zymobiomics dna miniprep kit  (Zymo Research)


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    Name:
    ZymoBIOMICS DNA Miniprep Kit
    Description:
    The ZymoBIOMICS DNA Kits are designed for purifying DNA from a variety of sample inputs that is immediately ready for microbiome or metagenome analyses The ZymoBIOMICS lysis system eliminates bias associated with unequal lysis efficiencies of different organisms e g Gram negative positive bacteria fungus protozoans and algae making it ideal for microbial community profiling Uniform mechanical lysis of all microbes is achieved by bead beating with the innovative ultra high density BashingBeads This kit is equipped with our OneStep PCR Inhibitor removal technology enabling PCR amplification from DNA derived from inhibitor rich environmental samples Purified DNA is ideal for all downstream applications including PCR arrays 16S rRNA gene sequencing and shotgun sequencing DNA Size is 15 20 kb
    Catalog Number:
    d4300t
    Price:
    None
    Applications:
    DNA Purification
    Size:
    50 units
    Category:
    Life Science Reagents and Media
    Buy from Supplier


    Structured Review

    Zymo Research zymobiomics dna miniprep kit
    ZymoBIOMICS DNA Miniprep Kit
    The ZymoBIOMICS DNA Kits are designed for purifying DNA from a variety of sample inputs that is immediately ready for microbiome or metagenome analyses The ZymoBIOMICS lysis system eliminates bias associated with unequal lysis efficiencies of different organisms e g Gram negative positive bacteria fungus protozoans and algae making it ideal for microbial community profiling Uniform mechanical lysis of all microbes is achieved by bead beating with the innovative ultra high density BashingBeads This kit is equipped with our OneStep PCR Inhibitor removal technology enabling PCR amplification from DNA derived from inhibitor rich environmental samples Purified DNA is ideal for all downstream applications including PCR arrays 16S rRNA gene sequencing and shotgun sequencing DNA Size is 15 20 kb
    https://www.bioz.com/result/zymobiomics dna miniprep kit/product/Zymo Research
    Average 99 stars, based on 424 article reviews
    Price from $9.99 to $1999.99
    zymobiomics dna miniprep kit - by Bioz Stars, 2020-10
    99/100 stars

    Images

    1) Product Images from "The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles"

    Article Title: The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

    Journal: Methods and Protocols

    doi: 10.3390/mps3020039

    HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.
    Figure Legend Snippet: HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.

    Techniques Used: DNA Extraction

    Complete linkage hierarchical clustering showing the relative abundances of bacterial taxa in the HM sample spiked with ZMCS. ( A ) Kit A DNA extraction protocol as per manufacturer’s recommendations and ( B ) Kit A DNA extraction protocol in which the initial steps (steps 1 to 4) involving degradation and digestion of host DNA were omitted. Samples were processed in duplicate. WM: whole milk, SM: skim milk, ZMCS: Zymobiomics Microbial Community Standard reference.
    Figure Legend Snippet: Complete linkage hierarchical clustering showing the relative abundances of bacterial taxa in the HM sample spiked with ZMCS. ( A ) Kit A DNA extraction protocol as per manufacturer’s recommendations and ( B ) Kit A DNA extraction protocol in which the initial steps (steps 1 to 4) involving degradation and digestion of host DNA were omitted. Samples were processed in duplicate. WM: whole milk, SM: skim milk, ZMCS: Zymobiomics Microbial Community Standard reference.

