Strain identifier

BacDive ID: 6384

Type strain: Yes

Species: Pediococcus damnosus

Strain Designation: Be1, Be.1

Strain history: CIP <- 1986, NCFB <- Queen Elizabeth College, London, UK <- D.H. Williamson, Brewing Res. Trust., UK: strain Be.1

NCBI tax ID(s): 51663 (species)

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

@ref: 8722

BacDive-ID: 6384

DSM-Number: 20331

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped

description: Pediococcus damnosus Be1 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from lager beer yeast.

NCBI tax id

  • NCBI tax id: 51663
  • Matching level: species

strain history

@refhistory
8722<- NCDO <- E. Coster, Be1 <- D.H. Williamson
67770ATCC 29358 <-- NCDO 1832 <-- Q. E. C. Univ. London <-- D. H. Williamson.
118851CIP <- 1986, NCFB <- Queen Elizabeth College, London, UK <- D.H. Williamson, Brewing Res. Trust., UK: strain Be.1

doi: 10.13145/bacdive6384.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Pediococcus
  • species: Pediococcus damnosus
  • full scientific name: Pediococcus damnosus Claussen 1903 (Approved Lists 1980)

@ref: 8722

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Pediococcus

species: Pediococcus damnosus

full scientific name: Pediococcus damnosus Claussen 1903

strain designation: Be1, Be.1

type strain: yes

Morphology

cell morphology

  • @ref: 118851
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8722PEDIOCOCCUS DAMNOSUS MEDIUM (DSMZ Medium 231)yeshttps://mediadive.dsmz.de/medium/231Name: PEDIOCOCCUS DAMNOSUS MEDIUM (DSMZ Medium 231) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Yeast extract 5.0 g/l Na-acetate 5.0 g/l K2HPO4 2.0 g/l (NH4)3 citrate 2.0 g/l Tween 80 1.0 g/l Cysteine hydrochloride 0.5 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
41846MEDIUM 43 - for Lactobacillus hamsteri and Lactobacillus ruminisyesDistilled water make up to (900.000 ml);Man Rogosa Sharp broth (55.000 g);Cysteine hydrochloride 5 % solution - M0172 (100.000 ml)
118851CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperaturerange
8722positivegrowth26mesophilic
41846positivegrowth25mesophilic
50930positivegrowth30mesophilic
67770positivegrowth26mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8722microaerophile
50930anaerobe

murein

  • @ref: 8722
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118851nitrate+reduction17632
118851nitrite-reduction16301

metabolite production

  • @ref: 118851
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
118851oxidase-
118851catalase-1.11.1.6
118851urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118851-++--------+---++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8722----------++++---------+++++----+------+----------
8722----------++++---------+++++----+------+----------
8722----------++++---------+++++----+------+----------
8722----------++++---------+++++----+------+----------
8722----------++++---------+/--+++----+/-------+----------
8722----------++++---------+++++----+------+----------

Isolation, sampling and environmental information

isolation

@refsample type
8722lager beer yeast
50930Lager beer yeast
67770Lager beer yeast
118851Food, Lager beer yeast

isolation source categories

  • Cat1: #Host
  • Cat2: #Yeast

taxonmaps

  • @ref: 69479
  • File name: preview.99_218.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_156;97_167;98_186;99_218&stattab=map
  • Last taxonomy: Pediococcus
  • 16S sequence: AJ318414
  • Sequence Identity:
  • Total samples: 13042
  • soil counts: 421
  • aquatic counts: 624
  • animal counts: 11554
  • plant counts: 443

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87221Risk group (German classification)
1188511Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pediococcus damnosus clone P11 16S ribosomal RNA gene, partial sequenceAF404721517ena51663
20218Pediococcus damnosus clone P11 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF405365531ena51663
20218Pediococcus damnosus 16S rRNA gene, strain DSM 20331AJ3184141561ena51663
20218Pediococcus damnosus DNA for 16S rRNA, partial sequenceD876781497ena51663

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pediococcus damnosus DSM 20331GCA_001437255contigncbi51663
66792Pediococcus damnosus strain DSM 2033151663.50wgspatric51663
66792Pediococcus damnosus DSM 203312675903387draftimg51663

GC content

@refGC-contentmethod
872237.1
6777040thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes96.47no
anaerobicno93.909no
halophileyes89.182no
spore-formingno93.828no
glucose-utilyes92.624no
aerobicno97.743no
thermophileno98.821yes
flagellatedno98.631no
motileno94.843no
glucose-fermentyes88.943no

External links

@ref: 8722

culture collection no.: DSM 20331, ATCC 29358, NCDO 1832, WDCM 00022, CCUG 32251, LMG 11484, NCIMB 12010, CIP 102264, CCM 3453, JCM 5886, BCRC 12840, CECT 793, CGMCC 1.2692, KCTC 3770, NBRC 107867, VKM B-1602, VTT E-91459, CCUG 21535

straininfo link

  • @ref: 75857
  • straininfo: 3818

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166726Pediococcus cellicola sp. nov., a novel lactic acid coccus isolated from a distilled-spirit-fermenting cellar.Zhang B, Tong H, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.63778-02005China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Genotype, Lactic Acid/*metabolism, Molecular Sequence Data, Pediococcus/*classification/genetics/isolation & purification/metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Wine/*microbiologyGenetics
Phylogeny17012570Pediococcus ethanolidurans sp. nov., isolated from the walls of a distilled-spirit-fermenting cellar.Liu L, Zhang B, Tong H, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.64407-02006Alcoholic Beverages/*microbiology, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Ethanol/metabolism, Fermentation, Genes, rRNA, Genotype, Lactic Acid/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Pediococcus/*classification/genetics/*isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNAGenetics
Enzymology32539960Inactivation kinetics of beer spoilage bacteria (Lactobacillus brevis, Lactobacillus casei, and Pediococcus damnosus) during acid washing of brewing yeast.Munford ARG, Chaves RD, Sant'Ana ASFood Microbiol10.1016/j.fm.2020.1035132020Beer/*microbiology, Bioreactors/microbiology, Fermentation, Food Contamination/prevention & control, Food Microbiology, Hydrogen-Ion Concentration, Kinetics, Lactobacillaceae/classification/*drug effects/growth & development/metabolism, Phosphoric Acids/*pharmacology, Yeasts/*growth & development/metabolismBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8722Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20331)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20331
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
41846Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13931
50930Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32251)https://www.ccug.se/strain?id=32251
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/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
75857Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3818.1StrainInfo: A central database for resolving microbial strain identifiers
118851Curators of the CIPCollection of Institut Pasteur (CIP 102264)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102264