Strain identifier

BacDive ID: 6379

Type strain: No

Species: Pediococcus acidilactici

Strain history: K. Doi NGRI 0510Q.

NCBI tax ID(s): 1229281 (strain), 1254 (species)

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General

@ref: 8393

BacDive-ID: 6379

DSM-Number: 19927

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, human pathogen

description: Pediococcus acidilactici DSM 19927 is a microaerophile, mesophilic human pathogen that was isolated from Ryegrass silage.

NCBI tax id

NCBI tax idMatching level
1229281strain
1254species

strain history

@refhistory
8393<- Katsumi Doi, Kyushu University, Japan; NGRI 0510Q
67770K. Doi NGRI 0510Q.

doi: 10.13145/bacdive6379.20230509.8.1

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: 8393

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

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no96.043
69480100positive

Culture and growth conditions

culture medium

  • @ref: 8393
  • name: MRS MEDIUM (DSMZ Medium 11)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/11
  • composition: 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

culture temp

@refgrowthtypetemperaturerange
8393positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 8393
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.99

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
68371gentiobiose+builds acid from28066
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
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
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-rhamnose-builds acid from62345
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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8393----+++---++++--------++++++-----------+----------
8393----+++---++++--------+-++++-----------+----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8393Ryegrass silageIshigaki Island, OkinawaJapanJPNAsia
67770Ryegrass silage

isolation source categories

Cat1Cat2Cat3
#Environmental#Microbial community
#Host#Plants#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: LC311071
  • Sequence Identity:
  • Total samples: 20009
  • soil counts: 1156
  • aquatic counts: 1242
  • animal counts: 16677
  • plant counts: 934

Safety information

risk assessment

  • @ref: 8393
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8393Pediococcus lolii gene for 16S ribosomal RNA, complete sequenceAB3629851540ena1229281
67770Pediococcus acidilactici gene for 16S ribosomal RNA, partial sequence, strain: JCM 15055LC3110711516ena1254

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pediococcus acidilactici DSM 19927GCA_001437115scaffoldncbi1254
66792Pediococcus acidilactici strain FDAARGOS_10071254.394completepatric1254
66792Pediococcus lolii strain DSM 19927476270.3wgspatric1254
66792Pediococcus lolii DSM 199272663762867draftimg1254

GC content

@refGC-contentmethod
839341.0
6777041high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno89no
motileno95.301no
gram-positiveyes96.751no
anaerobicno93.523yes
aerobicno96.813yes
halophileyes92.127no
spore-formingno95.747no
thermophileno99.174yes
glucose-utilyes94.677no
flagellatedno98.952no
glucose-fermentyes88.672no

External links

@ref: 8393

culture collection no.: DSM 19927, JCM 15055, LMG 27029, NGRI 0510Q, BCRC 80335

straininfo link

  • @ref: 75852
  • straininfo: 362581

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
Phylogeny23225319Pediococcus lolii DSM 19927T and JCM 15055T are strains of Pediococcus acidilactici.Wieme A, Cleenwerck I, Van Landschoot A, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.046201-02012Amplified Fragment Length Polymorphism Analysis, Bacterial Typing Techniques, DNA, Bacterial/genetics, Lolium/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pediococcus/*classification/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silage/*microbiology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationGenetics
Genetics23405350Draft Genome Sequence of Pediococcus lolii NGRI 0510Q(T) Isolated from Ryegrass Silage.Doi K, Mori K, Tashiro K, Fujino Y, Nagayoshi Y, Hayashi Y, Kuhara S, Ohshima TGenome Announc10.1128/genomeA.00156-122013Phylogeny

Reference

@idauthorscataloguedoi/urltitle
8393Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19927)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19927
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
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
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)
75852Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362581.1StrainInfo: A central database for resolving microbial strain identifiers