Strain identifier

BacDive ID: 6396

Type strain: Yes

Species: Pediococcus cellicola

Strain Designation: Z-8

Strain history: CIP <- 2005, X. Dong, Chinese Academy Sciences, Beijing, China: strain Z-8

NCBI tax ID(s): 319652 (species)

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

@ref: 7171

BacDive-ID: 6396

DSM-Number: 17757

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

description: Pediococcus cellicola Z-8 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from distilled pirit-fermenting cellar.

NCBI tax id

  • NCBI tax id: 319652
  • Matching level: species

strain history

@refhistory
7171<- X. Dong; Z-8 <- B. Zhang and X. Dong
67770CGMCC 1.3787 <-- B. Zhang Z-8.
117235CIP <- 2005, X. Dong, Chinese Academy Sciences, Beijing, China: strain Z-8

doi: 10.13145/bacdive6396.20230509.8.1

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 cellicola
  • full scientific name: Pediococcus cellicola Zhang et al. 2005

@ref: 7171

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Pediococcus

species: Pediococcus cellicola

full scientific name: Pediococcus cellicola Zhang et al. 2005

strain designation: Z-8

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31543positive0.8 µm0.8 µmcoccus-shapedno
69480positive100
117235positivecoccus-shapedno

colony morphology

  • @ref: 117235
  • hemolysis ability: 1

pigmentation

  • @ref: 31543
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7171MRS 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
33271MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
117235CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
7171positivegrowth30mesophilic
31543positivegrowth13-44
31543positiveoptimum33.5mesophilic
33271positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
31543positivegrowth6.0-6.8
31543positiveoptimum6.4

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7171microaerophile
31543facultative anaerobe
117235facultative anaerobe

spore formation

@refspore formationconfidence
31543no
69481no100
69480no99.991

observation

  • @ref: 31543
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31543168082-dehydro-D-gluconate+carbon source
3154322599arabinose+carbon source
3154317057cellobiose+carbon source
3154316236ethanol+carbon source
3154328757fructose+carbon source
3154328260galactose+carbon source
3154317234glucose+carbon source
3154317716lactose+carbon source
3154317306maltose+carbon source
3154337684mannose+carbon source
3154337657methyl D-glucoside+carbon source
31543506227N-acetylglucosamine+carbon source
3154326546rhamnose+carbon source
3154333942ribose+carbon source
3154317992sucrose+carbon source
3154327082trehalose+carbon source
3154318222xylose+carbon source
315434853esculin+hydrolysis
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
11723517632nitrate-reduction
11723516301nitrite-reduction

metabolite production

  • @ref: 117235
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
117235oxidase-
117235alcohol dehydrogenase-1.1.1.1
117235catalase-1.11.1.6
117235lysine decarboxylase-4.1.1.18
117235ornithine decarboxylase-4.1.1.17
117235urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117235----++-----++--++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117235---------++++-+----+++++++++---+------+--+-------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7171distilled pirit-fermenting cellarHebei ProvinceChinaCHNAsia
67770Distilled-spirit-fermenting cellar
117235Distilled spirit fermenting cellarHebeiChinaCHNAsia2004

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Fermented
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_8281.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_156;97_167;98_186;99_8281&stattab=map
  • Last taxonomy: Pediococcus cellicola
  • 16S sequence: LC258134
  • Sequence Identity:
  • Total samples: 647
  • soil counts: 85
  • aquatic counts: 10
  • animal counts: 526
  • plant counts: 26

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71711Risk group (German classification)
1172351Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7171Pediococcus cellicola strain Z-8 16S ribosomal RNA gene, partial sequenceAY9567881542ena319652
67770Pediococcus cellicola gene for 16S ribosomal RNA, partial sequence, strain: JCM 14152LC2581341457ena319652

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pediococcus cellicola strain DSM 17757319652.3wgspatric319652
66792Pediococcus cellicola strain NBRC 106103319652.4wgspatric319652
66792Pediococcus cellicola DSM 177572657245420draftimg319652
67770Pediococcus cellicola NBRC 106103GCA_007989045contigncbi319652
67770Pediococcus cellicola DSM 17757GCA_001438655contigncbi319652

GC content

@refGC-contentmethod
717138.1
3154337
6777037thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes95.605yes
anaerobicno88.892yes
halophileyes90.28no
spore-formingno94.948yes
glucose-utilyes91.601yes
motileno93.939yes
flagellatedno98.546yes
aerobicno97.113no
thermophileno99.425yes
glucose-fermentyes86.757no

External links

@ref: 7171

culture collection no.: DSM 17757, AS 1.3787, LMG 22956, JCM 14152, CGMCC 1.3787, KCTC 13055, NBRC 106103, CIP 108990

straininfo link

  • @ref: 75869
  • straininfo: 265617

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166726Pediococcus cellicola sp. nov., a novel lactic acid coccus isolated from a distilled-spirit-fermenting cellar.Zhang B, Tong H, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.63778-02005China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Genotype, Lactic Acid/*metabolism, Molecular Sequence Data, Pediococcus/*classification/genetics/isolation & purification/metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Wine/*microbiologyGenetics
Phylogeny17012570Pediococcus ethanolidurans sp. nov., isolated from the walls of a distilled-spirit-fermenting cellar.Liu L, Zhang B, Tong H, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.64407-02006Alcoholic Beverages/*microbiology, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Ethanol/metabolism, Fermentation, Genes, rRNA, Genotype, Lactic Acid/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Pediococcus/*classification/genetics/*isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7171Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17757)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17757
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
31543Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2783528776041
33271Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6680
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
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
75869Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265617.1StrainInfo: A central database for resolving microbial strain identifiers
117235Curators of the CIPCollection of Institut Pasteur (CIP 108990)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108990