Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens

Abstract

The intestinal disease coccidiosis, caused by Eimeria parasites, impacts nutrient absorption in broiler chickens, leading to weight gain depression and major losses in the poultry industry. To develop alternatives to antibiotics for treating infected chickens, the gut microbiota has been researched because of its association with health factors such as nutrient exchange, immune system modulation, digestive system physiology, and pathogen exclusion. The aim of this study was to determine the effect of Eimeria acervulina infection on the luminal and mucosal microbiota of both the duodenum (DuoL and DuoM) and jejunum (JejL and JejM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. 16S rRNA amplicon sequencing was utilized to characterize the microbiota and analyze differences in alpha and beta diversity between infected (IF) and control (C) birds at each time point. Alpha diversity differed between IF and C birds in DuoM and JejM microbiota. Combined with beta diversity results, DuoM microbiota appeared to be affected by infection in the longer-term, while JejM microbiota were affected in the shorter-term. Relative abundances of bacterial taxa known for short-chain fatty acid (SCFA) production, such as Lachnospiraceae, Subdoligranulum, and Peptostreptococcaceae, tended to be lower in IF birds for all four microbiota. Moreover, predicted functional abundances showed MetaCyc pathways related to SCFA production, especially butyrate, may be influenced by these differences in bacterial relative abundance. Our findings expand understanding of how Eimeria infection affects luminal and mucosal microbiota in the duodenum and jejunum, and further research on metagenomic function may provide insights on the degree of influence duodenal and jejunal bacteria have on chicken health.

Keywords: 16S; Coccidiosis; broiler chickens; duodenum; jejunum; microbiota.

Figure 1

Relative abundances of bacterial taxa at the genus level in duodenal luminal (DuoL), duodenal mucosal (DuoM), jejunal luminal (JejL), and jejunal mucosal (JejM) microbiota (n = 48 samples for each column). The 15 most abundant taxa overall are indicated in the legend.

Figure 2

Comparisons of: (A) evenness between control and Eimeria acervulina-infected birds in duodenal luminal (DuoL) microbiota; (B) Faith’s phylogenetic diversity (Faith PD, richness) between control and Eimeria acervulina-infected birds in jejunal luminal (JejL) microbiota. Stars (*) denote statistically significant (p < 0.05) differences.

Figure 3

Comparisons of alpha diversity metrics between Eimeria acervulina-infected birds and control birds at multiple time points in duodenal mucosal (DuoM) microbiota, (A) Faith’s phylogenetic diversity (Faith PD, richness), and in jejunal mucosal (JejM) microbiota: (B) number of observed features (ASVs), (C) Faith’s phylogenetic diversity (richness), and (D) evenness. Stars (*) denote statistically significant (p < 0.05) differences between groups.

Figure 4

Principal coordinate analysis (PCoA) based on: (A) unweighted UniFrac distance matrix of duodenal luminal (DuoL) microbiota, (B) unweighted UniFrac and (C) weighted UniFrac distance matrices of duodenal mucosal (DuoM) microbiota, and (D) unweighted UniFrac distance matrix of jejunal mucosal microbiota (JejM). Stars (*) on legend denote microbiota were significantly different (PERMANOVA, p < 0.05) on those days. Longer distances between points indicate microbiota profiles were different, while shorter distances between points indicate profiles were similar.

Figure 5

Linear discriminant analysis effect size (LEfSe) in: (A) duodenal luminal (DuoL) microbiota, (B) duodenal mucosal (DuoM) microbiota, (C) jejunal luminal (JejL) microbiota, and (D) jejunal mucosal (JejM) microbiota. Positive effect size indicates higher relative abundance in Eimeria acervulina-infected birds, while negative effect size indicates higher relative abundance in control birds.

Figure 6

Effect of Eimeria acervulina-infection on mean proportion (%) of predicted MetaCyc pathways (up to the top 15 shown) in the (A) duodenal luminal (DuoL), (B) duodenal mucosal (DuoM), (C) jejunal luminal (JejL), and (D) jejunal mucosal (JejM) bacterial populations.