Table 1.
NE frequency and mean lesion score by groups.
Fig 1.
Microbiota composition in jejunum and cecum with different treatments.
Each bar represents the average relative abundance of each bacterial taxon within a group. The top 5 and 10 abundant taxa are shown at the level of phylum and genus, respectively. (A) Abundant phyla in jejunum and ceca by groups; (B) Abundant genera in jejunum and ceca by groups; (C) Abundant genera in jejunal and cecal samples. LS stands for lesion score of NE.
Fig 2.
Differential abundance of genera between jejunal and cecal groups analyzed by metagenomeSeq.
In the jejunum, Lactobacillus in CP1 treatment (AJ) was significantly decreased compared to the control: EJ (A); Clostridium sensu stricto 1 in CP1+Eimeria (BJ) and Lauric acid supplementation (CJ) were both significantly higher than EJ (B); In Eimeria-treated group (DJ), Weissella and Staphylococcus both showed significantly abundant compared to BJ and EJ; For Escherichia Shigella, only BJ presented significantly abundant compare to DJ (E). In the cecum, lauric acid supplementation (CC) promoted significant higher abundance than CP1 treatment (AC); Eisenbergiella in CP1+Eimeria (BJ) was significantly abundant compared to the control: EC (F). * p ≤ 0.05 and ** p ≤ 0.01.
Fig 3.
Comparison of microbial diversity between groups in jejunum and cecum using different measures of alpha diversity.
(A) Shannon index, (B) Simpson index (C), abundance-based coverage estimator (ACE) index, and (D) Chao1 index. Results are shown as mean ± SEM. Kruskal-Wallis test: * p ≤ 0.05, ** p ≤ 0.01, and *** p ≤ 0.001.
Fig 4.
Comparison of the compositions and similarities of jejunal and cecal microbiota with different treatments.
(A) Weighted Unifrac principal coordinate analysis (PCoA); (B) principal component analysis (PCA); (C) cluster analysis by unweighted paired-group method using arithmetic means (UPGMA) using unweighted Unifrac distance; (D) heat map analysis at the genus level.
Fig 5.
Principal component analysis and hierarchical clustering of contributory genus to NE assemblage (in red circle) and to the dissimilarity between groups.
Fig 6.
Heat map analysis of contributory taxa to NE at the genus level in jejunal (A) and cecal (B) samples. (C) Heat map of gut bacteria with the relative abundance of OTUS by z score and represented bacterial taxa information, including phylum, family, genus, and species. Top 26 taxa was shown.
Fig 7.
LEfSe identified the most differentially abundant clades at all taxonomic levels between jejunal groups using the LDA score of 4.
Differentially abundant taxa in group BJ versus EJ (A) and CJ versus EJ (B).