Strain identifier

BacDive ID: 3061

Type strain: No

Species: Olsenella umbonata

Strain Designation: A2

Strain history: M. Kraatz A2 <-- J. R. Wallace.

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General

@ref: 16368

BacDive-ID: 3061

DSM-Number: 22619

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic

description: Olsenella umbonata A2 is an obligate anaerobe, mesophilic bacterium that was isolated from ruminal fluid of a rumen-fistulated sheep.

strain history

@refhistory
16368<- M. Kraatz, Faculty Vet. Med., Free Univ. Berlin, Germany; A2 <- J. R. Wallace
67770M. Kraatz A2 <-- J. R. Wallace.

doi: 10.13145/bacdive3061.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Coriobacteriales
  • family: Atopobiaceae
  • genus: Olsenella
  • species: Olsenella umbonata
  • full scientific name: Olsenella umbonata Kraatz et al. 2011

  • synonyms

    • @ref: 20215
    • synonym: Parafannyhessea umbonata

@ref: 16368

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Atopobiaceae

genus: Olsenella

species: Olsenella umbonata

full scientific name: Olsenella umbonata Kraatz et al. 2011 emend. Nouioui et al. 2018

strain designation: A2

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.206
6948099.999positive

colony morphology

  • @ref: 61631
  • incubation period: 1-4 days

Culture and growth conditions

culture medium

  • @ref: 16368
  • 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

@refgrowthtypetemperaturerange
16368positivegrowth37mesophilic
61631positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16368obligate anaerobe
61631anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no97
69480no99.989

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine+hydrolysis
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
16368-+---+----+/-------+-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16368ruminal fluid of a rumen-fistulated sheepScotland, Aberdeen, Rowett Research InstituteUnited KingdomGBREurope
61631Sheep ruminal fluid,rumenfistulated sheepScotland,Aberdeen,Rowett Research InsUnited KingdomGBREurope2004-07-01
67770Ruminal fluid of a sheepAberdeenUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body-Site#Organ#Rumen
#Host Body Product#Fluids#Rumen fluid

taxonmaps

  • @ref: 69479
  • File name: preview.99_27321.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_150;96_1373;97_3530;98_4466;99_27321&stattab=map
  • Last taxonomy: Olsenella umbonata subclade
  • 16S sequence: AJ251324
  • Sequence Identity:
  • Total samples: 14191
  • soil counts: 512
  • aquatic counts: 902
  • animal counts: 12522
  • plant counts: 255

Safety information

risk assessment

  • @ref: 16368
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16368
  • description: Olsenella umbonata partial 16S rRNA gene, strain A2
  • accession: AJ251324
  • length: 1433
  • database: ena
  • NCBI tax ID: 604330

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Olsenella umbonata strain DSM 22619604330.4wgspatric604330
66792Parafannyhessea umbonata DSM 226192606217797draftimg604330
67770Parafannyhessea umbonata DSM 22619GCA_900101655contigncbi604330

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
gram-positiveyes93.806no
anaerobicyes99.048yes
halophileno84.033no
spore-formingno94.632no
glucose-utilyes86.017no
thermophileno91.166yes
flagellatedno97.017no
aerobicno97.252no
motileno89.266no
glucose-fermentyes78.891no

External links

@ref: 16368

culture collection no.: DSM 22619, CCUG 58212, JCM 16157

straininfo link

  • @ref: 72581
  • straininfo: 402570

literature

  • topic: Phylogeny
  • Pubmed-ID: 20435744
  • title: Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa.
  • authors: Kraatz M, Wallace RJ, Svensson L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.022954-0
  • year: 2010
  • mesh: Actinobacteria/*classification/genetics/*isolation & purification/physiology, Anaerobiosis, Animals, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Jejunum/*microbiology, Lactic Acid/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNA, Sheep/*microbiology, Swine/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
16368Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22619)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22619
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
61631Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58212)https://www.ccug.se/strain?id=58212
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
72581Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402570.1StrainInfo: A central database for resolving microbial strain identifiers