The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing
Figure 6
PCA of Relative Taxon Abundance
Principal component analysis (PCA) of log2-transformed normalized abundance for 1,450 V3 refOTUs with normalized total abundance of at least ten (same data as in Figure 4A). Cp-associated samples are shown with open symbols, other samples with filled symbols.
(A) PCA axis 1 (accounting for 35.3% of intersample variation) separates the samples of individual B from those of individuals A and C; PCA axis 2 (18.2% of intersample variation) separates Cp-associated samples from others. The separation of the Cp-associated samples from others is greatest for individual A, intermediate for B, and least for C, consistent with the heatmaps (Figure 4) and diversity statistics (Figure 5).
(B) PCA axis 3 (9.7% of intersample variation) captures temporal variability in non-Cp samples of individual A, and to a lesser extent, individual C. Three samples collected from individual A in the week prior to Cp treatment cluster together at one extreme of the range of axis 3 values.
(C) PCA axis 2 versus PCA axis 3.
(D) Scree plot showing the proportion of variance explained by the first 5 PCA axes; the dashed line at 0.059 indicates the amount of variance expected for each axis with random, uncorrelated data.