Strain identifier
BacDive ID: 6381
Type strain:
Species: Pediococcus acidilactici
Strain Designation: B213c, B213 c. Barley
Strain history: CIP <- 1990, DSM <- W. Back: strain B213 c. Barley
NCBI tax ID(s): 862514 (strain), 1254 (species)
General
@ref: 8690
BacDive-ID: 6381
DSM-Number: 20284
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, human pathogen
description: Pediococcus acidilactici B213c is an anaerobe, mesophilic human pathogen that was isolated from barley.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1254 | species |
862514 | strain |
strain history
@ref | history |
---|---|
8690 | <- W. Back, B213c |
67770 | NRIC 0115 <-- DSM 20284 <-- W. Back B213c. |
115999 | CIP <- 1990, DSM <- W. Back: strain B213 c. Barley |
doi: 10.13145/bacdive6381.20230509.8.1
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 acidilactici
- full scientific name: Pediococcus acidilactici Lindner 1887 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Pediococcus lolii
@ref: 8690
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Lactobacillaceae
genus: Pediococcus
species: Pediococcus acidilactici
full scientific name: Pediococcus acidilactici Lindner 1887 emend. Judicial Commission 1996
strain designation: B213c, B213 c. Barley
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 95.403 | ||
69480 | 100 | positive | ||
115999 | positive | coccus-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8690 | MRS MEDIUM (DSMZ Medium 11) | yes | https://mediadive.dsmz.de/medium/11 | Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 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 |
39737 | MEDIUM 41- for Lactobacillus, Leuconostoc, Weissella, Pediococcus, Sporolactobacillus inulinus | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp broth (55.000 g) | |
115999 | CIP Medium 41 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8690 | positive | growth | 30 | mesophilic |
39737 | positive | growth | 37 | mesophilic |
50918 | positive | growth | 30-37 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
115999 | positive | growth | 25-45 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
50918 | anaerobe |
50918 | microaerophile |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.989 |
murein
- @ref: 8690
- 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 | 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 | 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 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
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-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 |
115999 | nitrate | - | reduction | 17632 |
115999 | nitrite | - | reduction | 16301 |
metabolite tests
- @ref: 115999
- Chebi-ID: 15688
- metabolite: acetoin
- voges-proskauer-test: +
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 |
115999 | alcohol dehydrogenase | + | 1.1.1.1 |
115999 | amylase | - | |
115999 | catalase | - | 1.11.1.6 |
115999 | lysine decarboxylase | - | 4.1.1.18 |
115999 | ornithine decarboxylase | - | 4.1.1.17 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 50918 C16:0 34.3 16 50918 C18:0 4 18 50918 C16:1 ω7c/C15:0 ISO 2OH 4.3 15.85 50918 C18:1 ω7c /12t/9t 39.5 17.824 50918 C18:1 ω9c 2.4 17.769 50918 C18:2 ω6,9c/C18:0 ANTE 9.2 17.724 50918 C19:0 CYCLO ω9c 6.2 18.87 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
115999 | - | - | - | - | - | + | - | - | - | - | + | + | - | + | - | - | + | + | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8690 | - | - | - | - | + | + | + | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | - | - | + | + | + | - | - | - | - | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - |
8690 | - | - | - | - | + | + | + | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | - | + | + | + | + | - | - | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - |
8690 | - | - | - | - | + | + | + | - | - | - | + | + | + | + | - | + | - | - | - | - | - | - | + | - | + | + | + | + | - | - | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | +/- | - | - |
115999 | - | - | - | + | + | + | - | - | - | + | + | + | + | - | +/- | - | - | - | - | - | - | + | + | + | + | + | + | - | +/- | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
8690 | barley |
50918 | Barley |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
taxonmaps
- @ref: 69479
- File name: preview.99_601.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_382;97_430;98_490;99_601&stattab=map
- Last taxonomy: Pediococcus acidilactici
- 16S sequence: LC097074
- Sequence Identity:
- Total samples: 20009
- soil counts: 1156
- aquatic counts: 1242
- animal counts: 16677
- plant counts: 934
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
8690 | yes, in single cases | 1 | Risk group (German classification) |
115999 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pediococcus acidilactici partial 16S rRNA gene, strain DSMZ 20284 | AJ249535 | 530 | ena | 862514 |
20218 | Pediococcus acidilactici 16S ribosomal RNA | M58833 | 1526 | ena | 1254 |
8690 | Pediococcus acidilactici 16S rRNA gene, strain DSM 20284 (T) | AJ305320 | 1569 | ena | 862514 |
67770 | Pediococcus acidilactici gene for 16S ribosomal RNA, partial sequence, strain: JCM 8797 | LC097074 | 1516 | ena | 1254 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pediococcus acidilactici DSM 20284 | GCA_000146325 | scaffold | ncbi | 862514 |
66792 | Pediococcus acidilactici JCM 8797 | GCA_014651255 | contig | ncbi | 1254 |
66792 | Pediococcus acidilactici DSM 20284 | 862514.3 | wgs | patric | 862514 |
66792 | Pediococcus acidilactici strain CCUG 32235 | 1254.351 | wgs | patric | 1254 |
