Table 1.
Sequencing summary of CeL and CeM microbiota datasets processed in QIIME 2. QC = quality control via DADA2, ASVs = amplicon sequence variants.
Fig 1.
Summary of bacterial composition (relative abundance, %) for samples in each group from
(A) CeL and (B) CeM microbiota at the genus level. In each legend, the 10 most common genera overall are listed.
Fig 2.
Comparisons of alpha diversity metrics in the cecal luminal microbiota:
(A) Shannon diversity and (B) observed features (ASVs). Stars (*) denote significant differences (* = P < 0.05, ** = P < 0.01).
Fig 3.
Comparison of the observed features (ASVs) alpha diversity metric in the cecal mucosal microbiota.
Stars (*) denote significant differences (* = P < 0.05).
Fig 4.
Principal coordinate analysis (PCoA) comparing Eimeria maxima-infected birds and control birds at multiple time points based on (A) unweighted UniFrac distance matrix in CeL microbiota, (B) weighted UniFrac distance matrix in CeL microbiota, (C) unweighted UniFrac distance matrix in CeM microbiota, and (D) weighted UniFrac distance matrix in CeM microbiota.
Fig 5.
Differential bacterial abundance analysis using linear discriminant analysis effect size (LEfSe) in: (A) cecal luminal and (B) cecal mucosal microbiota.
Positive effect size (red bars) indicates higher relative abundance in Eimeria maxima-infected birds, while negative effect size (green bars) indicates higher relative abundance in control birds.
Fig 6.
Effect of Eimeria maxima-infection on the differential mean proportion (%) of predicted MetaCyc pathways in the (A) cecal luminal and (B) cecal mucosal microbiota.