Fig. 2
From: An accurate and efficient experimental approach for characterization of the complex oral microbiota
Taxonomic richness is greater for V1–V3 compared to V3–V4 based on four different OTU picking approaches. Alpha rarefaction plots for V1–V3 and V3–V4 hypervariable regions were generated at the species level using the “observed number of OTUs,” a minimum rarefaction level of 1, maximum rarefaction level of 100,001, and a step size of 5,000. Sequence sampling was repeated 10 times for each sample size. OTUs were picked based on the a closed-reference OTU picking method against the Greengenes or b HOMD database, and c the de novo OTU picking with uchime or d ChimeraSlayer chimera removal. The x-axis shows the number of sampled sequences, and the y-axis represents the number of observed OTUs. Red lines depict taxonomic richness detected using the V3–V4 amplicon, and blue lines correspond to the V1–V3 amplicon. Error bars exhibit the standard error of mean diversity at each rarefaction level across multiple iterations