Microbiome diversity in CC hens. Diversity was measured as Chao1, Shannon, and Simpson in the ceca and lung of hens in a conventional cage (CC, dashed column) environment at early (white), peak (light gray), and late (dark gray) lay. (A) Chao1 in the ceca, (B) Chao1 in the lung, (C) Shannon in the ceca, (D) Shannon in the lung, (E) Simpson in the ceca, (F) Simpson in the lung, (G) Brey–Curtis distance beta diversity in the ceca, and (H) Bray–Curtis distance beta diversity in the lung. Bars represent the interquartile range from 20 hens/group. Statistical significance (P < 0.05) was determined using a one-way ANOVA with Tukey's method for multiple testing correction. ∗, P < 0.05; ∗∗, P < 0.01; ∗∗∗, P < 0.0001.