Mitochondrial haplotypes are associated with gut microbiota composition and growth-related traits in Qinghai Bamei pigs

The gut microbial is shaped by host genetics and the environment factor, and may be associated with growth-related traits. In this study, 108 adult Qinghai Bamei pigs reared under identical conditions were analyzed to evaluate associations among mitochondrial haplotypes, gut microbiota, and growth-related traits. Haplotype based on mitochondrial DNA (mtDNA) D-loop variation identified six haplotypes, with haplotype diversity ( Hd ) and nucleotide diversity ( Pi ) values of 0.553 and 0.199%, respectively, indicating high population genetic diversity ( Hd > 0.5). Three major haplotypes (Hap1, n = 68; Hap2, n = 12; Hap5, n = 22) were selected for gut microbiota comparison. Significantly differences in diversity were observed among haplotypes ( P < 0.05). At the phylum-level, Hap1 and Hap2 were enriched in Christensenellaceae_R-7_group and Treponema ( P < 0.05), whereas Hap5 was enriched in norank_f_Muribaculaceae and Prevotellaceae_NK3B31_group ( P < 0.05). The co-occurrence network analyses show that the network structure is simplest in Hap 1 groups and much more complex in Hap 2 and 5 groups. Functional analysis suggested the abundance of enzymes in glycolysis/gluconeogenesis, starch and sucrose and butanoate metabolism were significantly higher in Hap1. The abundance of enzymes in secondary bile acid biosynthesis pathway was significantly higher in Hap5. Correlation analysis further suggested that the higher abundances of Christensenellaceae_R-7_group and Treponema in Hap1 and Hap2 were associated with microbial metabolic profiles and improved growth-related traits, including higher 20-day body weight and adult body measurements, compared with Hap5 (P < 0.05). Six haplotypes were identified in the mtDNA D-loop region of Qinghai Bamei pigs in this study. The tested pig populations displayed significant inter-haplotype differences in intestinal microbial structure, metabolic functions and growth traits. In particular, Hap1 and Hap2 group had elevated abundances of Christensenellaceae_R-7_group , Treponema , showing excellent growth performance. By contrast, the Hap5 group harbored higher levels of norank_f_Muribaculaceae , Prevotellaceae_NK3B31_group , along with higher abundance of enzymes of bile acid metabolism pathway. Overall, host mitochondrial hap and intestinal microbiota co-regulate porcine growth traits, although the underlying molecular mechanisms require further investigation.