Comprehensive Multi-Omic Evaluation of the Microbiota and Metabolites in the Colons of Diverse Swine Breeds

Abstract

Pigs stand as a vital cornerstone in the realm of human sustenance, and the intricate composition of their intestinal microbiota wields a commanding influence over their nutritional and metabolic pathways. We employed multi-omic evaluations to identify microbial evidence associated with differential growth performance and metabolites, thereby offering theoretical support for the implementation of efficient farming practices for Tibetan pigs and establishing a robust foundation for enhancing pig growth and health. In this work, six Duroc × landrace × yorkshi (DLY) pigs and six Tibetan pigs were used for the experiment. Following humane euthanasia, a comprehensive analysis was undertaken to detect the presence of short-chain fatty acids (SCFAs), microbial populations, and metabolites within the colonic environment. Additionally, metabolites present within the plasma were also assessed. The outcomes of our analysis unveiled the key variables affecting the microbe changes causing the observed differences in production performance between these two distinct pig breeds. Specifically, noteworthy discrepancies were observed in the microbial compositions of DLY pigs, characterized by markedly higher levels of Alloprevotella and Prevotellaceae_UCG-003 (p < 0.05). These disparities, in turn, resulted in significant variations in the concentrations of acetic acid, propionic acid, and the cumulative SCFAs (p < 0.05). Consequently, the DLY pigs exhibited enhanced growth performance and overall well-being, which could be ascribed to the distinct metabolite profiles they harbored. Conversely, Tibetan pigs exhibited a significantly elevated relative abundance of the NK4A214_group, which consequently led to a pronounced increase in the concentration of L-cysteine. This elevation in L-cysteine content had cascading effects, further manifesting higher levels of taurine within the colon and plasma. It is noteworthy that taurine has the potential to exert multifaceted impacts encompassing microbiota dynamics, protein and lipid metabolism, as well as bile acid metabolism, all of which collectively benefit the pigs. In light of this, Tibetan pigs showcased enhanced capabilities in bile acid metabolism. In summation, our findings suggest that DLY pigs excel in their proficiency in short-chain fatty acid metabolism, whereas Tibetan pigs exhibit a more pronounced competence in the realm of bile acid metabolism. These insights underscore the potential for future studies to leverage these breed-specific differences, thereby contributing to the amelioration of production performance within these two distinct pig breeds.

Keywords: SCFA; gut; microbiota; nutrition; pigs.

Figure 1

Differential microbiome in colon of two breeds of pigs. (A) Venn diagrams of two groups. (B) Chao1 index of two groups. (C) Shannon index of two groups. (D) NMDS results of two groups. (E) PCoA results of two groups. (F) Community analysis of two groups at the phylum level. (G) Top 10 differential microbes of two groups at phylum level. (H) Community analysis of two groups at genus level. (I) Top 10 differential microbes of two groups at genus level. Data are presented as mean ± SD and statistical significance was determined by the Wilcoxon rank-sum test; DLY pigs; TP, Tibetan pig; * p ≤ 0.05; n = 6.

Figure 2

Differential metabolites in colon of two breeds of pigs. (A) OPLS-DA results of two groups. (B) PCA results of two groups. (C) Volcano plot of two groups. (D) Number of differential metabolites of two groups. (E) Top 27 possible pathways of metabolites of two groups. DLY pigs; TP, Tibetan pig; n = 6.

Figure 3

Differential metabolites in plasma of two breeds of pigs. (A) OPLS-DA results of two groups. (B) PCA results of two groups. (C) Volcano plot of two groups. (D) Number of differential metabolites of two groups. (E) Top 10 possible pathways of metabolites of two groups. DLY pigs; TP, Tibetan pig; n = 6.

Figure 4

Differential concentrations of SCFAs in colons of two breeds of pigs. (A) Acetic acid (ug/g), (B) propionic acid (ug/g), (C) Isobutyric acid (ug/g), (D) Butyric acid (ug/g), (E) Isovaleric acid (ug/g), (F) Pentanoic acid (ug/g), (G) Hexanoic acid (ug/g), (H) total SCFAs (ug/g) in the colonic samples from DLY and TP pigs. (I) Percentages of SCFAs in DLY pigs. (J) Percentages of SCFAs in Tibetan pigs. Data are presented as mean ± SD and statistical significance was determined by the Wilcoxon rank-sum test; DLY pigs; TP, Tibetan pig; * represents significant difference (* p ≤ 0.05), ** p ≤ 0.01, n = 6.

Figure 5

Differential expressions of related genes in mucosa of two breeds pigs. (A) mRNA expression of FXR5. (B) mRNA expression of TGR5. (C) mRNA expression of GPR41. (D) mRNA expression of GPR43. (E) mRNA expression GPR109. (F) mRNA expression SLC5A8. (G) mRNA expression SLC16A1. Data are presented as mean ± SD and statistical significance was determined by the Wilcoxon rank-sum test; DLY pigs; TP, Tibetan pig; * represents significant difference (* p ≤ 0.05), ** p ≤ 0.01 and *** p ≤ 0.001; n = 6.

Figure 6

Correlation analysis of microbial communities, colonic metabolites, and plasmatic metabolites. (A) Interactions between colonic microbes and plasmatic metabolites. (B) Interactions between colonic microbes and colonic metabolites. (C) Interactions between colonic metabolites and plasmatic metabolites. (D) Interactions between colonic or plasmatic taurine and plasmatic metabolites. Correlations were determined by the spearman test, blue represents a negative correlation, red represents a positive correlation, n = 6. * p < 0.05, ** p < 0.01, and *** p < 0.001.

Figure 7

Correlations between lithocholic acid and microbial communities, metabolites, or receptor related genes. (A) Interactions between lithocholic acid and colonic microbes. (B) Interactions between lithocholic acid and plasmatic metabolites. (C) Interactions between lithocholic acid and colonic metabolites. (D) Interactions between lithocholic acid and related genes. Correlations were determined by the spearman test, blue represents a negative correlation, red represents a positive correlation, n = 6. * p < 0.05, ** p < 0.01, and *** p < 0.001.

Figure 8

Correlations between short-chain fatty acids, microbial communities, and receptor-related genes. (A) Interactions between colonic microbes and SCFAs. (B) Interactions between SCFAs and related genes. (C) Interactions between colonic microbes and related genes. Correlations were determined by the spearman test, blue represents a negative correlation, red represents a positive correlation, n = 6. * p < 0.05, ** p < 0.01, and *** p < 0.001.