66792 | Pediococcus acidilactici strain FDAARGOS_1133 | 1254.398 | complete | patric | 1254 |
66792 | Pediococcus acidilactici strain JCM 8797 | 1254.384 | wgs | patric | 1254 |
66792 | Pediococcus acidilactici DSM 20284 | 649989981 | draft | img | 862514 |
67770 | Pediococcus acidilactici CCUG 32235 | GCA_012396515 | contig | ncbi | 1254 |
66792 | Pediococcus acidilactici NCFB2767 | GCA_029823335 | contig | ncbi | 1254 |
GC content
- @ref: 8690
- GC-content: 42.8
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 95.344 | no |
gram-positive | yes | 96.922 | no |
anaerobic | no | 93.677 | no |
aerobic | no | 97.641 | no |
halophile | yes | 93.072 | no |
spore-forming | no | 96.429 | no |
thermophile | no | 98.904 | yes |
glucose-util | yes | 94.074 | no |
flagellated | no | 98.918 | no |
glucose-ferment | yes | 90.129 | no |
External links
@ref: 8690
culture collection no.: DSM 20284, KCTC 13734, LMG 11384, CCUG 32235, NCIMB 12174, CIP 103408, JCM 8797, CGMCC 1.2696, KCTC 3771, LMG 11348, NBRC 109619, NCFB 2767, NRIC 0115
straininfo link
- @ref: 75854
- straininfo: 297036
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19406783 | Pediococcus lolii sp. nov., isolated from ryegrass silage. | Doi K, Nishizaki Y, Fujino Y, Ohshima T, Ohmomo S, Ogata S | Int J Syst Evol Microbiol | 10.1099/ijs.0.005793-0 | 2009 | Bacterial Typing Techniques, DNA, Bacterial/analysis/genetics, Genes, rRNA, Japan, Lolium/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pediococcus/*classification/genetics/isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silage/*microbiology, Species Specificity | Genetics |
Metabolism | 21784921 | Characterization of two distinct glycosyl hydrolase family 78 alpha-L-rhamnosidases from Pediococcus acidilactici. | Michlmayr H, Brandes W, Eder R, Schumann C, del Hierro AM, Kulbe KD | Appl Environ Microbiol | 10.1128/AEM.05317-11 | 2011 | Acyclic Monoterpenes, Enzyme Inhibitors/metabolism, Enzyme Stability, Ethanol/metabolism, Gene Expression, Glycoside Hydrolases/genetics/*metabolism, Hydrogen-Ion Concentration, Kinetics, Monoterpenes/metabolism, Pediococcus/*enzymology, Recombinant Proteins/genetics/metabolism, Terpenes/metabolism, Wine | Enzymology |
Enzymology | 22261863 | Characterization of D-lactate dehydrogenase from Pediococcus acidilactici that converts phenylpyruvic acid into phenyllactic acid. | Mu W, Yu S, Jiang B, Li X | Biotechnol Lett | 10.1007/s10529-012-0847-1 | 2012 | Animals, Biotransformation, Cats, Chromatography, Affinity, Cloning, Molecular, Enzyme Stability, Escherichia coli/enzymology/genetics, Gene Expression, Hydrogen-Ion Concentration, Kinetics, Lactate Dehydrogenases/chemistry/*genetics/*metabolism, Lactates/*metabolism, Pediococcus/*enzymology/*genetics, Phenylpyruvic Acids/*metabolism, Recombinant Proteins/isolation & purification/metabolism, Temperature | Metabolism |
Metabolism | 24609135 | Lipid-lowering effects of Pediococcus acidilactici M76 isolated from Korean traditional makgeolli in high fat diet-induced obese mice. | Moon YJ, Baik SH, Cha YS | Nutrients | 10.3390/nu6031016 | 2014 | Adipose Tissue/metabolism, Alanine Transaminase/blood, Alcoholic Beverages/*microbiology, Animals, Aspartate Aminotransferases/blood, Body Weight, Cholesterol/blood, *Diet, High-Fat, Energy Intake, *Hypolipidemic Agents, Insulin/blood, Leptin/blood, Lipogenesis/physiology, Liver/metabolism, Male, Mice, Mice, Inbred C57BL, Mice, Obese, Obesity/metabolism/therapy, PPAR gamma/genetics/metabolism, Pediococcus/*isolation & purification, RNA, Messenger/genetics/metabolism, Triglycerides/blood | Phylogeny |
Metabolism | 29678738 | Autochthonous lactic acid bacteria isolated from pig faeces in Thailand show probiotic properties and antibacterial activity against enteric pathogenic bacteria. | Sirichokchatchawan W, Pupa P, Praechansri P, Am-In N, Tanasupawat S, Sonthayanon P, Prapasarakul N | Microb Pathog | 10.1016/j.micpath.2018.04.031 | 2018 | Amidohydrolases, Animals, Anti-Bacterial Agents/*pharmacology, Bacterial Infections/microbiology/prevention & control, Bile Acids and Salts, Enterobacteriaceae/*drug effects/pathogenicity, Feces/*microbiology, Gastric Juice, Gastrointestinal Microbiome, Hydrogen-Ion Concentration, Hydrophobic and Hydrophilic Interactions, Lactobacillales/*metabolism, Lactobacillus plantarum/metabolism, Muramidase, Pediococcus acidilactici/metabolism, Pediococcus pentosaceus/metabolism, Phenol, Probiotics/*pharmacology, Swine, Thailand | Pathogenicity |
Phylogeny | 32201563 | Molecular identification and phylogenetic analysis of GABA-producing lactic acid bacteria isolated from indigenous dadih of West Sumatera, Indonesia. | Anggraini L, Marlida Y, Wizna W, Jamsari J, Mirzah M, Adzitey F, Huda N | F1000Res | 10.12688/f1000research.16224.3 | 2018 | Indonesia, *Lactobacillales/genetics/metabolism, *Phylogeny, RNA, Ribosomal, 16S, *gamma-Aminobutyric Acid | Metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8690 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20284) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20284 | |||
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 | |
39737 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15203 | ||||
50918 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 32235) | https://www.ccug.se/strain?id=32235 | |||
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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75854 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297036.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
115999 | Curators of the CIP | Collection of Institut Pasteur (CIP 103408) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103408 |