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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 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/bacdive6381.20230509.8.1

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

@refmotilityconfidencegram staincell shape
69480no95.403
69480100positive
115999positivecoccus-shaped

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

@refgrowthtypetemperaturerange
8690positivegrowth30mesophilic
39737positivegrowth37mesophilic
50918positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
115999positivegrowth25-45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50918anaerobe
50918microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.989

murein

  • @ref: 8690
  • 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
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
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
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-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
115999nitrate-reduction17632
115999nitrite-reduction16301

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
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
115999alcohol dehydrogenase+1.1.1.1
115999amylase-
115999catalase-1.11.1.6
115999lysine decarboxylase-4.1.1.18
115999ornithine decarboxylase-4.1.1.17

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 20284AJ249535530ena862514
20218Pediococcus acidilactici 16S ribosomal RNAM588331526ena1254
8690Pediococcus acidilactici 16S rRNA gene, strain DSM 20284 (T)AJ3053201569ena862514
67770Pediococcus acidilactici gene for 16S ribosomal RNA, partial sequence, strain: JCM 8797LC0970741516ena1254

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

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.344no
gram-positiveyes96.922no
anaerobicno93.677no
aerobicno97.641no
halophileyes93.072no
spore-formingno96.429no
thermophileno98.904yes
glucose-utilyes94.074no
flagellatedno98.918no
glucose-fermentyes90.129no

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
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
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