Strain identifier
BacDive ID: 22996
Type strain: 
Species: Budvicia diplopodorum
Strain Designation: D9
Strain history: <- B. A. Knapp, Inst. Microbiology, Univ. Innsbruck, Austria; D9
NCBI tax ID(s): 1119056 (species)
version 8.1 (current version)
General
@ref: 19199
BacDive-ID: 22996
DSM-Number: 21983
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Budvicia diplopodorum D9 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from Gut of Cylindroiulus fulviceps .
NCBI tax id
- NCBI tax id: 1119056
- Matching level: species
strain history
- @ref: 19199
- history: <- B. A. Knapp, Inst. Microbiology, Univ. Innsbruck, Austria; D9
doi: 10.13145/bacdive22996.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Budviciaceae
- genus: Budvicia
- species: Budvicia diplopodorum
- full scientific name: Budvicia diplopodorum Lang et al. 2013
@ref: 19199
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Budviciaceae
genus: Budvicia
species: Budvicia diplopodorum
full scientific name: Budvicia diplopodorum Lang et al. 2013
strain designation: D9
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30467 | negative | 2.75 µm | 0.8 µm | rod-shaped | yes | |
| 69480 | negative | 99.91 |
Culture and growth conditions
culture medium
- @ref: 19199
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 19199 | positive | growth | 28 | mesophilic |
| 30467 | positive | growth | 04-34 | |
| 30467 | positive | optimum | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 30467
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30467 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.593 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30467 | NaCl | positive | growth | 0-1 % |
| 30467 | NaCl | positive | optimum | 1 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30467 | 16947 | citrate | + | carbon source |
| 30467 | 24265 | gluconate | + | carbon source |
| 30467 | 25115 | malate | + | carbon source |
| 30467 | 29864 | mannitol | + | carbon source |
| 30467 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 30467
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
- @ref: 30467
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 19199
- sample type: Gut of Cylindroiulus fulviceps (Diplopoda)
- host species: Cylindroiulus fulviceps
- geographic location: Tyrol, Kaserstatt Alm, 2000 m above sea-level
- country: Austria
- origin.country: AUT
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Arthropoda | #Insecta |
| #Host Body-Site | #Gastrointestinal tract | #Stomach |
Safety information
risk assessment
- @ref: 19199
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19199
- description: Budvicia diplopodorum partial 16S rRNA gene, type strain DSM 21983T
- accession: HE574451
- length: 1536
- database: ena
- NCBI tax ID: 1119056
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Budvicia diplopodorum D9 | GCA_009800925 | contig | ncbi | 1119056 |
| 66792 | Budvicia diplopodorum strain D9 | 1119056.3 | wgs | patric | 1119056 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 19199 | 48.3 | high performance liquid chromatography (HPLC) |
| 30467 | 48.3 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 57.932 | yes |
| flagellated | no | 93.639 | no |
| gram-positive | no | 97.733 | yes |
| anaerobic | no | 94.934 | yes |
| aerobic | no | 72.383 | yes |
| halophile | no | 94.555 | yes |
| spore-forming | no | 95.282 | no |
| thermophile | no | 99.565 | yes |
| glucose-util | yes | 87.765 | no |
| glucose-ferment | yes | 83.026 | no |
External links
@ref: 19199
culture collection no.: DSM 21983, CCM 7845
straininfo link
- @ref: 87242
- straininfo: 402483
literature
- topic: Phylogeny
- Pubmed-ID: 22407790
- title: Budvicia diplopodorum sp. nov. and emended description of the genus Budvicia.
- authors: Lang E, Schumann P, Knapp BA, Kumar R, Sproer C, Insam H
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.036749-0
- year: 2012
- mesh: Animals, Arthropods/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/genetics/isolation & purification, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 19199 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21983) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21983 | |||
| 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 | |||
| 30467 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26802 | 28776041 | |
| 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) | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 87242 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID402483.1 | StrainInfo: A central database for resolving microbial strain identifiers |