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Simple Summary: Pigs play a crucial role in human sustenance, with their intestinal microbiota composition significantly influencing their nutrition and metabolism. Recent research has focused on understanding these differences among various swine breeds to attain improved food quality and safety. We sought the microbial evidence of differential performances of Tibetan pigs. In this study, six Duroc × Landrace × Yorkshire (DLY) pigs and six Tibetan pigs at 200 days of age were examined. Analysis revealed distinct microbial compositions in DLY pigs, with higher levels of Alloprevotella and Prevotellaceae_UCG-003. This resulted in variations in short-chain fatty acids (SCFAs) concentrations, contributing to enhanced growth performance. Tibetan pigs exhibited increased abundance of NK4A214_group, leading to higher L-cysteine levels and the subsequent elevation of taurine in the colon and plasma. Taurine influences microbiota dynamics and metabolism, particularly in bile acid metabolism, showcasing Tibetan pigs' proficiency in this area. Overall, DLY pigs excel in SCFA metabolism, while Tibetan pigs exhibit competence in bile acid metabolism. Leveraging these breed-specific differences could improve production performance in these pig breeds. 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. [ABSTRACT FROM AUTHOR]

Simple Summary: Whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed in this study. Population genetic analyses, including Principal Component Analysis (PCA), phylogenic tree, genetic differentiation, deleterious variant, contribution to meta-population genetic diversity and selective sweep were performed. Limited genetic differentiation was identified among these Tibetan pig populations. Most deleterious variants were low-frequency mutations and population specific. Contribution to the meta-population was largest in the TT population, based on gene and allelic diversity. Genes under selection were involved in hypoxia adaptation, hard palate development, facial appearance, and perception of smell. Several geographically isolated populations of Tibetan pigs inhabit the high-altitude environment of the Tibetan Plateau. Their genetic relationships, contribution to the pool of genetic diversity, and their origin of domestication are unclear. In this study, whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed. Population genetic analyses revealed limited genetic differentiation among the Tibetan pig populations. Evidence from deleterious variant analysis indicated that population-specific deleterious variants were the major component of all mutational loci. Contribution to the meta-population was largest in the TT (Qinghai-Tibet Plateau) population, based on gene diversity or allelic diversity. Selective sweep analysis revealed numerous genes, including RXFP1, FZD1, OR1F1, TBX19, MSTN, ESR1, MC1R, HIF3A, and EGLN2 which are involved in lung development, hard palate development, coat color, hormone metabolism, facial appearance, and perception of smell. These findings increase our understanding of the origins and domestication of the Tibetan pig, and help optimize the strategy for their conservation. [ABSTRACT FROM AUTHOR]