Strain identifier

BacDive ID: 3062

Type strain: Yes

Species: Olsenella umbonata

Strain Designation: lac31

Strain history: <- CCUG <- Mareike Kraatz, Faculty Vet. Med., Free Univ.(FUB), Berlin, Germany, lac31

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General

@ref: 16369

BacDive-ID: 3062

DSM-Number: 22620

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic, rod-shaped

description: Olsenella umbonata lac31 is an obligate anaerobe, mesophilic, rod-shaped bacterium that was isolated from jejunal mucosa of a domestic pig.

strain history

@refhistory
16369<- M. Kraatz, Faculty Vet. Med., Free Univ. Berlin, Germany; lac31
67770M. Kraatz lac31.
67771<- CCUG <- Mareike Kraatz, Faculty Vet. Med., Free Univ.(FUB), Berlin, Germany, lac31

doi: 10.13145/bacdive3062.20230509.8.1

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: 16369

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: lac31

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771rod-shapedno
67771positive
69480no95.858
69480positive100

colony morphology

  • @ref: 61724
  • incubation period: 2 days

Culture and growth conditions

culture medium

  • @ref: 16369
  • 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
16369positivegrowth37mesophilic
61724positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16369obligate anaerobe
61724anaerobe
67771anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
67771no
69481no100
69480no99.987

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
16369-+---+----------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16369jejunal mucosa of a domestic pigBerlin-Dahlem, Institute of Animal NutritionGermanyDEUEurope
61724Pig jejunal mucosa,healthy 62-day old animalBerlinGermanyDEUEurope2006-12-25
67770Mucosal jejunum of a pigBerlinGermanyDEUEurope
67771From the mucosal jejunum of a pig, healthy 62 day old animalInstitute of Animal Nutrition, Berlin-DahlemGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body-Site#Gastrointestinal tract#Small intestine

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: LC519857
  • Sequence Identity:
  • Total samples: 14191
  • soil counts: 512
  • aquatic counts: 902
  • animal counts: 12522
  • plant counts: 255

Safety information

risk assessment

  • @ref: 16369
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16369Olsenella umbonata partial 16S rRNA gene, type strain lac31TFN1784631428ena604330
67771Olsenella umbonata JCM 16156 gene for 16S rRNA, partial sequenceLC5198571456ena604330

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parafannyhessea umbonata DSM 22620GCA_900105025chromosomencbi604330
66792Olsenella umbonata strain DSM 22620604330.5completepatric604330
66792Parafannyhessea umbonata DSM 226202636416177draftimg604330

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes94.063yes
anaerobicyes99.12yes
halophileno87.455no
spore-formingno94.937yes
glucose-utilyes85.65no
thermophileno89.09yes
flagellatedno97.42yes
aerobicno97.248yes
motileno91.327no
glucose-fermentyes73.942no

External links

@ref: 16369

culture collection no.: DSM 22620, CCUG 58604, JCM 16156, KCTC 15140

straininfo link

  • @ref: 72582
  • straininfo: 405938

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20435744Olsenella 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.Kraatz M, Wallace RJ, Svensson LInt J Syst Evol Microbiol10.1099/ijs.0.022954-02010Actinobacteria/*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/*microbiologyGenetics
Phylogeny25634945Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces.Li X, Jensen RL, Hojberg O, Canibe N, Jensen BBInt J Syst Evol Microbiol10.1099/ijs.0.0000832015Actinobacteria/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Cresols/*metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Fermentation, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Skatole/*metabolism, Sus scrofa/*microbiologyMetabolism
Phylogeny29458507Parolsenella catena gen. nov., sp. nov., isolated from human faeces.Sakamoto M, Iino T, Hamada M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0026452018Actinobacteria/*classification/genetics/isolation & purification, Adult, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Humans, Japan, Male, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny31135332Olsenella faecalis sp. nov., an anaerobic actinobacterium isolated from human faeces.Han KI, Lee KC, Eom MK, Kim JS, Suh MK, Park SH, Lee JH, Kang SW, Park JE, Oh BS, Yu SY, Choi SH, Lee DH, Yoon H, Kim BY, Yang SJ, Lee JSInt J Syst Evol Microbiol10.1099/ijsem.0.0034692019Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, Glycolipids/chemistry, Humans, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNAPathogenicity
Phylogeny34914571Reclassification of Olsenella gallinarum as Thermophilibacter gallinarum comb. nov. and description of Thermophilibacter immobilis sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese Luzhou-flavour Baijiu.Lu LF, Yang Y, Zheng L, Zhang R, Liu GQ, Tu TY, Xu T, Luo X, Ran MF, Zhang LQ, Wang ST, Shen CH, Zhang YGInt J Syst Evol Microbiol10.1099/ijsem.0.0051922021Actinobacteria/*classification/isolation & purification, Alcoholic Beverages, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Fermentation, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny36288087Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae.Morinaga K, Kusada H, Sakamoto S, Murakami T, Toyoda A, Mori H, Meng XY, Takashino M, Murotomi K, Tamaki HInt J Syst Evol Microbiol10.1099/ijsem.0.0055962022Animals, Mice, RNA, Ribosomal, 16S/genetics, Phylogeny, Base Composition, DNA, Bacterial/genetics, Bacterial Typing Techniques, *Lactic Acid, *Peptones, Sequence Analysis, DNA, Fatty Acids/chemistry, Hydrogen, Formates, Butyrates, Glucose, IntestinesTranscriptome

Reference

@idauthorscataloguedoi/urltitle
16369Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22620)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22620
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
61724Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58604)https://www.ccug.se/strain?id=58604
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
72582Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405938.1StrainInfo: A central database for resolving microbial strain identifiers