Figure 2
Beta diversity shifts of turkey cecal (A,D), ileal (B,E), and jejunal (C,F) microbiome through time and as affected by BMD treatment as estimated by the Bray-Curtis measure. A non-metric multidimensional scaling (NMDS) ordination was calculated (Fig. S1) for each gut ___location (indicated at top of each figure) individually (A–C) with stress indicated below each figure. Ellipses indicate the 95% confidence interval with the symbol at the centroid of all replicate samples of a treatment group (indicated by symbol shape) on each day (indicated by color). Individual replicate data points are omitted for clarity but all data points are shown in Fig. S1. The cecal and ileal communities mature through the 12-week span of this experiment, while the jejunal community matures to a lesser extent. Statistical testing (PERMANOVA) for differences in beta diversity due to BMD treatment are indicated in (panels D,E). The F value indicates the degree of difference between the two communities compared. Symbol shapes indicate the pairwise treatment beta groups tested and symbol color indicates if the beta diversity was statistically different. P-values were adjusted by using the false discovery rate method for multiple comparisons. BMD treatment resulted in different cecal bacterial communities at every time point considered, but fewer differences were observed in the ileal bacterial communities, and nearly no differences were observed in the jejunal bacterial communities due to BMD treatment. ctrl, no antibiotic control; sub, subtherapeutic BMD dose; ther, therapeutic BMD dose.
