Strain identifier
BacDive ID: 6396
Type strain:
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)
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
@ref | history |
---|---|
7171 | <- X. Dong; Z-8 <- B. Zhang and X. Dong |
67770 | CGMCC 1.3787 <-- B. Zhang Z-8. |
117235 | CIP <- 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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31543 | positive | 0.8 µm | 0.8 µm | coccus-shaped | no | |
69480 | positive | 100 | ||||
117235 | positive | coccus-shaped | no |
colony morphology
- @ref: 117235
- hemolysis ability: 1
pigmentation
- @ref: 31543
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7171 | MRS MEDIUM (DSMZ Medium 11) | yes | https://mediadive.dsmz.de/medium/11 | 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 |
33271 | MEDIUM 40- for Lactobacillus and Leuconostoc | yes | Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g) | |
117235 | CIP Medium 40 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7171 | positive | growth | 30 | mesophilic |
31543 | positive | growth | 13-44 | |
31543 | positive | optimum | 33.5 | mesophilic |
33271 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31543 | positive | growth | 6.0-6.8 |
31543 | positive | optimum | 6.4 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
7171 | microaerophile |
31543 | facultative anaerobe |
117235 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31543 | no | |
69481 | no | 100 |
69480 | no | 99.991 |
observation
- @ref: 31543
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31543 | 16808 | 2-dehydro-D-gluconate | + | carbon source |
31543 | 22599 | arabinose | + | carbon source |
31543 | 17057 | cellobiose | + | carbon source |
31543 | 16236 | ethanol | + | carbon source |
31543 | 28757 | fructose | + | carbon source |
31543 | 28260 | galactose | + | carbon source |
31543 | 17234 | glucose | + | carbon source |
31543 | 17716 | lactose | + | carbon source |
31543 | 17306 | maltose | + | carbon source |
31543 | 37684 | mannose | + | carbon source |
31543 | 37657 | methyl D-glucoside | + | carbon source |
31543 | 506227 | N-acetylglucosamine | + | carbon source |
31543 | 26546 | rhamnose | + | carbon source |
31543 | 33942 | ribose | + | carbon source |
31543 | 17992 | sucrose | + | carbon source |
31543 | 27082 | trehalose | + | carbon source |
31543 | 18222 | xylose | + | carbon source |
31543 | 4853 | esculin | + | hydrolysis |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | + | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | + | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | + | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | + | builds acid from |
68371 | 4853 | esculin | + | builds acid from |
68371 | 18305 | arbutin | + | builds acid from |
68371 | 27613 | amygdalin | + | builds acid from |
68371 | 59640 | N-acetylglucosamine | + | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | + | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | + | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | + | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | + | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
117235 | 17632 | nitrate | - | reduction |
117235 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 117235
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | + | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
117235 | oxidase | - | |
117235 | alcohol dehydrogenase | - | 1.1.1.1 |
117235 | catalase | - | 1.11.1.6 |
117235 | lysine decarboxylase | - | 4.1.1.18 |
117235 | ornithine decarboxylase | - | 4.1.1.17 |
117235 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
117235 | - | - | - | - | + | + | - | - | - | - | - | + | + | - | - | + | + | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
117235 | - | - | - | - | - | - | - | - | - | + | + | + | + | - | + | - | - | - | - | + | + | + | + | + | + | + | + | + | - | - | - | + | - | - | - | - | - | - | + | - | - | + | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
7171 | distilled pirit-fermenting cellar | Hebei Province | China | CHN | Asia | |
67770 | Distilled-spirit-fermenting cellar | |||||
117235 | Distilled spirit fermenting cellar | Hebei | China | CHN | Asia | 2004 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
7171 | 1 | Risk group (German classification) |
117235 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
7171 | Pediococcus cellicola strain Z-8 16S ribosomal RNA gene, partial sequence | AY956788 | 1542 | ena | 319652 |
67770 | Pediococcus cellicola gene for 16S ribosomal RNA, partial sequence, strain: JCM 14152 | LC258134 | 1457 | ena | 319652 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pediococcus cellicola strain DSM 17757 | 319652.3 | wgs | patric | 319652 |
66792 | Pediococcus cellicola strain NBRC 106103 | 319652.4 | wgs | patric | 319652 |
66792 | Pediococcus cellicola DSM 17757 | 2657245420 | draft | img | 319652 |
67770 | Pediococcus cellicola NBRC 106103 | GCA_007989045 | contig | ncbi | 319652 |
67770 | Pediococcus cellicola DSM 17757 | GCA_001438655 | contig | ncbi | 319652 |
GC content
@ref | GC-content | method |
---|---|---|
7171 | 38.1 | |
31543 | 37 | |
67770 | 37 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 95.605 | yes |
anaerobic | no | 88.892 | yes |
halophile | yes | 90.28 | no |
spore-forming | no | 94.948 | yes |
glucose-util | yes | 91.601 | yes |
motile | no | 93.939 | yes |
flagellated | no | 98.546 | yes |
aerobic | no | 97.113 | no |
thermophile | no | 99.425 | yes |
glucose-ferment | yes | 86.757 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16166726 | Pediococcus cellicola sp. nov., a novel lactic acid coccus isolated from a distilled-spirit-fermenting cellar. | Zhang B, Tong H, Dong X | Int J Syst Evol Microbiol | 10.1099/ijs.0.63778-0 | 2005 | China, 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/*microbiology | Genetics |
Phylogeny | 17012570 | Pediococcus ethanolidurans sp. nov., isolated from the walls of a distilled-spirit-fermenting cellar. | Liu L, Zhang B, Tong H, Dong X | Int J Syst Evol Microbiol | 10.1099/ijs.0.64407-0 | 2006 | Alcoholic 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, DNA | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7171 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17757) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17757 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
31543 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27835 | 28776041 | ||
33271 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6680 | |||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68371 | Automatically annotated from API 50CH acid | ||||||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
75869 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265617.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
117235 | Curators of the CIP | Collection of Institut Pasteur (CIP 108990) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108990 |