<p><span class="html-italic">Boxplots of the alpha diversity measurements of ileal microbiota from hens in late-lay and peak lay housed in cage-free (CF) and enriched colony (EC) systems.</span> Gold denotes the diversities from hens in late-lay, and red denotes the diversities from hens in peak lay. The parameters displayed are Observed which represents the number of different taxa observed in the sample, Chao1 which represents species richness within a sample, Shannon which represents the Shannon index or an estimate of both species richness and species evenness within a sample, and Simpson which represents species evenness within a sample.</p> Full article ">Figure 2
<p><span class="html-italic">Principal coordinate analysis comparing the ileal microbiota of hens in cage-free (CF) and enriched colony (EC) systems as well as hens in late-lay and peak lay.</span> Gold denotes hens in late-lay, and red denotes hens in peak lay. Circles denote hens in CF systems, and triangles denote hens in EC systems.</p> Full article ">Figure 3
<p><span class="html-italic">Relative abundance of phyla of ileal microbiota of hens in cage-free (CF) and enriched colony (EC) systems as well as hens in late-lay and peak lay.</span> (<b>A</b>) Percent of relative abundance of phyla for housing system. (<b>B</b>) Percent of relative abundance of phyla for late-lay and peak-lay hens.</p> Full article ">Figure 4
<p><span class="html-italic">Relative abundance of top 15 genera of ileal microbiota of hens in cage-free (CF) and enriched colony (EC) systems as well as hens in late-lay and peak lay.</span> (<b>A</b>) Percent of relative abundance of genera for housing system. (<b>B</b>) Percent of relative abundance of genera for late-lay and peak-lay hens.</p> Full article ">Figure 5
<p><span class="html-italic">Changes in ileal microbiota from hens in enriched colonies (EC) and cage-free (CF) systems across peak and late-lay.</span> Each graph depicts different significant (<span class="html-italic">p</span> < 0.05, q < 0.05) interaction for individual operational taxonomic unit (OTU). Gold lines represent average relative counts from ileal sample collected from enriched colonies. Red lines represent average relative counts from ileal sample collected from cage-free system.</p> Full article ">