Analysis of Intestinal Microbiota Differences and Functional Prediction Between Sichuan-Tibetan Black Pigs and Landrace Pigs

This study aimed to investigate the structural differences and functional potential of the gut microbiota between Sichuan-Tibetan black pigs (<i>n</i> = 5) and Landrace pigs (<i>n</i> = 5) under identical rearing conditions. Fecal samples were collected and subjected to 16S rRNA gene sequencing followed by comprehensive bioinformatics analysis. The results revealed 963 and 910 operational taxonomic units (OTUs) in Sichuan-Tibetan black pigs and Landrace pigs, respectively, with 808 OTUs shared between the two breeds. While both breeds shared Firmicutes, Bacteroidota, and Proteobacteria as the dominant phyla, significant compositional differences were observed at the genus level. Sichuan-Tibetan black pigs exhibited higher abundance of <i>Escherichia-Shigella</i>, <i>Streptococcus</i>, <i>Prevotella</i>, <i>Parabacteroides</i>, and <i>Collinsella</i>, whereas Landrace pigs were enriched in <i>Bacteroides</i>. Alpha diversity analysis showed no significant differences in Shannon, Simpson, or ACE indices, though the Chao index differed markedly between the two groups. Beta diversity analysis (PCoA and NMDS) confirmed distinct microbial community structures between the breeds. Functional prediction analysis demonstrated that metabolic pathways dominated in both groups, but with notable functional differentiation: the microbiota of Sichuan-Tibetan black pigs showed significant enrichment in biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and amino acid biosynthesis; whereas, Landrace pigs were characterized by enhanced carbon and energy metabolism pathways. Additionally, BugBase phenotype prediction revealed significant differences in stress tolerance, cell wall properties, and oxygen utilization capabilities between the two groups. These findings provide valuable insights into the breed-specific characteristics of gut microbiota in swine and establish a foundation for further research on host-microbe interactions and their implications for animal health and nutrition.