Table 1.
Features of the six DNA extraction methods used.
Table 2.
Bacterial strains and cultivation condition used.
Table 3.
Comparison of DNA yields of type strains obtained using six DNA extraction methods.
Table 4.
16S rRNA gene copy numbers, expected and observed proportions of 16S rRNA gene sequence reads for each type strain.
Figure 1.
Boxplot of Euclidean distances between observed and expected species proportions.
Euclidean distances between observed and expected proportions were calculated for each of eight replicates of each method.
Figure 2.
Boxplot of Euclidean distances between observed and grand proportions.
To calculate grand proportions, the total counts of 16S rRNA gene reads of each species were calculated for eight replicates of each method. Then grand proportions were calculated based on total counts of 16S rRNA gene reads of each species per method. Grand proportions were used to calculate Euclidean distances between observed and grand proportions.
Figure 3.
DNA extractions using different enzymatic lysis modes.
The mean concentrations (columns) were calculated based on nine replicated extractions per sample per mode. Pair-wise comparisons of DNA concentrations between modes per sample were performed by using Wilcoxon rank sum test. Bonferroni correction was used for multiple testing. Letters at the top of columns indicate whether there is significantly difference between columns per sample. Means with the same letter are not significantly different.