Gut Fungal Community Modulates Fat Deposition in Ningxiang Pigs: Species-Specific Regulation via the Glucose–SCFAs Metabolic Axis

Despite limited understanding of gut fungal roles in fat deposition among indigenous pig breeds, a comparative study between high-fat-accumulating Ningxiang (NX) pigs and lean-type Duroc × Landrace × Yorkshire (DLY) pigs reveals a fungal-driven regulatory mechanism. NX pigs exhibited significantly higher fat percentage, elevated serum glucose, and markedly reduced total colonic short-chain fatty acids (SCFAs) compared to DLY pigs (all p < 0.001), with butyrate showing the most pronounced decrease. Beta-diversity confirmed distinct fungal communities (p = 0.002), where NX pigs were enriched with Aspergillus and Penicillium, while DLY pigs harbored dominant Rhodotorula. Strong correlations were observed: NX-enriched fungi positively correlated with glucose and negatively with SCFAs, whereas Rhodotorula strongly associated with SCFAs (p < 0.001). FUNGuild analysis linked Aspergillus/Penicillium to enhanced polysaccharide degradation and glucose bioavailability. The findings propose a gut fungal-mediated “Glucose–SCFAs axis”: NX-enriched fungi elevate glucose (promoting lipogenesis) and suppress SCFAs (reducing butyrate-mediated adipocyte inhibition), whereas Rhodotorula in DLY pigs enhances SCFAs-induced lipolysis. Crucially, we demonstrate that fungal modulation primarily drives fat deposition differences between breeds, offering novel probiotics/antifungal strategies for precision swine breeding.