Strain identifier

BacDive ID: 6397

Type strain: Yes

Species: Pediococcus stilesii

Strain Designation: FAIR-E-180, FAIR-E 180

Strain history: CIP <- 2006, CCUG <- 2005, LMG <- W. H. Holzapfel, Fed. Res. Cent. Nutrition and Food, Karlsruhe, Germany

NCBI tax ID(s): 331679 (species)

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General

@ref: 7228

BacDive-ID: 6397

DSM-Number: 18001

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

description: Pediococcus stilesii FAIR-E-180 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from white maize grains.

NCBI tax id

  • NCBI tax id: 331679
  • Matching level: species

strain history

@refhistory
7228<- M. Vancanneyt < W.H. Holzapfel, strain BFE 1652
67770CCUG 51290 <-- LMG 23082 <-- W. H. Holzapfel; Inst. for Hyg. and Toxicol., Germany; BFE 1652.
123319CIP <- 2006, CCUG <- 2005, LMG <- W. H. Holzapfel, Fed. Res. Cent. Nutrition and Food, Karlsruhe, Germany

doi: 10.13145/bacdive6397.20230509.8.1

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 stilesii
  • full scientific name: Pediococcus stilesii Franz et al. 2006

@ref: 7228

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Pediococcus

species: Pediococcus stilesii

full scientific name: Pediococcus stilesii Franz et al. 2006

strain designation: FAIR-E-180, FAIR-E 180

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
31637positive0.6-1.2 µmcoccus-shapedno
123319positivecoccus-shapedno

colony morphology

  • @ref: 123319
  • hemolysis ability: 1

pigmentation

  • @ref: 31637
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7228MRS 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
40127MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and NeisseriayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
123319CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
7228positivegrowth30mesophilic
31637positivegrowth35-48
31637positiveoptimum35-48
40127positivegrowth37mesophilic
59133positivegrowth30mesophilic
59133positivegrowth37mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepH
31637positivegrowth4.5-8
31637positiveoptimum4.5-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7228microaerophile
31637aerobe
59133anaerobe
59133microaerophile
123319facultative anaerobe

spore formation

  • @ref: 31637
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31637NaClpositivegrowth10 %
31637NaClpositiveoptimum10 %

observation

  • @ref: 31637
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3163717057cellobiose+carbon source
3163728757fructose+carbon source
3163728260galactose+carbon source
3163717234glucose+carbon source
3163717306maltose+carbon source
3163737684mannose+carbon source
31637506227N-acetylglucosamine+carbon source
3163733942ribose+carbon source
3163717814salicin+carbon source
68371Potassium 2-ketogluconate-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
12331917632nitrate-reduction
12331916301nitrite-reduction

metabolite production

  • @ref: 123319
  • 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
123319oxidase-
123319alcohol dehydrogenase-1.1.1.1
123319catalase-1.11.1.6
123319lysine decarboxylase-4.1.1.18
123319ornithine decarboxylase-4.1.1.17
123319urease-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
123319-----++---++----++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123319+/----+----++++--------+++++++----------+--+----+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7228white maize grainsLagosNigeriaNGAAfrica
59133Maize,white graines after 3 days of steepingLagosNigeriaNGAAfrica
67770White maize grains
123319Plant, Maize, white grains after 3 days of steepingLagosNigeriaNGAAfrica1997

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72281Risk group (German classification)
1233191Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7228
  • description: Pediococcus stilesii 16S rRNA gene, type strain LMG 23082T
  • accession: AJ973157
  • length: 1529
  • database: ena
  • NCBI tax ID: 331679

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pediococcus stilesii strain DSM 18001331679.3wgspatric331679
66792Pediococcus stilesii DSM 180012667527983draftimg331679
67770Pediococcus stilesii DSM 18001GCA_001437075contigncbi331679

GC content

@refGC-contentmethod
722838
6777038thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes96.071yes
anaerobicno94.992no
halophileyes93.897yes
spore-formingno95.462yes
glucose-utilyes91.207yes
motileno95.372yes
flagellatedno98.327no
thermophileno99.305yes
aerobicno97.633no
glucose-fermentyes90.169no

External links

@ref: 7228

culture collection no.: DSM 18001, CCUG 51290, LMG 23082, CIP 109142, JCM 30772, BCRC 17601, FAIR-E 180, NCIMB 14315, BFE 1652

straininfo link

  • @ref: 75870
  • straininfo: 94605

literature

  • topic: Phylogeny
  • Pubmed-ID: 16449434
  • title: Pediococcus stilesii sp. nov., isolated from maize grains.
  • authors: Franz CMAP, Vancanneyt M, Vandemeulebroecke K, De Wachter M, Cleenwerck I, Hoste B, Schillinger U, Holzapfel WH, Swings J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63944-0
  • year: 2006
  • mesh: Bacterial Proteins/analysis, Bacterial Typing Techniques, DNA Fingerprinting/methods, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Pediococcus/*classification/genetics/growth & development/*isolation & purification, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Zea mays/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7228Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18001)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18001
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
31637Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2792028776041
40127Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6851
59133Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51290)https://www.ccug.se/strain?id=51290
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
75870Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID94605.1StrainInfo: A central database for resolving microbial strain identifiers
123319Curators of the CIPCollection of Institut Pasteur (CIP 109142)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109142