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

SIMPLE SUMMARY: Enterotype (ET) is defined based on different gut microbial community composition. It has been considered as a critical factor strongly associated with the porcine feed efficiency and growth characteristic. However, little is known about whether the ET clustering depends on the pig breeds and the effects of the different enterotypes on the butyrate metabolism in pigs. Therefore, we studied Jinhua pig’s enterotype by using 16S rRNA high throughput sequencing, and then analyzed the interaction between enterotype and butyrate production. Results showed that we identified three ETs driven by discriminative genera dominated by Lactobacillus, Clostridium sensu stricto 1, and Bacteroides, respectively. Significant differences in the fecal contents of butyrate production and butyrate-producing bacteria were observed among ETs. These findings present a first overview of the enterotypes clustering in Jinhua pigs and provide new insights into the relationship between the different ETs and intestinal butyrate production. 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.