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Items: 4

1.
Fig. 1

Fig. 1. From: An accurate and efficient experimental approach for characterization of the complex oral microbiota.

Box plots of Euclidean distances between observed and expected relative species abundances support accurate assessment of true bacterial mock community composition. Euclidean distances between observed and expected relative species abundances of a mock bacterial community were calculated for four technical replicates of the V1–V3 and V3–V4 regions using OTUs picked with the closed-reference protocol against Greengenes (GG) and HOMD. The x-axis represents the different amplicon/OTU picking method used, and the y-axis represents the distance from expected values

Wei Zheng, et al. Microbiome. 2015;3:48.
2.
Fig. 3

Fig. 3. From: An accurate and efficient experimental approach for characterization of the complex oral microbiota.

Boxplots of Pielou’s index J for V1–V3 and V3–V4 OTUs support a negative relationship between observed oral sample species richness and evenness. Pielou’s index J was estimated independently for all generated taxa summaries at the species level to evaluate species evenness detected by the V1–V3 and V3–V4 regions. Analysis was based on OTUs 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 value for Pielou’s index J, and the y-axis presents the amplicon regions tested. J takes values between 0 and 1, with values closer to 1 representing more even quantities of the different species within a community

Wei Zheng, et al. Microbiome. 2015;3:48.
3.
Fig. 2

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

Wei Zheng, et al. Microbiome. 2015;3:48.
4.
Fig. 4

Fig. 4. From: An accurate and efficient experimental approach for characterization of the complex oral microbiota.

Procrustes analyses demonstrates significant correlation between oral bacterial composition obtained with the V1–V3 and V3–V4 regions. Procrustes analysis of the bacterial composition of V1–V3 (red) and V3–V4 (blue) regions was calculated using the unweighted UniFrac metric. β-diversity distances were computed at the genus level using 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. For a given sample, red lines connect to 16S sequence data from the V1–V3 region while blue lines connect to points generated from the V3–V4 sequence data. The M 2 fit reported is from a Procrustes transformation over the first two principal coordinates, while the P value is calculated from an empirically determined distribution of M 2 values over 10,000 Monte Carlo simulations.

Wei Zheng, et al. Microbiome. 2015;3:48.

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