Strain identifier

BacDive ID: 6380

Type strain: No

Species: Pediococcus acidilactici

Strain Designation: P-60

Strain history: CIP <- 1954, NCIB <- R.P. Tittsler, Pediococcus cerevisiae <- E. Snell, Leuconostoc mesenteroides: strain P-60

NCBI tax ID(s): 1254 (species)

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General

@ref: 8649

BacDive-ID: 6380

DSM-Number: 20238

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, Gram-positive, coccus-shaped, human pathogen

description: Pediococcus acidilactici P-60 is a facultative anaerobe, spore-forming, Gram-positive human pathogen of the family Lactobacillaceae.

NCBI tax id

  • NCBI tax id: 1254
  • Matching level: species

strain history

@refhistory
8649<- ATCC <- R.P. Tittsler (Pediococcus cerevisiae) <- E.E. Snell, P-60 (Leuconostoc mesenteroides)
67770IAM 1233 <-- ATU L-12 <-- ATCC 8042 <-- R. P. Tittsler ("Pediococcus cerevisiae") <-- E. E. Snell P-60 (Leuconostoc mesenteroides).
116001CIP <- 1954, NCIB <- R.P. Tittsler, Pediococcus cerevisiae <- E. Snell, Leuconostoc mesenteroides: strain P-60

doi: 10.13145/bacdive6380.20240916.9.1

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: 8649

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: P-60

type strain: no

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116001positivecoccus-shapedno
69480no92.5
69480positive93.549

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8649MRS 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
35224MEDIUM 41- for Lactobacillus, Leuconostoc, Weissella, Pediococcus, Sporolactobacillus inulinusyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp broth (55.000 g)
116001CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41
116001CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperature
8649positivegrowth30
35224positivegrowth37
67770positivegrowth30
116001positivegrowth25-45

Physiology and metabolism

oxygen tolerance

  • @ref: 116001
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69480no91.376
69481yes97

murein

  • @ref: 8649
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

observation

  • @ref: 67770
  • observation: Assay of Panthenol, amino acids, pantothenic acid, pyridoxal (vitamin B6 requirement)

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
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
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose+builds acid from17057
68371esculin+builds acid from4853
68371amygdalin-builds acid from27613
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
116001nitrate-reduction17632
116001nitrite-reduction16301

metabolite tests

  • @ref: 116001
  • 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
116001oxidase-
116001alcohol dehydrogenase+1.1.1.1
116001amylase-
116001catalase-1.11.1.6
116001lysine decarboxylase-4.1.1.18
116001ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116001-+---+----++-+--++--

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8649----+++---++++--------+-+/-++/-+----+------+--+-------
8649----+++---++++-+/-------+-++++----+------+/---+-------

Isolation, sampling and environmental information

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: LC311073
  • 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
8649yes, in single cases1Risk group (German classification)
1160011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pediococcus acidilactici clone P15 16S ribosomal RNA gene, partial sequenceAF404724516nuccore1254
20218Pediococcus acidilactici clone P15 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF405368529nuccore1254
20218Pediococcus acidilactici partial 16S rRNA gene, strain DSMZ 20238AJ249539530nuccore1254
67770Pediococcus acidilactici gene for 16S ribosomal RNA, partial sequence, strain: JCM 20119LC3110731513nuccore1254
124043Pediococcus acidilactici gene for 16S rRNA, partial sequence, strain: NBRC 3076.AB6800061502nuccore1254

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pediococcus acidilactici strain ATCC 80421254.155completepatric1254
66792Pediococcus acidilactici strain FDAARGOS_10081254.395completepatric1254
66792Pediococcus acidilactici strain NCIMB 69901254.101plasmidpatric1254
66792Pediococcus acidilactici ATCC 80422847224930completeimg1254
67770Pediococcus acidilactici ATCC 8042GCA_004355265completencbi1254

GC content

@refGC-content
864938.0
6777038

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes97no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes93.549no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.332yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.768yes
69480spore-formingspore-formingAbility to form endo- or exosporesno91.376no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.496yes
69480flagellatedmotile2+Ability to perform flagellated movementno92.5no

External links

@ref: 8649

culture collection no.: DSM 20238, ATCC 8042, CCM 2425, NCDO 521, NCIMB 6990, NCIMB 7881, NCIMB 8018, NCIMB 8031, JCM 20119, ATU L-12, IAM 1233, IFO 3076, NBRC 3076, NCTC 6990, NISL 7202, CIP 54.167

