Strain identifier

BacDive ID: 1768

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refmotilityconfidencegram stain
69480no92.096
69480100positive

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

@refoxygen toleranceconfidence
16621anaerobe
69480anaerobe99.48

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose+fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan-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

@refvalueactivityec
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase+4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
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

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bombiscardovia coagulans DSM 22924GCA_002259585contigncbi686666
66792Bombiscardovia coagulans strain DSM 22924686666.4wgspatric686666
66792Bombiscardovia coagulans DSM 229242788500098draftimg686666

GC content

  • @ref: 16621
  • GC-content: 46.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes90.471no
anaerobicyes95.838yes
halophileyes51.608no
spore-formingno94.643no
glucose-utilyes89.226no
thermophileno92.796yes
flagellatedno97.322no
motileno94.432no
aerobicno96.856yes
glucose-fermentyes72.299no

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

@idauthorscataloguedoi/urltitlejournalpubmed
16621Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22924)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22924
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68380Automatically annotated from API rID32A
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71415Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407803.1StrainInfo: A central database for resolving microbial strain identifiers