Strain identifier

BacDive ID: 17141

Type strain: Yes

Species: Pectinatus frisingensis

Strain Designation: V1

Strain history: <- VTT <- A. Haikara, V1

NCBI tax ID(s): 865 (species)

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General

@ref: 2588

BacDive-ID: 17141

DSM-Number: 6306

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

description: Pectinatus frisingensis V1 is an anaerobe, mesophilic bacterium that was isolated from turbid beer.

NCBI tax id

  • NCBI tax id: 865
  • Matching level: species

strain history

  • @ref: 2588
  • history: <- VTT <- A. Haikara, V1

doi: 10.13145/bacdive17141.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Selenomonadales
  • family: Selenomonadaceae
  • genus: Pectinatus
  • species: Pectinatus frisingensis
  • full scientific name: Pectinatus frisingensis Schleifer et al. 1990

@ref: 2588

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Selenomonadaceae

genus: Pectinatus

species: Pectinatus frisingensis

full scientific name: Pectinatus frisingensis Schleifer et al. 1990

strain designation: V1

type strain: yes

Morphology

colony morphology

@refincubation period
25881-2 days
557644 days
557643 days

Culture and growth conditions

culture medium

  • @ref: 2588
  • name: MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/232
  • composition: Name: MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232; with strain-specific modifications) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Lactate 5.0 g/l Yeast extract 5.0 g/l Na-acetate 5.0 g/l K2HPO4 2.0 g/l (NH4)2 citrate 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
2588positivegrowth28mesophilic
55764positivegrowth30mesophilic
55764positivegrowth28-30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2588anaerobe
55764anaerobe

murein

  • @ref: 2588
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

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-
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
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

@refADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNEGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerAURERAF
2588-----+---+----+/-------------
2588----++---+-------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
2588turbid beerFinlandFINEurope
55764Turbid beer

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Engineered#Food production#Beverage

Safety information

risk assessment

  • @ref: 2588
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pectinatus frisingensis strain ATCC33332 16S ribosomal RNA gene, partial sequenceAF3730271498ena865
20218Pectinatus frisingensis strain ATCC 33332 16S ribosomal RNA gene, partial sequenceAY659948472ena865
20218Pectinatus frisingensis partial 16S rRNA gene, strain CCM 6217HF5583841522ena865
20218Pectinatus frisingensis DNA, 16S/23S rRNA intergenic spacer regionAB022063624ena865
20218Pectinatus frisingensis DNA, 16S/23S rRNA intergenic spacer regionAB022064442ena865

Genome sequences

  • @ref: 66792
  • description: Pectinatus frisingensis strain MB174
  • accession: 865.10
  • assembly level: wgs
  • database: patric
  • NCBI tax ID: 865

GC content

@refGC-contentmethod
258839.0thermal denaturation, midpoint method (Tm)
258836.0Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes82.868no
flagellatedno69.872no
gram-positiveno94.609no
anaerobicyes99.589yes
halophileno97.384no
spore-formingno68.457no
glucose-utilyes82.222no
aerobicno98.601yes
thermophileno82.612yes
glucose-fermentyes58.835no

External links

@ref: 2588

culture collection no.: DSM 6306, ATCC 33332, CCM 6217, VTT E-79100, CCUG 43283

straininfo link

  • @ref: 86140
  • straininfo: 44950

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology12846837Structure of the exceptionally large nonrepetitive carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-82164.Vinogradov E, Petersen BO, Sadovskaya I, Jabbouri S, Duus JO, Helander IMEur J Biochem10.1046/j.1432-1033.2003.03682.x2003Acetic Acid/chemistry, Acetylation, Bacteria, Anaerobic/*chemistry/genetics, Carbohydrate Conformation, Carbohydrate Sequence, Electrophoresis, Polyacrylamide Gel/methods, Glycosides/chemistry, Hydrolysis, Lipopolysaccharides/*chemistry, Methylglycosides/isolation & purification, Molecular Sequence Data, Nuclear Magnetic Resonance, BiomolecularGenetics
Phylogeny16585679Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus.Juvonen R, Suihko MLInt J Syst Evol Microbiol10.1099/ijs.0.63699-02006Beer/*microbiology, Megasphaera/*classification/genetics/isolation & purification/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Pectinatus/*classification, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/analysis/geneticsGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2588Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6306)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6306
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
55764Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43283)https://www.ccug.se/strain?id=43283
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)
68380Automatically annotated from API rID32A
86140Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44950.1StrainInfo: A central database for resolving microbial strain identifiers