    Techniques Used: DNA Extraction

    2) Product Images from "The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles"

    Article Title: The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

    Journal: Methods and Protocols

    doi: 10.3390/mps3020039

    Relative abundances of bacterial taxa extracted by skim milk and whole milk in comparison to the commercial ZMCS composition. The horizontal line in each box indicates the relative abundance of the organism in question in the commercial ZMCS as given by the manufacturer. p > 0.05 shows a non-statistically significant difference in relative abundance of each bacterial taxon in the human milk (HM) sample spiked with ZMCS as extracted by skim milk and whole milk. p -values were generated by Anova test in stats package of R and adjusted using Benjamini–Hochberg’s false discovery rate. ZMCS = Zymobiomics Microbial Community Standard.
    Figure Legend Snippet: Relative abundances of bacterial taxa extracted by skim milk and whole milk in comparison to the commercial ZMCS composition. The horizontal line in each box indicates the relative abundance of the organism in question in the commercial ZMCS as given by the manufacturer. p > 0.05 shows a non-statistically significant difference in relative abundance of each bacterial taxon in the human milk (HM) sample spiked with ZMCS as extracted by skim milk and whole milk. p -values were generated by Anova test in stats package of R and adjusted using Benjamini–Hochberg’s false discovery rate. ZMCS = Zymobiomics Microbial Community Standard.

    Techniques Used: Generated

    Complete linkage hierarchical clustering showing the relative abundances of bacterial taxa in the HM sample spiked with ZMCS. ( A ) Kit A DNA extraction protocol as per manufacturer’s recommendations and ( B ) Kit A DNA extraction protocol in which the initial steps (steps 1 to 4) involving degradation and digestion of host DNA were omitted. Samples were processed in duplicate. WM: whole milk, SM: skim milk, ZMCS: Zymobiomics Microbial Community Standard reference.
    Figure Legend Snippet: Complete linkage hierarchical clustering showing the relative abundances of bacterial taxa in the HM sample spiked with ZMCS. ( A ) Kit A DNA extraction protocol as per manufacturer’s recommendations and ( B ) Kit A DNA extraction protocol in which the initial steps (steps 1 to 4) involving degradation and digestion of host DNA were omitted. Samples were processed in duplicate. WM: whole milk, SM: skim milk, ZMCS: Zymobiomics Microbial Community Standard reference.

    Techniques Used: DNA Extraction

    3) Product Images from "The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles"

    Article Title: The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

    Journal: Methods and Protocols

    doi: 10.3390/mps3020039

    HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.
    Figure Legend Snippet: HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.

    Techniques Used: DNA Extraction

    4) Product Images from "The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles"

    Article Title: The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

    Journal: Methods and Protocols

    doi: 10.3390/mps3020039

    HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.
    Figure Legend Snippet: HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.

    Techniques Used: DNA Extraction

    5) Product Images from "The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles"

    Article Title: The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

    Journal: Methods and Protocols

    doi: 10.3390/mps3020039

    HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.
    Figure Legend Snippet: HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.

    Techniques Used: DNA Extraction

    Relative abundances of bacterial taxa extracted by skim milk and whole milk in comparison to the commercial ZMCS composition. The horizontal line in each box indicates the relative abundance of the organism in question in the commercial ZMCS as given by the manufacturer. p > 0.05 shows a non-statistically significant difference in relative abundance of each bacterial taxon in the human milk (HM) sample spiked with ZMCS as extracted by skim milk and whole milk. p -values were generated by Anova test in stats package of R and adjusted using Benjamini–Hochberg’s false discovery rate. ZMCS = Zymobiomics Microbial Community Standard.
    Figure Legend Snippet: Relative abundances of bacterial taxa extracted by skim milk and whole milk in comparison to the commercial ZMCS composition. The horizontal line in each box indicates the relative abundance of the organism in question in the commercial ZMCS as given by the manufacturer. p > 0.05 shows a non-statistically significant difference in relative abundance of each bacterial taxon in the human milk (HM) sample spiked with ZMCS as extracted by skim milk and whole milk. p -values were generated by Anova test in stats package of R and adjusted using Benjamini–Hochberg’s false discovery rate. ZMCS = Zymobiomics Microbial Community Standard.

