Strain identifier

BacDive ID: 6399

Type strain: Yes

Species: Pediococcus argentinicus

Strain history: CCUG 54535 <-- LMG 23999 <-- K. De Bruyne; Gent Univ., Belgium; R-24310 <-- L. De Vuyst; Vrije Univ., Belgium <-- Centro de Referencia para Lactobacilos (CERELA, CONICET), Argentina.

NCBI tax ID(s): 480391 (species)

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General

@ref: 16656

BacDive-ID: 6399

DSM-Number: 23026

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

description: Pediococcus argentinicus DSM 23026 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from fermented wheat flour.

NCBI tax id

  • NCBI tax id: 480391
  • Matching level: species

strain history

@refhistory
16656<- CCUG <- K. De Bruyne, LMG <- CERELA, San Miguel de Tucumán, Argentina
67770CCUG 54535 <-- LMG 23999 <-- K. De Bruyne; Gent Univ., Belgium; R-24310 <-- L. De Vuyst; Vrije Univ., Belgium <-- Centro de Referencia para Lactobacilos (CERELA, CONICET), Argentina.

doi: 10.13145/bacdive6399.20230509.8.1

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 argentinicus
  • full scientific name: Pediococcus argentinicus De Bruyne et al. 2008

@ref: 16656

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Pediococcus

species: Pediococcus argentinicus

full scientific name: Pediococcus argentinicus De Bruyne et al. 2008

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
32642positive0.7-1 µmcoccus-shapedno
69480no95.079
69480positive100

colony morphology

  • @ref: 60219
  • incubation period: 1-2 days

pigmentation

  • @ref: 32642
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16656
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16656positivegrowth30mesophilic
32642positivegrowth40thermophilic
32642positiveoptimum40thermophilic
60219positivegrowth28mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32642positivegrowth04-08acidophile
32642positiveoptimum04-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16656microaerophile
32642aerobe
60219aerobe

spore formation

@refspore formationconfidence
32642no
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
32642NaClpositivegrowth0-6 %
32642NaClpositiveoptimum0-6 %

observation

  • @ref: 32642
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3264217057cellobiose+carbon source
3264228757fructose+carbon source
3264228260galactose+carbon source
3264217234glucose+carbon source
3264229864mannitol+carbon source
3264237684mannose+carbon source
32642506227N-acetylglucosamine+carbon source
3264217814salicin+carbon source
3264217992sucrose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-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
6837128066gentiobiose+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
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-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
6837116813galactitol-builds acid from
6837162345L-rhamnose-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
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

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
16656-----+----++++----+-+-+++++++--++------+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
16656fermented wheat flourArgentinaARGMiddle and South America
60219Wheat flour,commercialArgentinaARGMiddle and South America1990-09-01
67770Argentinean fermented wheat flour

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production

taxonmaps

  • @ref: 69479
  • File name: preview.99_2982.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_382;97_430;98_490;99_2982&stattab=map
  • Last taxonomy: Pediococcus argentinicus
  • 16S sequence: AM709786
  • Sequence Identity:
  • Total samples: 3318
  • soil counts: 219
  • aquatic counts: 279
  • animal counts: 2443
  • plant counts: 377

Safety information

risk assessment

  • @ref: 16656
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16656
  • description: Pediococcus argentinicus 16S rRNA gene
  • accession: AM709786
  • length: 1492
  • database: ena
  • NCBI tax ID: 480391

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pediococcus argentinicus strain CCUG 54535480391.6wgspatric480391
66792Pediococcus argentinicus strain DSM 23026480391.4wgspatric480391
66792Pediococcus argentinicus strain NBRC 107827480391.5wgspatric480391
66792Pediococcus argentinicus DSM 230262660238258draftimg480391
67770Pediococcus argentinicus NBRC 107827GCA_007992295contigncbi480391
67770Pediococcus argentinicus CCUG 54535GCA_012396535contigncbi480391
67770Pediococcus argentinicus DSM 23026GCA_001437605scaffoldncbi480391

GC content

@refGC-contentmethod
1665640.8
6777040.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes94.809yes
anaerobicno94.493yes
halophileyes91.307no
spore-formingno95.544yes
glucose-utilyes91.319no
aerobicno96.774no
thermophileno99.247no
flagellatedno98.621no
motileno95.038no
glucose-fermentyes89.439no

External links

@ref: 16656

culture collection no.: DSM 23026, CCUG 54535, CRL 776, LMG 23999, JCM 30771, NBRC 107827

straininfo link

  • @ref: 75872
  • straininfo: 358774

literature

  • topic: Phylogeny
  • Pubmed-ID: 19060081
  • title: Pediococcus argentinicus sp. nov. from Argentinean fermented wheat flour and identification of Pediococcus species by pheS, rpoA and atpA sequence analysis.
  • authors: De Bruyne K, Franz CM, Vancanneyt M, Schillinger U, Mozzi F, de Valdez GF, De Vuyst L, Vandamme P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65833-0
  • year: 2008
  • mesh: Argentina, Fermentation, Flour/*microbiology, Genes, Bacterial/*genetics, Molecular Sequence Data, Pediococcus/*classification/*genetics/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Triticum/microbiology
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16656Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23026)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23026
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
32642Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2885328776041
60219Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54535)https://www.ccug.se/strain?id=54535
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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)
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
75872Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID358774.1StrainInfo: A central database for resolving microbial strain identifiers