Different levels of SCFAs in the colon content of two different species pig
The concentrations of SCFAs in the colon of pigs in two groups are shown in Figure 1. Compared with Tibetan pigs, Duroc × landrace × yorkshire pigs had significantly higher concentrations of acetic acid (P < 0.05), propionic acid (P < 0.01) and total SCFAs (P < 0.05) (Figure 1A, B and D), and Duroc × landrace × yorkshire pigs had higher concentrations of butyric acid but not significant (P = 0.078) (Figure 1C). For other SCFAs, there were no significant differences (P > 0.05), but the trends showed that compared with Tibetan pig, duroc × landrace × yorkshire had higher concentrations of isobutyric acid and hexanoic acid (Supplementary Figure 1). The percentage of SCFAs concentration are similar for both two breeds which are higher acetic acid (65.22% and 61.72%), propionic acid (16.50% and 16.59%) and butyric acid (10.58% and 11.39%), while other SCFAs concentration are lower than 5% (Figure 1E and F).
Metabotropic receptor related gene level expression in mucosa
The mRNA expressions of metabotropic receptor related genes are shown in Figure 2. Tibetan pig had higher gene expression. In specific, Tibetan pigs had significantly higher gene expressions of FXR5 (P < 0.001) and TGR5 (P < 0.05) (Figure 2A and B). Meanwhile, duroc × landrace × yorkshire pigs had significantly higher gene expressions of GPR41 and GPR43 (P < 0.01) (Figure 2C and D). For the expression of SLC5A8, Tibetan pigs had higher level but not significant (P = 0.087) (Supplementary Figure 2B). For the expressions of other genes, there are no significant differences (P > 0.05) (Supplementary Figure 2A and C).
Differences in Colonic Luminal Microbiome between duroc × landrace × yorkshire and Tibetan pigs
The microbes in colon of pigs in two groups are shown in Figure 3. There were 2397 types of same microbes from more than 3300 types in pigs of two groups (Figure 3A). In α-diversity result, Duroc × landrace × yorkshire pigs had more microbes compare with Tibetan pigs (P < 0.05) (Figure 3B and C), and for β-diversity, pigs in these two groups were different (Figure 3D and E). At phylum level, duroc × landrace × yorkshire pigs had significantly higher Bacteroidetes, Fibrobacterota, and Campilobacterota but significantly lower Firmicutes and Deferribacterota, and Gemmatimonadota, Myxococcota, and Acidobacteriota only proliferated in Tibetan pigs. (Figure 3F and G). In top ten abundant different microbial communities on genus level, Tibetan pigs had 4 kinds of microbes with lower abundances which were p-251-o5, Prevotellaceae_UCG-003, Alloprevotella and Lachnospiraceae_NK4A136_group, and 6 kinds of microbes with higher abundances which were UCG-002, Prevotellaceae_NK3B31_group, UCG-005, NK4A214_group, dgA-11_gut_group, and Streptococcus (Figure 3H and I).
The differences in colon metabolite between duroc × landrace × yorkshire and Tibetan pigs
The different metabolites in colon between two breeds pigs are shown in Figure 4. PCA score-plots, OPLS-DA, and PLS-DA showed that two breeds pigs had different metabolites (Figure 4A, B and C), and the parameters of this model had enough predictive power which were R2 = (0.0, 0.875) and Q2 = (0.0, -0.331) (Figure 4D). Moreover, compared with duroc × landrace × yorkshire pigs, Tibetan pigs had 59 up-regulated and 10 down-regulated metabolites (Figure 4E and F). These different metabolites were related to various pathways such as glycine, cysteine, and methionine metabolism and CoA biosynthesis (Figure 4 G and H).
In specific, main different metabolites are shown in Supplementary Table 2. In Tibetan pigs, the relative levels of two amino acids (tranexamic acid and ornithine), three carbohydrates (maltotriose, D-tagatose and methyl beta-d-glucopyranoside) and five other compounds were significantly lower than which in duroc × landrace × yorkshire pigs. Meanwhile, in Tibetan pigs, the relative levels of 12 amino acids (4-aminobutyric acid, 4-hydroxyproline, alpha-aminoadipic acid, aminomalonate, Dl-dopa, L-aspartic acid, L-cysteine, L-methionine, L-phenylalanine, L-threonine, sarcosine and serine), three benzoic acids (phthalic acid, syringic acid and hydroxypropionic acid), one bile acid (lithocholic acid), three carbohydrates (digalacturonic acid, erythronic acid and gluconic acid), 13 fatty acids (2-hydroxy-2-methylbutanoic acid, 2-isopropylmalic acid, 3-methyladipic acid, citramalic acid, elaidic acid, heptadecanoic acid, hexadecanedioic acid, nonadecanoic acid, oleic acid, palmitic acid, pentacosanoic acid, sebacic acid and tridecanoic acid), one organosulfonic acid (taurine) and 26 other compounds were significantly higher than those in duroc × landrace × yorkshire pigs.
The differences in plasma metabolite between duroc × landrace × yorkshire and Tibetan pigs
The different metabolites in plasma between two breeds pigs are shown in Figure 5. PCA score-plots, OPLS-DA, and PLS-DA showed that two breeds pigs had different metabolites (Figure 5A, B and C), and the parameters of this model had enough predictive power which were R2 = (0.0, 0.918) and Q2 = (0.0, -0.188) (Figure 5D). What is more, compared with duroc × landrace × yorkshire pigs, Tibetan pigs had 38 up-regulated and 30 down-regulated metabolites (Figure 5E and F). These different metabolites were related to various pathways such as purine, galactose, and cysteine metabolism and TCA cycle (Figure 5 G and H).
In specific, main different metabolites are shown in Supplementary Table 3. In Tibetan pigs, the relative levels of five amino acids (bicine, L-histidine, homocystine, L-cystine and L-asparagine), seven carbohydrates (D-tagatose, D-arabinose, maltotriose, coniferin, L-sorbose, 1,5-anhydroglucitol and D-fructose), two fatty acids (hexadecanedioic acid and tetradecanedioic acid), one Organosulfonic acid (taurine) and 24 other compounds were significantly higher than which in duroc × landrace × yorkshire pigs. In addition, in Tibetan pigs, the relative levels of five amino acids (2-aminoheptanedioic acid, N-carbamoylaspartate, aminomalonate, creatinine and pipecolic acid), six carbohydrates (glucosamine, D-fructose-1-phosphate, glucose-1-phosphate, arabinofuranose, glucose and 3-phosphoglyceric acid), two fatty acids (beta-hydroxymyristic acid and lauric acid) and 17 other compounds were significantly lower than those in duroc × landrace × yorkshire pigs.
Correlation between Microbial Communities and their Metabolites.
Correlations between metabotropic receptor related gene, top 15 different microbes in colon and SCFAs concentration are shown in Figure 6. In specific, the relative abundances of 2 microbes, which were UCG-002 and UCG-005, showed similar trends which were positively correlated with the expression of FXR5 and GTR5, and negatively correlated with the expression of GPR41 and GPR43. Meanwhile, the relative abundance of NK4A214_group also showed negatively correlated with the expression of GPR41 and GPR43. What is more, the concentrations of acetic acid and propanoic acid were positively associated with the expressions of GPR41 and GPR43, and negatively associated with the relative abundances of UCG-002 and NK4A214_group.