Strain identifier
BacDive ID: 6384
Type strain:
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)
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
@ref | history |
---|---|
8722 | <- NCDO <- E. Coster, Be1 <- D.H. Williamson |
67770 | ATCC 29358 <-- NCDO 1832 <-- Q. E. C. Univ. London <-- D. H. Williamson. |
118851 | CIP <- 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
@ref | name | growth | link | composition |
---|---|---|---|---|
8722 | PEDIOCOCCUS DAMNOSUS MEDIUM (DSMZ Medium 231) | yes | https://mediadive.dsmz.de/medium/231 | Name: 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 |
41846 | MEDIUM 43 - for Lactobacillus hamsteri and Lactobacillus ruminis | yes | Distilled water make up to (900.000 ml);Man Rogosa Sharp broth (55.000 g);Cysteine hydrochloride 5 % solution - M0172 (100.000 ml) | |
118851 | CIP Medium 41 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8722 | positive | growth | 26 | mesophilic |
41846 | positive | growth | 25 | mesophilic |
50930 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 26 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
8722 | microaerophile |
50930 | anaerobe |
murein
- @ref: 8722
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | salicin | + | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
118851 | nitrate | + | reduction | 17632 |
118851 | nitrite | - | reduction | 16301 |
metabolite production
- @ref: 118851
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
118851 | oxidase | - | |
118851 | catalase | - | 1.11.1.6 |
118851 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118851 | - | + | + | - | - | - | - | - | - | - | - | + | - | - | - | + | + | - | - | - |
API 50CHac
@ref | Q | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8722 | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | - | + | + | + | + | + | - | - | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
8722 | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | - | + | + | + | + | + | - | - | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
8722 | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | - | + | + | + | + | + | - | - | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
8722 | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | - | + | + | + | + | + | - | - | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
8722 | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | - | +/- | - | + | + | + | - | - | - | - | +/- | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
8722 | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | - | + | + | + | + | + | - | - | - | - | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
8722 | lager beer yeast |
50930 | Lager beer yeast |
67770 | Lager beer yeast |
118851 | Food, 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
@ref | biosafety level | biosafety level comment |
---|---|---|
8722 | 1 | Risk group (German classification) |
118851 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pediococcus damnosus clone P11 16S ribosomal RNA gene, partial sequence | AF404721 | 517 | ena | 51663 |
20218 | Pediococcus damnosus clone P11 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | AF405365 | 531 | ena | 51663 |
20218 | Pediococcus damnosus 16S rRNA gene, strain DSM 20331 | AJ318414 | 1561 | ena | 51663 |
20218 | Pediococcus damnosus DNA for 16S rRNA, partial sequence | D87678 | 1497 | ena | 51663 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pediococcus damnosus DSM 20331 | GCA_001437255 | contig | ncbi | 51663 |
66792 | Pediococcus damnosus strain DSM 20331 | 51663.50 | wgs | patric | 51663 |
66792 | Pediococcus damnosus DSM 20331 | 2675903387 | draft | img | 51663 |
GC content
@ref | GC-content | method |
---|---|---|
8722 | 37.1 | |
67770 | 40 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | yes | 96.47 | no |
anaerobic | no | 93.909 | no |
halophile | yes | 89.182 | no |
spore-forming | no | 93.828 | no |
glucose-util | yes | 92.624 | no |
aerobic | no | 97.743 | no |
thermophile | no | 98.821 | yes |
flagellated | no | 98.631 | no |
motile | no | 94.843 | no |
glucose-ferment | yes | 88.943 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16166726 | Pediococcus cellicola sp. nov., a novel lactic acid coccus isolated from a distilled-spirit-fermenting cellar. | Zhang B, Tong H, Dong X | Int J Syst Evol Microbiol | 10.1099/ijs.0.63778-0 | 2005 | China, 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/*microbiology | Genetics |
Phylogeny | 17012570 | Pediococcus ethanolidurans sp. nov., isolated from the walls of a distilled-spirit-fermenting cellar. | Liu L, Zhang B, Tong H, Dong X | Int J Syst Evol Microbiol | 10.1099/ijs.0.64407-0 | 2006 | Alcoholic 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, DNA | Genetics |
Enzymology | 32539960 | Inactivation kinetics of beer spoilage bacteria (Lactobacillus brevis, Lactobacillus casei, and Pediococcus damnosus) during acid washing of brewing yeast. | Munford ARG, Chaves RD, Sant'Ana AS | Food Microbiol | 10.1016/j.fm.2020.103513 | 2020 | Beer/*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/metabolism | Biotechnology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8722 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20331) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20331 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
41846 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/13931 | ||||
50930 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 32251) | https://www.ccug.se/strain?id=32251 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
75857 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID3818.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
118851 | Curators of the CIP | Collection of Institut Pasteur (CIP 102264) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102264 |