Strain identifier
BacDive ID: 1768
Type strain:
Species: Bombiscardovia coagulans
Strain Designation: BLAPIII-AGV
Strain history: <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; BLAPIII-AGV
NCBI tax ID(s): 686666 (species)
General
@ref: 16621
BacDive-ID: 1768
DSM-Number: 22924
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Bombiscardovia coagulans BLAPIII-AGV is an anaerobe, mesophilic bacterium that was isolated from bumblebee digestive tract.
NCBI tax id
- NCBI tax id: 686666
- Matching level: species
strain history
- @ref: 16621
- history: <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; BLAPIII-AGV
doi: 10.13145/bacdive1768.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Bifidobacteriales
- family: Bifidobacteriaceae
- genus: Bombiscardovia
- species: Bombiscardovia coagulans
- full scientific name: Bombiscardovia coagulans Killer et al. 2014
@ref: 16621
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Bifidobacteriales
family: Bifidobacteriaceae
genus: Bombiscardovia
species: Bombiscardovia coagulans
full scientific name: Bombiscardovia coagulans Killer et al. 2014
strain designation: BLAPIII-AGV
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 92.096 | |
69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 16621
- name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104
- composition: Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
culture temp
- @ref: 16621
- growth: positive
- type: growth
- temperature: 37
- range: mesophilic
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
16621 | anaerobe | |
69480 | anaerobe | 99.48 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | + | fermentation |
68380 | 29985 | L-glutamate | + | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | + | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | + | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | + | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | phenylalanine arylamidase | + | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | L-arginine arylamidase | + | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | + | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | + | 3.2.1.55 |
68380 | beta-glucosidase | + | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16621 | - | - | + | + | - | + | + | + | - | - | - | + | + | - | - | - | - | + | + | - | + | + | - | + | - | - | + | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 16621
- sample type: bumblebee digestive tract
- country: Czech Republic
- origin.country: CZE
- continent: Europe
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Arthropoda | #Insecta |
#Host Body-Site | #Gastrointestinal tract |
taxonmaps
- @ref: 69479
- File name: preview.99_43127.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_19938;97_24746;98_31327;99_43127&stattab=map
- Last taxonomy: Bombiscardovia coagulans subclade
- 16S sequence: EU127550
- Sequence Identity:
- Total samples: 327
- soil counts: 7
- aquatic counts: 8
- animal counts: 311
- plant counts: 1
Safety information
risk assessment
- @ref: 16621
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16621
- description: Bombiscardovia coagulans strain BLAPIII-AGV 16S ribosomal RNA gene, partial sequence
- accession: EU127550
- length: 1420
- database: ena
- NCBI tax ID: 686666
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bombiscardovia coagulans DSM 22924 | GCA_002259585 | contig | ncbi | 686666 |
66792 | Bombiscardovia coagulans strain DSM 22924 | 686666.4 | wgs | patric | 686666 |
66792 | Bombiscardovia coagulans DSM 22924 | 2788500098 | draft | img | 686666 |
GC content
- @ref: 16621
- GC-content: 46.6
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 90.471 | no |
anaerobic | yes | 95.838 | yes |
halophile | yes | 51.608 | no |
spore-forming | no | 94.643 | no |
glucose-util | yes | 89.226 | no |
thermophile | no | 92.796 | yes |
flagellated | no | 97.322 | no |
motile | no | 94.432 | no |
aerobic | no | 96.856 | yes |
glucose-ferment | yes | 72.299 | no |
External links
@ref: 16621
culture collection no.: DSM 22924, ATCC BAA 1568
straininfo link
- @ref: 71415
- straininfo: 407803
literature
- topic: Phylogeny
- Pubmed-ID: 20950979
- title: Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees.
- authors: Killer J, Kopecny J, Mrazek J, Havlik J, Koppova I, Benada O, Rada V, Kofronova O
- journal: Syst Appl Microbiol
- DOI: 10.1016/j.syapm.2010.08.002
- year: 2010
- mesh: *Actinobacteria/classification/genetics/isolation & purification, Aldehyde-Lyases/metabolism, Animals, *Bacterial Typing Techniques, Base Composition/genetics, Base Sequence, Bees/*microbiology, Chaperonin 60/genetics, Cold Temperature, DNA, Bacterial/analysis/genetics, Fatty Acids/analysis/chemistry, Gastrointestinal Tract/microbiology, Lipids/chemistry, Molecular Sequence Data, Peptidoglycan/genetics, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16621 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22924) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22924 | |||
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 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68380 | Automatically annotated from API rID32A | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
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 | |||
71415 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407803.1 | StrainInfo: A central database for resolving microbial strain identifiers |