Strain identifier
BacDive ID: 132915
Type strain: 
Species: Snodgrassella alvi
Strain Designation: wkB2
Strain history: <- NCIMB <- W. K. Kwong, Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA; wkB2
NCBI tax ID(s): 1196083 (species)
version 8.1 (current version)
General
@ref: 24703
BacDive-ID: 132915
DSM-Number: 104735
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, rod-shaped
description: Snodgrassella alvi wkB2 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from gut of honey bee Apis mellifera, adult worker bees from lab-raised hives.
NCBI tax id
- NCBI tax id: 1196083
- Matching level: species
strain history
- @ref: 24703
- history: <- NCIMB <- W. K. Kwong, Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA; wkB2
doi: 10.13145/bacdive132915.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Neisseriales
- family: Neisseriaceae
- genus: Snodgrassella
- species: Snodgrassella alvi
- full scientific name: Snodgrassella alvi Kwong and Moran 2013
synonyms
- @ref: 20215
- synonym: Snodgrassella alvi
@ref: 24703
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Neisseriales
family: Neisseriaceae
genus: Snodgrassella
species: Snodgrassella alvi
full scientific name: Snodgrassella alvi Kwong and Moran 2013
strain designation: wkB2
type strain: yes
Morphology
cell morphology
- @ref: 30807
- gram stain: negative
- cell length: 1 µm
- cell width: 0.4 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 30807
- production: yes
multimedia
- @ref: 24703
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_104735.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 24703 | BHI MEDIUM (DSMZ Medium 215) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium215.pdf | |
| 24703 | COLUMBIA BLOOD AGAR (DSMZ Medium 429) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium429.pdf | |
| 24703 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | 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 |
|---|---|---|---|---|
| 24703 | positive | growth | 37 | mesophilic |
| 30807 | positive | optimum | 37 | mesophilic |
culture pH
- @ref: 30807
- ability: positive
- type: growth
- pH: 6-6.5
Physiology and metabolism
oxygen tolerance
- @ref: 30807
- oxygen tolerance: microaerophile
observation
- @ref: 30807
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30807 | 16947 | citrate | + | carbon source |
| 30807 | 25115 | malate | + | carbon source |
| 30807 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30807 | catalase | + | 1.11.1.6 |
| 30807 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 24703
- sample type: gut of honey bee Apis mellifera, adult worker bees from lab-raised hives
- host species: Apis mellifera
- geographic location: West Haven, Connecticut
- 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: 24703
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 30807 | Snodgrassella alvi strain wkB12 16S ribosomal RNA gene, complete sequence | JQ746645 | 1547 | nuccore | 1196083 |
| 24703 | Snodgrassella alvi strain wkB2 16S ribosomal RNA gene, complete sequence | JQ746650 | 1548 | ena | 1196094 |
| 24703 | Snodgrassella alvi strain wkB2 16S ribosomal RNA gene, complete sequence | JQ746651 | 1547 | ena | 1196094 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Snodgrassella alvi wkB2 | GCA_000600005 | complete | ncbi | 1196094 |
| 66792 | Snodgrassella alvi wkB2 | 1196094.4 | complete | patric | 1196094 |
| 66792 | Snodgrassella alvi wkB2 | 2585428136 | complete | img | 1196094 |
| 66792 | Snodgrassella alvi wkB2 | GCA_022870965 | complete | ncbi | 1196094 |
GC content
- @ref: 30807
- GC-content: 41.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 92.462 | no |
| flagellated | no | 96.383 | yes |
| gram-positive | no | 98.46 | yes |
| anaerobic | no | 98.021 | yes |
| halophile | no | 65.16 | no |
| spore-forming | no | 98.028 | no |
| glucose-util | no | 50 | no |
| aerobic | no | 89.018 | no |
| thermophile | no | 99.318 | yes |
| glucose-ferment | no | 77.588 | no |
External links
@ref: 24703
culture collection no.: DSM 104735, ATCC BAA 2449, NCIMB 14803, NRRL B-59751
straininfo link
- @ref: 91193
- straininfo: 407413
literature
- topic: Phylogeny
- Pubmed-ID: 23041637
- title: 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.
- authors: Kwong WK, Moran NA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.044875-0
- year: 2012
- mesh: 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
- topic2: Enzymology
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 | |||
| 24703 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-104735 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104735) | |||
| 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 | |||
| 91193 | 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-ID407413.1 |