Strain identifier
BacDive ID: 132150
Type strain: 
Species: Gilliamella apicola
Strain Designation: wkB1
Strain history: <- NCIMB <- W. Kwong, Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA
NCBI tax ID(s): 1196095 (species)
version 8.1 (current version)
General
@ref: 23940
BacDive-ID: 132150
DSM-Number: 104097
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, motile, rod-shaped
description: Gilliamella apicola wkB1 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from gut of honey bee (Apis mellifera.
NCBI tax id
- NCBI tax id: 1196095
- Matching level: species
strain history
- @ref: 23940
- history: <- NCIMB <- W. Kwong, Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA
doi: 10.13145/bacdive132150.20230509.8.1
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 apicola
- full scientific name: Gilliamella apicola Kwong and Moran 2013
synonyms
- @ref: 20215
- synonym: Gilliamella apicola
@ref: 23940
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Orbales
family: Orbaceae
genus: Gilliamella
species: Gilliamella apicola
full scientific name: Gilliamella apicola Kwong and Moran 2013
strain designation: wkB1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30807 | negative | 1.5 µm | 0.5 µm | rod-shaped | yes | |
| 69480 | negative | 99.619 | ||||
| 69480 | yes | 92.826 |
pigmentation
- @ref: 30807
- production: yes
Culture and growth conditions
culture medium
- @ref: 23940
- 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 |
|---|---|---|---|---|
| 23940 | positive | growth | 37 | mesophilic |
| 30807 | positive | optimum | 37 | mesophilic |
culture pH
- @ref: 30807
- ability: positive
- type: growth
- pH: 6.0-6.5
Physiology and metabolism
oxygen tolerance
- @ref: 30807
- oxygen tolerance: microaerophile
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.971 |
observation
- @ref: 30807
- observation: aggregates in clumps
Isolation, sampling and environmental information
isolation
- @ref: 23940
- sample type: gut of honey bee (Apis mellifera
- host species: Apis mellifera
- geographic location: West Haven
- country: USA
- origin.country: USA
- continent: North America
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Arthropoda | #Insecta |
| #Host Body-Site | #Gastrointestinal tract | #Stomach |
Safety information
risk assessment
- @ref: 23940
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 30807 | Gilliamella apicola strain wkB1 16S ribosomal RNA gene, complete sequence | JQ936674 | 1538 | nuccore | 1196095 |
| 23940 | JQ93674 | ena |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gilliamella apicola wkB1 | GCA_000599985 | complete | ncbi | 1196095 |
| 66792 | Gilliamella apicola DSM 104097 | GCA_003201455 | scaffold | ncbi | 1196095 |
| 66792 | Gilliamella apicola strain DSM 104097 | 1196095.342 | wgs | patric | 1196095 |
| 66792 | Gilliamella apicola wkB1 | 2574179809 | complete | img | 1196095 |
| 66792 | Gilliamella apicola DSM 104097 | 2756170265 | draft | img | 1196095 |
GC content
- @ref: 30807
- GC-content: 33.6
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 68.715 | no |
| flagellated | no | 79.472 | no |
| gram-positive | no | 97.337 | no |
| anaerobic | no | 93.599 | yes |
| halophile | no | 72.406 | no |
| spore-forming | no | 97.351 | no |
| glucose-util | yes | 75.102 | no |
| aerobic | no | 94.243 | no |
| thermophile | no | 97.71 | yes |
| glucose-ferment | yes | 73.15 | no |
External links
@ref: 23940
culture collection no.: DSM 104097, ATCC BAA 2448, NCIMB 14804
straininfo link
- @ref: 90506
- straininfo: 397885
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23041637 | Cultivation and characterization of the gut symbionts of honey bees and bumble bees: description of Snodgrassella alvi gen. nov., sp. nov., a member of the family Neisseriaceae of the Betaproteobacteria, and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov., a sister taxon to the order 'Enterobacteriales' of the Gammaproteobacteria. | Kwong WK, Moran NA | Int J Syst Evol Microbiol | 10.1099/ijs.0.044875-0 | 2012 | Animals, Bacterial Typing Techniques, Base Composition, Bees/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification, Gastrointestinal Tract/*microbiology, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Symbiosis, Ubiquinone/analysis | Enzymology |
| Phylogeny | 28442157 | 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. | Praet J, Cnockaert M, Meeus I, Smagghe G, Vandamme P | Syst Appl Microbiol | 10.1016/j.syapm.2017.03.003 | 2017 | 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 | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | 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 | |||
| 23940 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104097 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104097) | |||
| 30807 | 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 | 27138 | 28776041 | |
| 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 | |||
| 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 | |||
| 90506 | 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-ID397885.1 |