    Techniques Used: Generated

    Complete linkage hierarchical clustering showing the relative abundances of bacterial taxa in the HM sample spiked with ZMCS. ( A ) Kit A DNA extraction protocol as per manufacturer’s recommendations and ( B ) Kit A DNA extraction protocol in which the initial steps (steps 1 to 4) involving degradation and digestion of host DNA were omitted. Samples were processed in duplicate. WM: whole milk, SM: skim milk, ZMCS: Zymobiomics Microbial Community Standard reference.
    Figure Legend Snippet: Complete linkage hierarchical clustering showing the relative abundances of bacterial taxa in the HM sample spiked with ZMCS. ( A ) Kit A DNA extraction protocol as per manufacturer’s recommendations and ( B ) Kit A DNA extraction protocol in which the initial steps (steps 1 to 4) involving degradation and digestion of host DNA were omitted. Samples were processed in duplicate. WM: whole milk, SM: skim milk, ZMCS: Zymobiomics Microbial Community Standard reference.

    Techniques Used: DNA Extraction

    6) Product Images from "Evaluation of Extraction Methods for Clinical Metagenomic Assay"

    Article Title: Evaluation of Extraction Methods for Clinical Metagenomic Assay

    Journal: Microorganisms

    doi: 10.3390/microorganisms8081128

    Schematic presentation of the extraction protocols used for comparison in this study. DNA -Seq stand for DNA sequencing and RNA-Seq stand for RNA sequencing.
    Figure Legend Snippet: Schematic presentation of the extraction protocols used for comparison in this study. DNA -Seq stand for DNA sequencing and RNA-Seq stand for RNA sequencing.

    Techniques Used: DNA Sequencing, RNA Sequencing Assay

    7) Product Images from "Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota"

    Article Title: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota

    Journal: bioRxiv

    doi: 10.1101/2020.01.27.921619

    Distinct detections of microbe among the DNA extraction protocols. (A) A bar graph showing 23 significantly enriched taxa with ZymoBIOMICS, 3 with QIAamp DNA Mini Kit, and 3 with IndiSpin Pathogen Kit determined by the linear discriminant analysis (LDA) effect size (LEfSe) analyses [ 31 ]. (B) A taxonomic cladogram from the same LEfSe analyses showing that the significantly enriched microbiota in ZymoBIOMICS were composed of phylum Proteobacteria . Also note that Meiothermus (a member of the phylum Deinococcus-Thermus ) Hydrogenophilaceae (a member of the phylum Proteobacteria ), and Hydrogenophilus (a member of the phylum Proteobacteria ) are likely an extraction kit contaminant. Zy: ZymoBIOMICS DNA Miniprep Kit, Pro: QIAamp PowerFecal Pro DNA Kit, QIA: QIAamp DNA Mini Kit, IN: IndiSpin Pathogen Kit. g_: genus, f_: family, o_: order, c_: class, p_: phylum.
    Figure Legend Snippet: Distinct detections of microbe among the DNA extraction protocols. (A) A bar graph showing 23 significantly enriched taxa with ZymoBIOMICS, 3 with QIAamp DNA Mini Kit, and 3 with IndiSpin Pathogen Kit determined by the linear discriminant analysis (LDA) effect size (LEfSe) analyses [ 31 ]. (B) A taxonomic cladogram from the same LEfSe analyses showing that the significantly enriched microbiota in ZymoBIOMICS were composed of phylum Proteobacteria . Also note that Meiothermus (a member of the phylum Deinococcus-Thermus ) Hydrogenophilaceae (a member of the phylum Proteobacteria ), and Hydrogenophilus (a member of the phylum Proteobacteria ) are likely an extraction kit contaminant. Zy: ZymoBIOMICS DNA Miniprep Kit, Pro: QIAamp PowerFecal Pro DNA Kit, QIA: QIAamp DNA Mini Kit, IN: IndiSpin Pathogen Kit. g_: genus, f_: family, o_: order, c_: class, p_: phylum.

    Techniques Used: DNA Extraction

    Comparisons of alpha diversity between different DNA extraction protocols. The alpha diversity indices determined by Species richness and Phylogenetic diversity are significantly higher with ZymoBIOMICS in comparison with PowerFecalPro (p = 0.025 and 0.012, respectively, Dunn’s test with Benjamini-Hochberg-adjustment). IndiSpin also showed significantly higher diversity than that of PowerFecalPro using analysis of Species richness (p = 0.042, Dunn’s test with Benjamini-Hochberg-adjustment). No significant differences were observed in other alpha diversity indexes such as observed OTUs, Shannon’s diversity index, and Pielou’s Evenness. Zy: ZymoBIOMICS DNA Miniprep Kit, Pro: QIAamp PowerFecal Pro DNA Kit, QIA: QIAamp DNA Mini Kit, IN: IndiSpin Pathogen Kit.
    Figure Legend Snippet: Comparisons of alpha diversity between different DNA extraction protocols. The alpha diversity indices determined by Species richness and Phylogenetic diversity are significantly higher with ZymoBIOMICS in comparison with PowerFecalPro (p = 0.025 and 0.012, respectively, Dunn’s test with Benjamini-Hochberg-adjustment). IndiSpin also showed significantly higher diversity than that of PowerFecalPro using analysis of Species richness (p = 0.042, Dunn’s test with Benjamini-Hochberg-adjustment). No significant differences were observed in other alpha diversity indexes such as observed OTUs, Shannon’s diversity index, and Pielou’s Evenness. Zy: ZymoBIOMICS DNA Miniprep Kit, Pro: QIAamp PowerFecal Pro DNA Kit, QIA: QIAamp DNA Mini Kit, IN: IndiSpin Pathogen Kit.

    Techniques Used: DNA Extraction

    Taxonomic resolution among DNA extraction protocols. (A) Relative abundance of microbe at family level (left) and genus level (right) per DNA extraction method showed the pattern that variance of microbe composition per patient was higher than that per DNA extraction protocol. These patterns were confirmed by values of Adonis test ( q2-diversity adonis ); F.Model: 199.4, R2: 0.982, and p value: 0.001 for patients and F.Model: 2.9, R2: 0.003, and p value: 0.002 for DNA extraction [ 80 ] [ 81 ]. After all count data of taxonomy were converted to relative abundance as shown in the y-axis, the top ten taxonomy at each family and genus level were plotted in colored bar plot and other relatively few taxonomies were not plotted. The 20 patients ID were described in the x-axis. (B) Venn diagrams, considering only those OTUs with a frequency greater than 0.005% shown, revealed that ZymoBIOMICS had four unique taxa at family (left) and genus (right) taxonomic level. Thirty-one of 41 families and 45 of 57 genera were detected with all DNA extraction protocols.
    Figure Legend Snippet: Taxonomic resolution among DNA extraction protocols. (A) Relative abundance of microbe at family level (left) and genus level (right) per DNA extraction method showed the pattern that variance of microbe composition per patient was higher than that per DNA extraction protocol. These patterns were confirmed by values of Adonis test ( q2-diversity adonis ); F.Model: 199.4, R2: 0.982, and p value: 0.001 for patients and F.Model: 2.9, R2: 0.003, and p value: 0.002 for DNA extraction [ 80 ] [ 81 ]. After all count data of taxonomy were converted to relative abundance as shown in the y-axis, the top ten taxonomy at each family and genus level were plotted in colored bar plot and other relatively few taxonomies were not plotted. The 20 patients ID were described in the x-axis. (B) Venn diagrams, considering only those OTUs with a frequency greater than 0.005% shown, revealed that ZymoBIOMICS had four unique taxa at family (left) and genus (right) taxonomic level. Thirty-one of 41 families and 45 of 57 genera were detected with all DNA extraction protocols.

    Techniques Used: DNA Extraction

    8) Product Images from "The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles"

    Article Title: The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

    Journal: Methods and Protocols

    doi: 10.3390/mps3020039

    HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.
    Figure Legend Snippet: HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.

    Techniques Used: DNA Extraction

    9) Product Images from "The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles"

    Article Title: The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

    Journal: Methods and Protocols

    doi: 10.3390/mps3020039

    HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.
    Figure Legend Snippet: HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.

    Techniques Used: DNA Extraction

    10) Product Images from "Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota"

    Article Title: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota

    Journal: bioRxiv

    doi: 10.1101/2020.01.27.921619

    Distinct detections of microbe among the DNA extraction protocols. (A) A bar graph showing 23 significantly enriched taxa with ZymoBIOMICS, 3 with QIAamp DNA Mini Kit, and 3 with IndiSpin Pathogen Kit determined by the linear discriminant analysis (LDA) effect size (LEfSe) analyses [ 31 ]. (B) A taxonomic cladogram from the same LEfSe analyses showing that the significantly enriched microbiota in ZymoBIOMICS were composed of phylum Proteobacteria . Also note that Meiothermus (a member of the phylum Deinococcus-Thermus ) Hydrogenophilaceae (a member of the phylum Proteobacteria ), and Hydrogenophilus (a member of the phylum Proteobacteria ) are likely an extraction kit contaminant. Zy: ZymoBIOMICS DNA Miniprep Kit, Pro: QIAamp PowerFecal Pro DNA Kit, QIA: QIAamp DNA Mini Kit, IN: IndiSpin Pathogen Kit. g_: genus, f_: family, o_: order, c_: class, p_: phylum.
    Figure Legend Snippet: Distinct detections of microbe among the DNA extraction protocols. (A) A bar graph showing 23 significantly enriched taxa with ZymoBIOMICS, 3 with QIAamp DNA Mini Kit, and 3 with IndiSpin Pathogen Kit determined by the linear discriminant analysis (LDA) effect size (LEfSe) analyses [ 31 ]. (B) A taxonomic cladogram from the same LEfSe analyses showing that the significantly enriched microbiota in ZymoBIOMICS were composed of phylum Proteobacteria . Also note that Meiothermus (a member of the phylum Deinococcus-Thermus ) Hydrogenophilaceae (a member of the phylum Proteobacteria ), and Hydrogenophilus (a member of the phylum Proteobacteria ) are likely an extraction kit contaminant. Zy: ZymoBIOMICS DNA Miniprep Kit, Pro: QIAamp PowerFecal Pro DNA Kit, QIA: QIAamp DNA Mini Kit, IN: IndiSpin Pathogen Kit. g_: genus, f_: family, o_: order, c_: class, p_: phylum.

    Techniques Used: DNA Extraction

    Comparisons of alpha diversity between different DNA extraction protocols. The alpha diversity indices determined by Species richness and Phylogenetic diversity are significantly higher with ZymoBIOMICS in comparison with PowerFecalPro (p = 0.025 and 0.012, respectively, Dunn’s test with Benjamini-Hochberg-adjustment). IndiSpin also showed significantly higher diversity than that of PowerFecalPro using analysis of Species richness (p = 0.042, Dunn’s test with Benjamini-Hochberg-adjustment). No significant differences were observed in other alpha diversity indexes such as observed OTUs, Shannon’s diversity index, and Pielou’s Evenness. Zy: ZymoBIOMICS DNA Miniprep Kit, Pro: QIAamp PowerFecal Pro DNA Kit, QIA: QIAamp DNA Mini Kit, IN: IndiSpin Pathogen Kit.
    Figure Legend Snippet: Comparisons of alpha diversity between different DNA extraction protocols. The alpha diversity indices determined by Species richness and Phylogenetic diversity are significantly higher with ZymoBIOMICS in comparison with PowerFecalPro (p = 0.025 and 0.012, respectively, Dunn’s test with Benjamini-Hochberg-adjustment). IndiSpin also showed significantly higher diversity than that of PowerFecalPro using analysis of Species richness (p = 0.042, Dunn’s test with Benjamini-Hochberg-adjustment). No significant differences were observed in other alpha diversity indexes such as observed OTUs, Shannon’s diversity index, and Pielou’s Evenness. Zy: ZymoBIOMICS DNA Miniprep Kit, Pro: QIAamp PowerFecal Pro DNA Kit, QIA: QIAamp DNA Mini Kit, IN: IndiSpin Pathogen Kit.

    Techniques Used: DNA Extraction

    Taxonomic resolution among DNA extraction protocols. (A) Relative abundance of microbe at family level (left) and genus level (right) per DNA extraction method showed the pattern that variance of microbe composition per patient was higher than that per DNA extraction protocol. These patterns were confirmed by values of Adonis test ( q2-diversity adonis ); F.Model: 199.4, R2: 0.982, and p value: 0.001 for patients and F.Model: 2.9, R2: 0.003, and p value: 0.002 for DNA extraction [ 80 ] [ 81 ]. After all count data of taxonomy were converted to relative abundance as shown in the y-axis, the top ten taxonomy at each family and genus level were plotted in colored bar plot and other relatively few taxonomies were not plotted. The 20 patients ID were described in the x-axis. (B) Venn diagrams, considering only those OTUs with a frequency greater than 0.005% shown, revealed that ZymoBIOMICS had four unique taxa at family (left) and genus (right) taxonomic level. Thirty-one of 41 families and 45 of 57 genera were detected with all DNA extraction protocols.
    Figure Legend Snippet: Taxonomic resolution among DNA extraction protocols. (A) Relative abundance of microbe at family level (left) and genus level (right) per DNA extraction method showed the pattern that variance of microbe composition per patient was higher than that per DNA extraction protocol. These patterns were confirmed by values of Adonis test ( q2-diversity adonis ); F.Model: 199.4, R2: 0.982, and p value: 0.001 for patients and F.Model: 2.9, R2: 0.003, and p value: 0.002 for DNA extraction [ 80 ] [ 81 ]. After all count data of taxonomy were converted to relative abundance as shown in the y-axis, the top ten taxonomy at each family and genus level were plotted in colored bar plot and other relatively few taxonomies were not plotted. The 20 patients ID were described in the x-axis. (B) Venn diagrams, considering only those OTUs with a frequency greater than 0.005% shown, revealed that ZymoBIOMICS had four unique taxa at family (left) and genus (right) taxonomic level. Thirty-one of 41 families and 45 of 57 genera were detected with all DNA extraction protocols.

    Techniques Used: DNA Extraction

    11) Product Images from "How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis"

    Article Title: How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis

    Journal: International Journal of Molecular Sciences

    doi: 10.3390/ijms19103256

    Comparison of median levels of ( a ) DNA extraction yield, ( b ) coefficient of variation between replicates, ( c ) 16s rRNA gene real-time PCR results, and ( d ) coefficient of variation between replicates across dithiothreitol (DTT)-untreated sputum vs. DTT-treated (Experiment 1).
    Figure Legend Snippet: Comparison of median levels of ( a ) DNA extraction yield, ( b ) coefficient of variation between replicates, ( c ) 16s rRNA gene real-time PCR results, and ( d ) coefficient of variation between replicates across dithiothreitol (DTT)-untreated sputum vs. DTT-treated (Experiment 1).

    Techniques Used: DNA Extraction, Real-time Polymerase Chain Reaction

    12) Product Images from "How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis"

    Article Title: How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis

    Journal: International Journal of Molecular Sciences

    doi: 10.3390/ijms19103256

    Comparison of median levels of ( a ) DNA extraction yield, ( b ) coefficient of variation between replicates, ( c ) 16s rRNA gene real-time PCR results, and ( d ) coefficient of variation between replicates across dithiothreitol (DTT)-untreated sputum vs. DTT-treated (Experiment 1).
    Figure Legend Snippet: Comparison of median levels of ( a ) DNA extraction yield, ( b ) coefficient of variation between replicates, ( c ) 16s rRNA gene real-time PCR results, and ( d ) coefficient of variation between replicates across dithiothreitol (DTT)-untreated sputum vs. DTT-treated (Experiment 1).

    Techniques Used: DNA Extraction, Real-time Polymerase Chain Reaction

    13) Product Images from "The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles"

    Article Title: The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles

    Journal: Methods and Protocols

    doi: 10.3390/mps3020039

    HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.
    Figure Legend Snippet: HM samples cluster primarily based on the donor. Complete linkage unsupervised hierarchical clustering based on the relative abundances of bacteria genera in un-spiked HM samples show that DNA extraction kits and milk type affects bacterial profiles less when compared to the source. W: whole milk, S: skim milk; 1–10 represents each donor; kit B: ZR Fungal/Bacterial DNA MiniPrep™, kit C: QIAsymphony DSP DNA Kit, and kit D: ZymoBIOMICS™ DNA Miniprep Kit.

    Techniques Used: DNA Extraction

    Complete linkage hierarchical clustering showing the relative abundances of bacterial taxa in the HM sample spiked with ZMCS. ( A ) Kit A DNA extraction protocol as per manufacturer’s recommendations and ( B ) Kit A DNA extraction protocol in which the initial steps (steps 1 to 4) involving degradation and digestion of host DNA were omitted. Samples were processed in duplicate. WM: whole milk, SM: skim milk, ZMCS: Zymobiomics Microbial Community Standard reference.
    Figure Legend Snippet: Complete linkage hierarchical clustering showing the relative abundances of bacterial taxa in the HM sample spiked with ZMCS. ( A ) Kit A DNA extraction protocol as per manufacturer’s recommendations and ( B ) Kit A DNA extraction protocol in which the initial steps (steps 1 to 4) involving degradation and digestion of host DNA were omitted. Samples were processed in duplicate. WM: whole milk, SM: skim milk, ZMCS: Zymobiomics Microbial Community Standard reference.

    Techniques Used: DNA Extraction

    Related Articles

    DNA Extraction:

    Article Title: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota
    Article Snippet: .. DNA extraction protocols We selected four commercially available DNA extraction kits as the candidates for comparison: ZymoBIOMICS DNA Miniprep Kit (Zymo Research, D4300), QIAamp PowerFecal Pro DNA Kit (QIAGEN, 51804), QIAamp DNA Mini Kit (QIAGEN, 51304), and IndiSpin Pathogen Kit (Indical Bioscience, SPS4104). ..

    Article Title: The Influence of DNA Extraction and Lipid Removal on Human Milk Bacterial Profiles
    Article Snippet: .. Four commercial DNA extraction kits, QIAamp® DNA Microbiome Kit, ZR Fungal/Bacterial DNA MiniPrep™, QIAsymphony DSP DNA Kit and ZymoBIOMICS™ DNA Miniprep Kit, were assessed using milk collected from ten healthy lactating women. ..

    Article Title: Comparison of Bacterial Community Structure and Diversity in Traditional Gold Mining Waste Disposal Site and Rice Field by Using a Metabarcoding Approach
    Article Snippet: .. DNA Extraction, PCR Amplification, 454 Pyrosequencing, and High-Throughput Sequencing Data Processing The genomic DNAs (gDNAs) of bacteria were extracted from soil using ZymoBiomics DNA Mini kit (Zymo Research) according to the protocol provided by the manufacturer. .. Amplification of hypervariable V3-V4 regions of 16S rRNA were performed using MyTaq™ HS Red Mix (Bioline, BIO-25044) in Agilent SureCycler 8800 Thermal Cycler.

    Amplification:

    Article Title: Comparison of Bacterial Community Structure and Diversity in Traditional Gold Mining Waste Disposal Site and Rice Field by Using a Metabarcoding Approach
    Article Snippet: .. DNA Extraction, PCR Amplification, 454 Pyrosequencing, and High-Throughput Sequencing Data Processing The genomic DNAs (gDNAs) of bacteria were extracted from soil using ZymoBiomics DNA Mini kit (Zymo Research) according to the protocol provided by the manufacturer. .. Amplification of hypervariable V3-V4 regions of 16S rRNA were performed using MyTaq™ HS Red Mix (Bioline, BIO-25044) in Agilent SureCycler 8800 Thermal Cycler.

    Polymerase Chain Reaction:

    Article Title: Comparison of Bacterial Community Structure and Diversity in Traditional Gold Mining Waste Disposal Site and Rice Field by Using a Metabarcoding Approach
    Article Snippet: .. DNA Extraction, PCR Amplification, 454 Pyrosequencing, and High-Throughput Sequencing Data Processing The genomic DNAs (gDNAs) of bacteria were extracted from soil using ZymoBiomics DNA Mini kit (Zymo Research) according to the protocol provided by the manufacturer. .. Amplification of hypervariable V3-V4 regions of 16S rRNA were performed using MyTaq™ HS Red Mix (Bioline, BIO-25044) in Agilent SureCycler 8800 Thermal Cycler.

    Sequencing:

    Article Title: Comparison of Bacterial Community Structure and Diversity in Traditional Gold Mining Waste Disposal Site and Rice Field by Using a Metabarcoding Approach
    Article Snippet: .. DNA Extraction, PCR Amplification, 454 Pyrosequencing, and High-Throughput Sequencing Data Processing The genomic DNAs (gDNAs) of bacteria were extracted from soil using ZymoBiomics DNA Mini kit (Zymo Research) according to the protocol provided by the manufacturer. .. Amplification of hypervariable V3-V4 regions of 16S rRNA were performed using MyTaq™ HS Red Mix (Bioline, BIO-25044) in Agilent SureCycler 8800 Thermal Cycler.

    Incubation:

    Article Title: Deciphering Resistome and Virulome Diversity in a Porcine Slaughterhouse and Pork Products Through Its Production Chain
    Article Snippet: .. Bacterial samples, following 24 h incubation at 4°C, were centrifuged (14000 rpm for 10 min), and the DNA were extracted using ZymoBIOMICS DNA Miniprep Kit (Zymo Research, California, United States) according to the manufacturer’s instructions. .. Total DNA quantification and quality were assessed by a NanoDrop 2000 spectrophotometer (Thermo Scientific).

    DNA Sequencing:

    Article Title: 910 metagenome-assembled genomes from the phytobiomes of three urban-farmed leafy Asian greens
    Article Snippet: .. Metagenomic DNA sequencing and assemblyGenomic DNA was extracted from all the samples using the ZymoBIOMICS DNA miniprep kit (Zymo Research, Irvine, CA, USA). ..

    High Throughput Screening Assay:

    Article Title: Comparison of Bacterial Community Structure and Diversity in Traditional Gold Mining Waste Disposal Site and Rice Field by Using a Metabarcoding Approach
    Article Snippet: .. DNA Extraction, PCR Amplification, 454 Pyrosequencing, and High-Throughput Sequencing Data Processing The genomic DNAs (gDNAs) of bacteria were extracted from soil using ZymoBiomics DNA Mini kit (Zymo Research) according to the protocol provided by the manufacturer. .. Amplification of hypervariable V3-V4 regions of 16S rRNA were performed using MyTaq™ HS Red Mix (Bioline, BIO-25044) in Agilent SureCycler 8800 Thermal Cycler.

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  • 99
    Zymo Research zymobiomicstm dna miniprep kit
    Zymobiomicstm Dna Miniprep Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/zymobiomicstm dna miniprep kit/product/Zymo Research
    Average 99 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    zymobiomicstm dna miniprep kit - by Bioz Stars, 2020-10
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