The association between microbial community and ileal gene expression on intestinal wall thickness alterations in chickens

Abstract

The dynamic development of the animal intestine with a concurrent succession of microbiota and changes in microbial community and metabolite spectrum can exert far-reaching effects on host physiology. However, the precise mechanism of mutual response between microbiota and the gut is yet to be fully elucidated. Broilers with varying developmental degrees of intestinal wall thickness were selected, and they were divided into the thick group (H type) and the thin group (B type), using multiomics data integration analysis to reveal the fundamental regulatory mechanisms of gut-microbiota interplay. Our data showed, in broilers with similar body weight, the intestinal morphological parameters were improved in H type and the diversity of microbial communities is distinguishable from each other. The beneficial bacteria such as Bifidobacterium breve was increased whereas avian endogenous retrovirus EAV-HP was decreased in the H type compared with the B type. Furthermore, microbial metabolic potentials were more active, especially the biosynthesis of folate was improved in the H type. Similarly, the consolidation of absorption, immunity, metabolism, and development was noticed in the thick group. Correlation analysis indicated that the expression levels of material transport and immunomodulatory-related genes were positively correlated with the relative abundance of several probiotics such as B. breve, Lactobacillus saerimneri, and Butyricicoccus pullicaecorum. Our findings suggest that the chickens with well-developed ileal thickness own exclusive microbial composition and metabolic potential, which is closely related to small intestinal morphogenesis and homeostasis.

Keywords: broiler; ileal transcriptome; immune regulation; intestinal thickness; microbiota.

Figure 1

Observation of intestinal wall morphology in broilers. Representation of the ileal wall of the H type and B type under a light microscope ( × 40) at day 28, the rectangular frame indicating the villus and the arrow indicating the crypt. Sections were stained with hematoxylin and eosin. Scale bar = 250 μm.

Figure 2

Bacterial community variation in intestinal thickness. (A) The effect of intestinal thickness on the observed species number in ileal microbiota (97% similarity rate). The values are shown as median and quartile. (B) The effect of intestinal thickness on the Shannon index in ileal microbiota. The values are shown as median and quartile; ***, P < 0.001 (H type, n = 10; B type, n = 12). (C) Principal coordinate analysis (PCoA) plot based on the weighted Unifrac distance for all samples, on which the intestinal thickness (PCo1) made the 2 communities distinctly separated (H type, n = 10; B type, n = 12). (D) The histogram displaying 28 microorganisms with different intestinal thicknesses obtained by linear discriminant analysis effect size. Abbreviation: LDA, linear discriminant analysis.

Figure 3

The alterations of species composition in intestinal thickness. (A) Principal component analysis demonstrated all samples at the species level (H type, n = 10; B type, n = 10). (B) The clustered heat map of representative species in all samples. (C) STAMP analyzed the ileal microbiome and indicated a total of 7 species with a significant difference (H type, n = 10; B type, n = 10).

Figure 4

The switches of microbial metabolic potentiality with intestinal thickness. (A) The clustered heat map of microbial metabolic pathways in all samples, in which the color boxes indicate distinctive metabolic pathways. (B) STAMP analyzed the core metabolic potentialities of the ileal microbiome in chickens. (H type, n = 10; B type, n = 10).

Figure 5

Shapes of gene expression in intestinal thickness. (A) The volcano plot shows the differential gene expression in 2 groups, wherein each dot represents 1 gene. The golden dots represent upregulated genes in the H type, the purple dots represent upregulated genes in the B type. (B) The hub protein–protein interaction network, showing 51 nodes and 66 edges. Each node represents a protein, and the links between nodes represent known or predicted functional protein–protein interactions. The degree of a node indicates its number of links to other nodes. (C) Chord diagram mapping the core genes to connect with KEGG pathways.

Figure 6

The correlational response between gut genes and microbial species. (A) The Spearman correlational heat map of ileal gene expression and microbial species. (B) The abundance of microbial species as a conditional factor for redundancy analysis (RDA)(m). Each line represents a single species of microorganism in the coordinate system. The brown dots represent transcriptomic samples of the H type, and the cyan dots represent transcriptomic samples of the B type.

Fig S1

Effect of intestinal thickness on the bacterial composition. (A) The relative abundance of Top10 microbe at the phylum level. (B) The relative abundance of Top10 microbe at the genus level.

Fig S2

Influence of intestinal thickness on the species composition of ileal microbiota. The histogram shows the relative abundance of the microorganism at the species level.

Fig S3

Impact of intestinal thickness on the similarity of ileal transcriptome. PCA analyzed all transcriptome samples showing 32% differences in the PC1 axis and 12% differences in the PC2 axis (H type, n = 10; B type, n = 10). PCA, principal component analysis.