Figure 3. Comparison of β-diversity between libraries.

Plot of a Mantel correlation test comparing unweighted UniFrac distance matrices created using synthetic mock communities from paired, R1 and R2 reads (for both the V3–V5 and V6–V9 pairs) versus the distance matrix created from the corresponding full-length 16S synthetic mock communities. A higher correlation value means the distance matrices, and hence their β-diversity, are more closely related to the full-length communities. Here, the communities from paired reads are significantly closer to the full-length communities than the R1 and R2 communities (p<0.0001, Wilcoxon signed ranked test, using 100 synthetic mock communities), strongly suggesting that combining the use of paired reads leads to results closer to what is obtained from full-length reads, even when the chosen primers create non-overlapping reads.