Fig. 1

Overview of study design and summary of 16S rRNA data. A Birds are fed one of two diets (corn and wheat) in the presence and absence of AGPs to yield four conditions. Sets of five birds are harvested at days 10, 24, and 40. B From each bird, six intestinal sites were sampled for 16S rRNA analysis; two intestinal sites (jejunum and ceca) were sampled for metatranscriptomics and blood samples collected for metabolomics analysis. C Area plots showing major taxa identified in the six sampling sites of the chicken GI tract at days 10, 24, and 40 across 4 different treatments. Only taxa with an abundance > 1% were included. Note, relative to the older birds, the upper GI sites (gizzard, duodenum, and jejunum) of the 10-day-old birds featured a high proportion of reads mapping to Streptophyta, likely reflecting a reduced breakdown of the plant-based dietary components. D PCoA plots of weighted UniFrac distances for all samples and samples grouped by sampling sites, age, diet, and AGPs. For each plot, results from PERMANOVA and PERMDISP calculations are shown