Figure 3

Changes in relative abundance of putative pathogens by treatment and time. A) For each time point (7d, 21d, and 42 d post-hatch), the relative proportions are shown for each of the four treatments. Putative pathogens were defined using the intersection of independent taxonomic classifications with the RDP classifier and the Silva database as described in the methods. Sequences classified as Escherichia or Shigella by Silva are shown separately but not distinguished by RDP. Treatment designations are Ctl, control; FO, feed-only; WO, water-only; and FW, feed and water as described in the text. Note scale of Y axis. B) Number of gene copies of Clostridium as determined by quantitative-PCR for each time point. Treatments for each time point are grouped due to the non-significant effect of treatment as shown in Table 1. Quantitative loads of Clostridium were significantly higher at 21 d than 7d or 42 (p < 0.0001, one-sided t-tests),