Figure 5
Comparison of α- and β- diversity between the observed and the expected community structures from each experimental procedure. (A) Box plots of Bray-Curtis distances between the expected and the observed microbiome diversity. The highest reproducibility of oral microbiota structure was found in those featuring combination of mechanical and enzymatic lysis methods (M5 and M6), followed by M3, M4, M2 and M1. (B) Both Shannon and Simpson indices representing α diversity were significantly different among the DNA extraction methods (p < 0.001, Kruskal-Wallis test), yet no difference was found among hypervariable regions on both indices (p > 0.05, Kruskal-Wallis test). Regardless of the primer sets chosen, α diversity indices from M5, M6 and M3 were the closest to the expected microbiota structure (p > 0.05, Kruskal-Wallis test).
