Strain identifier

BacDive ID: 6387

Type strain: Yes

Species: Pediococcus parvulus

Strain Designation: S182, S 182

Strain history: CIP <- 1986, NCFB <- H.R. White, Queen Elizabeth College, London, UK: strain S 182

NCBI tax ID(s): 54062 (species)

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General

@ref: 8723

BacDive-ID: 6387

DSM-Number: 20332

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

description: Pediococcus parvulus S182 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from silage.

NCBI tax id

  • NCBI tax id: 54062
  • Matching level: species

strain history

@refhistory
8723<- NCDO <- H.R. White, S182
67770IAM 12291 (Pediococus pentosaceus) <-- K. Sakaguchi <-- H. R. White S-182 (Pediococcus parvulus).
67770ATCC 19371 <-- NCIB 9447 <-- E. Coster QEC 106 (S-182).
121602CIP <- 1986, NCFB <- H.R. White, Queen Elizabeth College, London, UK: strain S 182

doi: 10.13145/bacdive6387.20250331.9.3

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 parvulus
  • full scientific name: Pediococcus parvulus Günther and White 1961 (Approved Lists 1980)

@ref: 8723

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Pediococcus

species: Pediococcus parvulus

full scientific name: Pediococcus parvulus Günther and White 1961

strain designation: S182, S 182

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121602positivecoccus-shapedno
125438no91
125438positive94.362

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8723MRS 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
38095MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121602CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41
121602CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperature
8723positivegrowth30
38095positivegrowth30
49241positivegrowth30
49241positivegrowth37
67770positivegrowth30
121602positivegrowth25-37
121602nogrowth15
121602nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
49241microaerophile
121602facultative anaerobe
125439obligate aerobe97.1

murein

  • @ref: 8723
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12160217632nitrate-reduction
12160216301nitrite-reduction
12160217632nitrate+respiration
68371Potassium 5-ketogluconate-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
6837112936D-galactose-builds acid from
6837117754glycerol-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
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
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-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

metabolite tests

  • @ref: 121602
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382alkaline phosphatase+3.1.3.1
121602oxidase-
121602alcohol dehydrogenase-1.1.1.1
121602catalase-1.11.1.6
121602lysine decarboxylase-4.1.1.18
121602ornithine decarboxylase-4.1.1.17
68382esterase (C 4)-

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121602-+---+----++---++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8723-----------+++--------+--+--++--------------------
8723-----------+-+-----------+--+---------------------
121602----------+/-+/-+/---------+/---+/-+/-+/-+/-----------+/-----------

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
8723silage
49241Silage
67770Silage
121602Environment, Silage1962

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Animal feed
#Engineered#Biodegradation#Composting
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_6248.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_156;97_167;98_186;99_6248&stattab=map
  • Last taxonomy: Pediococcus parvulus
  • 16S sequence: LC071841
  • Sequence Identity:
  • Total samples: 4010
  • soil counts: 369
  • aquatic counts: 362
  • animal counts: 2941
  • plant counts: 338

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87231Risk group (German classification)
1216021Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus reuteri ATCC 19371 16S ribosomal RNA gene, partial sequenceAF429538515nuccore1598
20218Lactobacillus reuteri strain ATCC 19371 16S ribosomal RNA gene, partial sequence; 16S-23S intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF429625516nuccore1598
20218Pediococcus parvulus DNA for 16S ribosomal RNA, partial sequenceD885281447nuccore54062
20218Pediococcus parvulus gene for 16S rRNA, partial sequence, strain: NBRC 100673AB6812161501nuccore54062
67770Pediococcus parvulus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5889LC0718411474nuccore54062
67770Pediococcus parvulus gene for 16S ribosomal RNA, partial sequence, strain: JCM 20450LC2581551511nuccore54062

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pediococcus parvulus NBRC 100673GCA_007990205contigncbi54062
66792Pediococcus parvulus JCM 5889GCA_014651215contigncbi54062
66792Pediococcus parvulus strain DSM 2033254062.4wgspatric54062
66792Pediococcus parvulus strain JCM 588954062.14wgspatric54062
66792Pediococcus parvulus strain NBRC 10067354062.13wgspatric54062
66792Pediococcus parvulus DSM 203322775507230draftimg54062

GC content

@refGC-contentmethod
872341.6
6777041.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes94.362no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no88.81yes
125438spore-formingspore-formingAbility to form endo- or exosporesno89.376no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.344no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98no
125438motile2+flagellatedAbility to perform flagellated movementno91no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes58
125439BacteriaNetmotilityAbility to perform movementyes53
125439BacteriaNetgram_stainReaction to gram-stainingpositive80.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.1

External links

@ref: 8723

culture collection no.: CCUG 28439, CCM 3450, DSM 20332, ATCC 19371, NCDO 1634, NCIB 9447, JCM 20450, BCRC 12575, CECT 813, CGMCC 1.2694, CIP 102262, IAM 12291, IFO 12235, JCM 5889, KCTC 3615, LMG 11486, NBRC 100673, NBRC 12235, NCIMB 9447, VKM B-1604

straininfo link

  • @ref: 75860
  • straininfo: 3822

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/urltitlejournalpubmed
8723Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20332)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20332
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
38095Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/13929
49241Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28439)https://www.ccug.se/strain?id=28439
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
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
75860Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3822.1StrainInfo: A central database for resolving microbial strain identifiers
121602Curators of the CIPCollection of Institut Pasteur (CIP 102262)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102262
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1