Strain identifier

BacDive ID: 6381

Type strain: Yes

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)

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General

@ref: 8690

BacDive-ID: 6381

DSM-Number: 20284

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

description: Pediococcus acidilactici B213c is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from barley.

NCBI tax id

NCBI tax idMatching level
1254species
862514strain

strain history

@refhistory
8690<- W. Back, B213c
67770NRIC 0115 <-- DSM 20284 <-- W. Back B213c.
115999CIP <- 1990, DSM <- W. Back: strain B213 c. Barley

doi: 10.13145/bacdive6381.20250331.9.3

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

@refgram staincell shapemotilityconfidence
115999positivecoccus-shaped
125438no91
125438positive93.082

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8690MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: 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
39737MEDIUM 41- for Lactobacillus, Leuconostoc, Weissella, Pediococcus, Sporolactobacillus inulinusyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp broth (55.000 g)
115999CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperature
8690positivegrowth30
39737positivegrowth37
50918positivegrowth30-37
67770positivegrowth30
115999positivegrowth25-45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50918anaerobe
50918microaerophile

spore formation

  • @ref: 125438
  • spore formation: no
  • confidence: 92.328

murein

  • @ref: 8690
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11599917632nitrate-reduction
11599916301nitrite-reduction
68371Potassium 5-ketogluconate-builds acid from
683714853esculin+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose+builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

metabolite tests

  • @ref: 115999
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

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
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
115999alcohol dehydrogenase+1.1.1.1
115999amylase-
115999catalase-1.11.1.6
115999lysine decarboxylase-4.1.1.18
115999ornithine decarboxylase-4.1.1.17
68382esterase lipase (C 8)-

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50918C16:034.316
    50918C18:0418
    50918C16:1 ω7c/C15:0 ISO 2OH4.315.85
    50918C18:1 ω7c /12t/9t39.517.824
    50918C18:1 ω9c2.417.769
    50918C18:2 ω6,9c/C18:0 ANTE9.217.724
    50918C19:0 CYCLO ω9c6.218.87
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
115999-----+----++-+--++--

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8690----+++---++++--------+--+++----+---------+-------
8690----+++---++++--------+-++++----+------+--+-------
8690----+++---++++-+------+-++++----+------+--+----+/---
115999---+++---++++-+/-------++++++-+/---+------+--+----+--

Isolation, sampling and environmental information

isolation

@refsample type
8690barley
50918Barley

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

@refpathogenicity humanbiosafety levelbiosafety level comment
8690yes, in single cases1Risk group (German classification)
1159991Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pediococcus acidilactici partial 16S rRNA gene, strain DSMZ 20284AJ249535530nuccore862514
20218Pediococcus acidilactici 16S ribosomal RNAM588331526nuccore1254
8690Pediococcus acidilactici 16S rRNA gene, strain DSM 20284 (T)AJ3053201569nuccore862514
67770Pediococcus acidilactici gene for 16S ribosomal RNA, partial sequence, strain: JCM 8797LC0970741516nuccore1254

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pediococcus acidilactici DSM 20284GCA_000146325scaffoldncbi862514
66792Pediococcus acidilactici JCM 8797GCA_014651255contigncbi1254
66792Pediococcus acidilactici DSM 20284862514.3wgspatric862514
66792Pediococcus acidilactici strain CCUG 322351254.351wgspatric1254
66792Pediococcus acidilactici strain FDAARGOS_11331254.398completepatric1254
66792Pediococcus acidilactici strain JCM 87971254.384wgspatric1254
66792Pediococcus acidilactici DSM 20284649989981draftimg862514
67770Pediococcus acidilactici CCUG 32235GCA_012396515contigncbi1254
66792Pediococcus acidilactici NCFB2767GCA_029823335contigncbi1254

GC content

  • @ref: 8690
  • GC-content: 42.8

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe88.9
125439BacteriaNetgram_stainReaction to gram-stainingvariable81
125439BacteriaNetmotilityAbility to perform movementyes82.1
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes78.3
125438gram-positivegram-positivePositive reaction to Gram-stainingyes93.082no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no86.341no
125438spore-formingspore-formingAbility to form endo- or exosporesno92.328no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.976no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5yes
125438motile2+flagellatedAbility to perform flagellated movementno91no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406783Pediococcus lolii sp. nov., isolated from ryegrass silage.Doi K, Nishizaki Y, Fujino Y, Ohshima T, Ohmomo S, Ogata SInt J Syst Evol Microbiol10.1099/ijs.0.005793-02009Bacterial 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 SpecificityGenetics
Metabolism21784921Characterization 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 KDAppl Environ Microbiol10.1128/AEM.05317-112011Acyclic 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, WineEnzymology
Enzymology22261863Characterization of D-lactate dehydrogenase from Pediococcus acidilactici that converts phenylpyruvic acid into phenyllactic acid.Mu W, Yu S, Jiang B, Li XBiotechnol Lett10.1007/s10529-012-0847-12012Animals, 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, TemperatureMetabolism
Metabolism24609135Lipid-lowering effects of Pediococcus acidilactici M76 isolated from Korean traditional makgeolli in high fat diet-induced obese mice.Moon YJ, Baik SH, Cha YSNutrients10.3390/nu60310162014Adipose 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/bloodPhylogeny
Metabolism29678738Autochthonous 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 NMicrob Pathog10.1016/j.micpath.2018.04.0312018Amidohydrolases, 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, ThailandPathogenicity
Phylogeny32201563Molecular 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 NF1000Res10.12688/f1000research.16224.32018Indonesia, *Lactobacillales/genetics/metabolism, *Phylogeny, RNA, Ribosomal, 16S, *gamma-Aminobutyric AcidMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8690Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20284)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20284
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
39737Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15203
50918Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32235)https://www.ccug.se/strain?id=32235
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
75854Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297036.1StrainInfo: A central database for resolving microbial strain identifiers
115999Curators of the CIPCollection of Institut Pasteur (CIP 103408)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103408
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1