Strain identifier

BacDive ID: 17137

Type strain: Yes

Species: Pectinatus cerevisiiphilus

Strain history: <- S.Y. Lee, CCC B-1022

NCBI tax ID(s): 86956 (species)

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General

@ref: 8838

BacDive-ID: 17137

DSM-Number: 20467

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative

description: Pectinatus cerevisiiphilus DSM 20467 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from beer.

NCBI tax id

  • NCBI tax id: 86956
  • Matching level: species

strain history

  • @ref: 8838
  • history: <- S.Y. Lee, CCC B-1022

doi: 10.13145/bacdive17137.20230509.8.1

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 cerevisiiphilus
  • full scientific name: Pectinatus cerevisiiphilus Lee et al. 1978 (Approved Lists 1980)

@ref: 8838

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Selenomonadaceae

genus: Pectinatus

species: Pectinatus cerevisiiphilus

full scientific name: Pectinatus cerevisiiphilus Lee et al. 1978 emend. Schleifer et al. 1990

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.987

colony morphology

  • @ref: 8838
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 8838
  • name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/58
  • composition: Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

culture temp

  • @ref: 8838
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8838anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
69481no100
69480no99.683

murein

  • @ref: 8838
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

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
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
8838--++--+---+------------------
8838--++--+/----+/-------------------

Isolation, sampling and environmental information

isolation

  • @ref: 8838
  • sample type: beer

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Beverage
#Engineered#Food production#Fermented
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8905.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16010;96_4179;97_5115;98_6510;99_8905&stattab=map
  • Last taxonomy: Pectinatus cerevisiiphilus subclade
  • 16S sequence: FR870446
  • Sequence Identity:
  • Total samples: 2305
  • soil counts: 36
  • aquatic counts: 284
  • animal counts: 1978
  • plant counts: 7

Safety information

risk assessment

  • @ref: 8838
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pectinatus cerevisiiphilus DNA, 16S/23S rRNA intergenic spacer regionAB022061724ena86956
20218Pectinatus cerevisiiphilus DNA, 16S/23S rRNA intergenic spacer regionAB022062399ena86956
20218Pectinatus cerevisiiphilus strain ATCC29359 16S ribosomal RNA gene, partial sequenceAF3730261498ena86956
20218Pectinatus cerevisiiphilus strain ATCC 29359 16S ribosomal RNA gene, partial sequenceAY659945472ena86956
8838Pectinatus cerevisiiphilus partial 16S rRNA gene, type strain CECT 4927TFR8704461547ena86956

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pectinatus cerevisiiphilus DSM 20467GCA_004341685contigncbi86956
66792Pectinatus cerevisiiphilus strain DSM 2046786956.3wgspatric86956
66792Pectinatus cerevisiiphilus strain MB13486956.4wgspatric86956
66792Pectinatus cerevisiiphilus DSM 204672784746786draftimg86956

GC content

  • @ref: 8838
  • GC-content: 39.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes80.612no
flagellatedno76.454no
gram-positiveno94.025no
anaerobicyes99.312yes
halophileno95.913no
spore-formingno86.225no
thermophileno83.213yes
glucose-utilyes85.674no
aerobicno97.72no
glucose-fermentyes53.742no

External links

@ref: 8838

culture collection no.: DSM 20467, ATCC 29359, CCC B-1022

straininfo link

  • @ref: 86136
  • straininfo: 39490

literature

  • topic: Phylogeny
  • Pubmed-ID: 16585679
  • title: Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus.
  • authors: Juvonen R, Suihko ML
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63699-0
  • year: 2006
  • mesh: Beer/*microbiology, Megasphaera/*classification/genetics/isolation & purification/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Pectinatus/*classification, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/analysis/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8838Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20467)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20467
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
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
86136Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39490.1StrainInfo: A central database for resolving microbial strain identifiers