck S, Borremans W, Cleenwerck I, Smagghe G, De Vuyst L, Vandamme P | PLoS One | 10.1371/journal.pone.0165611 | 2016 | Acetic Acid/*metabolism, Animal Structures/*microbiology, Animals, Bacteria/drug effects/*genetics/growth & development/*isolation & purification, Bacterial Proteins/genetics/metabolism, Bees/*microbiology, Carbohydrate Metabolism, Cell Membrane/metabolism, Electron Transport, *Genome, Bacterial, Glucose/pharmacology, Metabolic Networks and Pathways, Metabolome/drug effects, Open Reading Frames/genetics, Sequence Analysis, DNA/*methods, Symbiosis/genetics | Genetics |
| Phylogeny | 28671528 | Bombella apis sp. nov., an acetic acid bacterium isolated from the midgut of a honey bee. | Yun JH, Lee JY, Hyun DW, Jung MJ, Bae JW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001921 | 2017 | Acetic Acid, Acetobacteraceae/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Bees/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phosphatidylethanolamines, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | 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 | |
| 22131 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28636 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28636) | |
| 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 | |
| 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 | |
| 88690 | 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-ID404319.1 |