Identification of Enterotype and Its Effects on Intestinal Butyrate Production in Pigs

Abstract

Gut microbiota is thought to play a crucial role in nutrient digestion for pigs, especially in processing indigestible polysaccharides in the diets to produce short-chain fatty acids (SCFAs). However, the link between microbiota community structure and phenotypic performances are poorly understood. In the present study, the fecal samples of 105 Jinhua pigs at 105 days of age were clustered into three enterotypes (ETs, ET1, ET2, and ET3) that are subpopulations of distinct bacterial community composition by using 16S rRNA high throughput sequencing. The α-diversity indices (the OTU number and Shannon index) were significantly different among the ETs (p < 0.001). At the genus level, the ET1 group was over-represented by Lactobacillus (17.49%) and Clostridium sensu stricto 1 (11.78%), the ET2 group was over-represented by Clostridium sensu stricto 1 (17.49%) and Bifidobacterium (11.78%), and the ET3 group was over-represented by Bacteroides (18.17%). Significant differences in the fecal contents of butyrate were observed among ETs, with the highest level detected in ET3 and the lowest in ET2 (p < 0.05). Consistently, more copies of the terminal genes for butyrate synthesis, butyrate kinase (Buk) and butyryl coenzyme A (CoA): acetate CoA transferase (But) were detected by qPCR in the fecal samples of the ET3 group as compared to other two groups (p < 0.05). In addition, of the two genes, But was demonstrated to be more relevant to the butyrate content (R = 0.7464) than Buk (R = 0.4905) by correlation analysis. In addition, based on the taxonomic analysis, we found that Faecalibacterium was the most relevant butyrate-producing genera with fecal butyrate contents in Jinhua pigs, followed by Butyricicoccus, Eubacterium, Butyricimonas, Blautia, and Anaerostipes, all of which showed significantly higher richness in ET3 than as compared to ET1 and ET2 (p < 0.05). Collectively, this work presents a first overview of the enterotypes clustering in Jinhua pigs and will help to unravel the functional implications of ETs for the pig's phenotypic performance and nutrient metabolism.

Keywords: Jinhua pig; butyrate; enterotype; gut microbiota.

Figure 1

Enterotype clustering in a cohort of 105 experimental Jinhua pigs. The fecal samples were clustered into three distinct ETs using the JSD distance metric based on the relative abundances of bacteria at the genus level. Abbreviation: ET, enterotype.

Figure 2

The α-diversity of the three enterotypes. The boxplot shown are means, ranges, and the first and third quartiles. Different letters indicate a significant difference (p < 0.05) with the 95% confidence interval. Abbreviation: ET, enterotype.

Figure 3

Differentially abundant bacterial genera in three enterotypes. The relative abundances of the 12 most abundant genera in three ETs were illustrated. Different letters indicate a significant difference (p < 0.05) with the 95% confidence interval. Abbreviation: ET, enterotype.

Figure 4

Correlation matrix showing the Spearman’s rank correlations among the most abundant genera. Spearman’s rank correlation coefficients (ρ) range from −1 to 1, corresponding to a strongly positive to a strongly negative correlation, respectively.

Figure 5

Butyrate contents (A) and the gene copies of butyrate kinase (B) and butyryl CoA: acetate CoA transferase (C) in the fecal samples of three ETs and their correlations as evaluated by Spearman’s rank correlation coefficients (D–F). The butyrate contents were expressed as mg/g of fresh feces. The abundance of functional genes was expressed as log10 gene copies of total DNA/g of fresh feces. Different letters indicate a significant difference (p < 0.05) with the 95% confidence interval. Abbreviation: ET, enterotype.

Figure 6

Differentially abundant butyrate-producing bacterial genera in three enterotypes. The relative abundances of the nine most abundant genera related to butyrate production in three ETs were illustrated. Different letters indicate a significant difference (p < 0.05) with the 95% confidence interval. Abbreviation: ET, enterotype.