straininfo link

  • @ref: 75853
  • straininfo: 92368

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny10734568Expanded bed adsorption as a unique unit operation for the isolation of bacteriocins from fermentation media.Callewaert R, De Vuyst LBioseparation1999Adsorption, Bacteriocins/*isolation & purification, Cell-Free System, Culture Media/*chemistry, *Fermentation, Hydrogen-Ion ConcentrationEnzymology
Phylogeny17395262pEOC01: a plasmid from Pediococcus acidilactici which encodes an identical streptomycin resistance (aadE) gene to that found in Campylobacter jejuni.O'Connor EB, O'Sullivan O, Stanton C, Danielsen M, Simpson PJ, Callanan MJ, Ross RP, Hill CPlasmid2007Base Sequence, Campylobacter jejuni/*genetics, Chromosome Mapping, Chromosomes, Bacterial, DNA, Bacterial/chemistry/genetics, Drug Resistance, Multiple, Bacterial/*genetics, *Genes, Bacterial, Molecular Sequence Data, Open Reading Frames, Pediococcus/*genetics, Phylogeny, Plasmids/drug effects/*genetics/isolation & purification, Repetitive Sequences, Nucleic Acid, Replication Origin, Sequence Analysis, DNA, Streptomycin/pharmacologyGenetics10.1016/j.plasmid.2007.02.002
Metabolism18772932Novel extracellular proteolytic activity in Pediococcus acidilactici ATCC 8042.Llorente-Bousquets A, Perez-Munguia S, Farres ACan J Microbiol2008Bacterial Proteins/chemistry/genetics/*metabolism, Molecular Weight, N-Acetylmuramoyl-L-alanine Amidase/chemistry/genetics/*metabolism, Pediococcus/chemistry/*enzymology/genetics/growth & development, Substrate SpecificityEnzymology10.1139/w08-055
Enzymology21707881Detection, cellular localization and antibacterial activity of two lytic enzymes of Pediococcus acidilactici ATCC 8042.Garcia-Cano I, Velasco-Perez L, Rodriguez-Sanoja R, Sanchez S, Mendoza-Hernandez G, Llorente-Bousquets A, Farres AJ Appl Microbiol2011Amino Acid Sequence, Anti-Bacterial Agents/*pharmacology, Bacterial Proteins/genetics/metabolism, Electrophoresis, Polyacrylamide Gel, Glycoside Hydrolases/genetics/metabolism, Gram-Negative Bacteria/*drug effects, Gram-Positive Bacteria/*drug effects, Microbial Sensitivity Tests, Molecular Sequence Data, N-Acetylmuramoyl-L-alanine Amidase/genetics/*metabolism, Pediococcus/*enzymology/genetics/growth & development, Tandem Mass SpectrometryMetabolism10.1111/j.1365-2672.2011.05088.x
Enzymology25940238Expression, purification, and characterization of a bifunctional 99-kDa peptidoglycan hydrolase from Pediococcus acidilactici ATCC 8042.Garcia-Cano I, Campos-Gomez M, Contreras-Cruz M, Serrano-Maldonado CE, Gonzalez-Canto A, Pena-Montes C, Rodriguez-Sanoja R, Sanchez S, Farres AAppl Microbiol Biotechnol2015Amino Acid Sequence, Chromatography, Gel, Cloning, Molecular, Enzyme Stability, Gene Expression, Hydrogen-Ion Concentration, Microbial Viability/drug effects, Micrococcus/drug effects, Molecular Sequence Data, Molecular Weight, N-Acetylmuramoyl-L-alanine Amidase/chemistry/genetics/*isolation & purification/*metabolism, Pediococcus/*enzymology, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Alignment, TemperaturePathogenicity10.1007/s00253-015-6593-2
Stress25951387Evaluating Pediococcus acidilactici and Enterococcus faecium NRRL B-2354 as Thermal Surrogate Microorganisms for Salmonella for In-Plant Validation Studies of Low-Moisture Pet Food Products.Ceylan E, Bautista DAJ Food Prot2015Animal Feed/analysis/*microbiology, Colony Count, Microbial, Enterococcus faecium/chemistry/*growth & development, Food Contamination/analysis, Food Handling/*methods, Hot Temperature, Kinetics, Pediococcus/chemistry/*growth & development, Salmonella/chemistry/*growth & development, Water/analysisEnzymology10.4315/0362-028X.JFP-14-271
Pathogenicity29446685Inactivation of Salmonella and Surrogate Bacteria on Cashews and Macadamia Nuts Exposed to Commercial Propylene Oxide Processing Conditions.Saunders T, Wu J, Williams RC, Huang H, Ponder MAJ Food Prot2018Anacardium/*microbiology, Epoxy Compounds/*pharmacology, Macadamia/*microbiology, Nuts/*microbiology, Salmonella/*drug effects10.4315/0362-028X.JFP-17-252
Stress31202412Assessment of Pediococcus acidilactici ATCC 8042 as potential Salmonella surrogate for thermal treatments of toasted oats cereal and peanut butter.Deen B, Diez-Gonzalez FFood Microbiol2019Arachis/*microbiology, Avena/*microbiology, Colony Count, Microbial, Consumer Product Safety/standards, Food Microbiology/*methods, Hot Temperature, Kinetics, *Microbial Viability, Pediococcus acidilactici/*physiology, Salmonella/physiology, *ThermotoleranceEnzymology10.1016/j.fm.2019.05.015
Pathogenicity31502493Encapsulation of Lactobacillus plantarum ATCC 8014 and Pediococcus acidilactici ATCC 8042 in a freeze-dried alginate-gum arabic system and its in vitro testing under gastrointestinal conditions.Sandoval-Mosqueda I, Llorente-Bousquets A, Montiel-Sosa JF, Corona L, Guadarrama-Alvarez ZJ Microencapsul2019Alginates/*chemistry, Cell Encapsulation, Cells, Immobilized/cytology, Freeze Drying, Gastrointestinal Tract/microbiology, Gum Arabic/*chemistry, Humans, Lactobacillus plantarum/*cytology, Microbial Viability, Pediococcus acidilactici/*cytology, Probiotics/analysis10.1080/02652048.2019.1660729
35185178Assessment of the prebiotic potential of seed coats from green gram (Vigna radiata) and black gram (Vigna mungo).Swaroopa C, Kashmira L, Vikas G, Rajan WJ Food Sci Technol202110.1007/s13197-021-05043-2

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8649Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20238)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20238
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
35224Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19222
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
75853Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92368.1StrainInfo: A central database for resolving microbial strain identifiers
116001Curators of the CIPCollection of Institut Pasteur (CIP 54.167)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2054.167
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy