Journal: International Journal of Molecular Sciences

Article Title: Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples

doi: 10.3390/ijms26115226

Figure Lengend Snippet: DNA concentration of amplicons obtained during bacterial library preparations with two protocols, home brew and VeriFi. Amplicons were quantified by Nano Drop ® ND-1000. Median values are indicated by the line in the box plot. The box extends from the 25th to the 75th percentile and whiskers indicate the minimum and maximum values. t -test was used to calculate p -values ( p -value *); ( A ) box plot showing DNA concentrations obtained during the amplification of the 16S rRNA V3–V4 regions, p -value = 0.026; ( B ) box plot showing DNA concentrations obtained during the barcoding step using Nextera TM primers, p -value = 1.6 × 10 −9 .

Article Snippet: VeriFi Library Amplification Mix for NGS Kit (PCR Biosystems simplifying research, London, UK, named VeriFi Kit) : The first PCR reaction was performed using the following reaction mixture: 1X VeriFiTM Hot Start Polymerase, 3 mM MgCl 2 , 1 mM dNTPs (PCR Biosystems simplifying research, London, UK), and 10 μM of each primer mix.

Techniques: Concentration Assay, Amplification

Journal: International Journal of Molecular Sciences

Article Title: Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples

doi: 10.3390/ijms26115226

Figure Lengend Snippet: Sequencing parameters of amplicons obtained using the two protocols of amplification, home brew and VeriFi. The box plots report the median value and the 25th and the 75th percentiles. Wilcoxon rank test was used to calculate p -values. ( A ) Box plot showing the number of reads per sample obtained for the three kits evaluated. ( B ) Figure showing the ASV frequencies for the three kits evaluated. ( C ) Box plot showing the number of chimeras obtained for the three kits evaluated.

Article Snippet: VeriFi Library Amplification Mix for NGS Kit (PCR Biosystems simplifying research, London, UK, named VeriFi Kit) : The first PCR reaction was performed using the following reaction mixture: 1X VeriFiTM Hot Start Polymerase, 3 mM MgCl 2 , 1 mM dNTPs (PCR Biosystems simplifying research, London, UK), and 10 μM of each primer mix.

Techniques: Sequencing, Amplification

Journal: International Journal of Molecular Sciences

Article Title: Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples

doi: 10.3390/ijms26115226

Figure Lengend Snippet: Analysis of alpha and beta diversity. Alpha diversity was based on the Shannon ( A ) and Simpson ( B ) indices. The pairwise Wilcoxon rank test, used to compare the two protocols of amplification, home brew and VeriFi, indicated no statistically significant differences. Beta diversity was calculated using the Bray–Curtis distance and represented by PCoA plot ( C ). PERMANOVA test is statistically significant, p -value = 0.035, R 2 = 0.082. The Bray–Curtis distance was represented by box plot ( D ). **, p value < 0.001.

Article Snippet: VeriFi Library Amplification Mix for NGS Kit (PCR Biosystems simplifying research, London, UK, named VeriFi Kit) : The first PCR reaction was performed using the following reaction mixture: 1X VeriFiTM Hot Start Polymerase, 3 mM MgCl 2 , 1 mM dNTPs (PCR Biosystems simplifying research, London, UK), and 10 μM of each primer mix.

Techniques: Amplification

Journal: International Journal of Molecular Sciences

Article Title: Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples

doi: 10.3390/ijms26115226

Figure Lengend Snippet: Protocol-dependent variations in the relative abundance of microbiota profiles at the phylum ( A , B ) and genus ( C , D ) levels. ( A , C ) Histograms of the relative abundances of the 7 most abundant phyla and 20 most abundant genera obtained by the sequencing of amplicons obtained during bacterial library preparations with two protocols, home brew and VeriFi. ( B , D ) Heatmap showing, for each sample, the relative abundance of the 7 most abundant phyla and 20 most abundant genera for each sample.

Article Snippet: VeriFi Library Amplification Mix for NGS Kit (PCR Biosystems simplifying research, London, UK, named VeriFi Kit) : The first PCR reaction was performed using the following reaction mixture: 1X VeriFiTM Hot Start Polymerase, 3 mM MgCl 2 , 1 mM dNTPs (PCR Biosystems simplifying research, London, UK), and 10 μM of each primer mix.

Techniques: Sequencing