Strain identifier

BacDive ID: 6395

Type strain: Yes

Species: Pediococcus claussenii

Strain Designation: P06, PO6

Strain history: <- DSM <- B Ziola, P06 <- D Bendiak

NCBI tax ID(s): 187452 (species)

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General

@ref: 5550

BacDive-ID: 6395

DSM-Number: 14800

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

description: Pediococcus claussenii P06 is a facultative anaerobe, mesophilic, coccus-shaped bacterium that was isolated from spoiled beer.

NCBI tax id

  • NCBI tax id: 187452
  • Matching level: species

strain history

@refhistory
5550<- B. Ziola; P06 <- D. Bendiak
67770DSM 14800 <-- B. Ziola P06 <-- D. Bendiak.
67771<- DSM <- B Ziola, P06 <- D Bendiak

doi: 10.13145/bacdive6395.20230509.8.1

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 claussenii
  • full scientific name: Pediococcus claussenii Dobson et al. 2002

@ref: 5550

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Pediococcus

species: Pediococcus claussenii

full scientific name: Pediococcus claussenii Dobson et al. 2002

strain designation: P06, PO6

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stain
67771coccus-shapedno
67771positive

Culture and growth conditions

culture medium

  • @ref: 5550
  • 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
5550positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 67771
  • spore formation: no

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
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-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
5550-----+-----+++----+---++/--++++---+------+/-----------
5550----------+++-----+---+++++++---+-----------------
5550-----+-----+++----+---+++++++---+------+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5550spoiled beerCanadaCANNorth America
67771From spoiled beerCanadaCANNorth America
67770Beer

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Environmental#Microbial community
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_1583.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_382;97_430;98_1250;99_1583&stattab=map
  • Last taxonomy: Pediococcus claussenii subclade
  • 16S sequence: LC258161
  • Sequence Identity:
  • Total samples: 9006
  • soil counts: 428
  • aquatic counts: 471
  • animal counts: 7644
  • plant counts: 463

Safety information

risk assessment

  • @ref: 5550
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pediococcus claussenii partial 16S rRNA gene, strain DSM 14800TAJ6215551472ena187452
5550Pediococcus claussenii clone P06 16S ribosomal RNA gene, partial sequenceAF404716518ena187452
67771Pediococcus claussenii gene for 16S ribosomal RNA, partial sequence, strain: JCM 18046LC2581611478ena187452

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pediococcus claussenii strain DSM 14800187452.24wgspatric187452
66792Pediococcus claussenii DSM 148002660237910draftimg187452
67771Pediococcus claussenii ATCC BAA-344GCA_000237995completencbi701521
67771Pediococcus claussenii DSM 14800GCA_001436905scaffoldncbi187452

GC content

@refGC-contentmethod
6777040.2-41.1high performance liquid chromatography (HPLC)
6777140.0-41.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.01no
gram-positiveyes94.969no
anaerobicno93.315yes
aerobicno96.76no
halophileyes89.415no
spore-formingno93.678yes
glucose-utilyes93.691no
flagellatedno98.622yes
thermophileno99.56yes
glucose-fermentyes89.602no

External links

@ref: 5550

culture collection no.: DSM 14800, ATCC BAA 344, JCM 18046, KCTC 3811, BCRC 17600, CECT 7027, LMG 21948, VTT E-032355

straininfo link

  • @ref: 75868
  • straininfo: 100851

literature

  • topic: Phylogeny
  • Pubmed-ID: 12508860
  • title: Phylogenetic analysis of the genus Pediococcus, including Pediococcus claussenii sp. nov., a novel lactic acid bacterium isolated from beer.
  • authors: Dobson CM, Deneer H, Lee S, Hemmingsen S, Glaze S, Ziola B
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-6-2003
  • year: 2002
  • mesh: Base Composition, Base Sequence, Beer/microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Food Microbiology, Molecular Sequence Data, Pediococcus/*classification/*genetics/isolation & purification/metabolism, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity
  • topic2: Biotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5550Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14800)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14800
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
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75868Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100851.1StrainInfo: A central database for resolving microbial strain identifiers