Table 1.
The details for nested and standard PCR design and number of successful PCR reactions in vagina and stool samples.
Fig 1.
Box plots comparing nested to standard PCRs in number of OTUs and Shannon’s index.
Note, *P<0.05, **P<0.01, ***P<0.001, the P values were calculated by the Wilcoxon Matched-Pairs Signed Ranks test.
Table 2.
Summary of number of OTUs which were detected by only either nested PCRs or standard PCR controls when compared with each other for the matched samples.
Fig 2.
Principal coordinates analysis (PCoA) of weighted UniFrac distance.
Proportion of variance explained by each axis is denoted in the corresponding axis labels. Each symbol (designated by the combination of color and shape) represents each subject with the open symbols for the nested PCRs and the closed symbols for the standard PCRs. For example, the blue circles represent subject 1 with open blue ones for two nested PCR results and closed blue ones for three standard PCR results.
Fig 3.
Clusters of stool samples based on bacterial genus relative abundance.
Heatmaps were based on the hierarchical clustering solution (Bray-Curtis) distance metric and average clustering method. Row represents different sample ID (The number before the period is the subject ID; The text after the period is the PCR method used.). Columns represent the predominant bacterial genera with mean relative abundance of 0.01 or greater. The colors in the heatmaps represent the relative abundance of each genus, as indicated in the upper left corner of each panel.
Fig 4.
Clusters of vagina samples based on bacterial genus relative abundance.
Heatmaps were based on the hierarchical clustering solution (Bray-Curtis) distance metric and average clustering method. Row represents different sample ID (The number before the period is the subject ID; The text after the period is the PCR method used.). Columns represent the predominant bacterial genera with mean relative abundance of 0.01 or greater. The colors in the heatmaps represent the relative abundance of each genus, as indicated in the upper left corner of each panel.
Fig 5.
Histogram of the LDA scores computed for microbial genera differentially abundant between nested and standard PCRs in stool samples.
The taxa shown in red are the ones with significantly higher abundance by nested PCRs while the taxa shown in green are the ones with significantly higher abundance by standard PCR. The g or f before the taxon name means genus or family.