Fig. 2

Alpha diversity of the ileal, cecal, and cloacal microbiota on day 35 between high and low RFI chickens. Differences in richness, overall diversity, and evenness were calculated using observed features (a), Pielou’s Evenness Index (b), and Shannon Index (c), respectively. Results were plotted using box and whisker plots, in which the middle line denoted the median value and the lower and upper hinges represented the first and third quartiles, respectively. Whiskers extended from the hinge to the highest or lowest value no farther than 1.5 × the interquartile range. Points outside of this range are considered outliers. Statistical significance was determined using Kruskal-Wallis test