Breed and housing system shape jejunal transcriptome and digesta microbiota in German Landrace and Saddleback pigs

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Background Sustainable pig farming balances animal welfare, productivity, and social acceptance. Organic systems offer enriched environments for the pigs and represent a model for sustainable production, but require an understanding of how breed, intestinal microbiome, and housing interact. In this study, we compared a commercial breed (German Landrace, GL) and a traditional breed (German Saddleback, GS) reared in different housing systems (Conventional, CON; Organic, ECO). Jejunal mucosa transcriptomes ( n = 56) and digesta microbiota ( n = 100) were collected from growing pigs at 70 days of life; 54 samples overlapped between the two datasets and were used for all integrated host–microbiome analyses. Data from RNA-seq and 16 S-seq were evaluated through differential expression analysis, microbial community profiling, and DIABLO-based data integration. Results Jejunal transcriptome variation was influenced primarily by breed. GL pigs exhibited a profile supporting anabolic pathways, including upregulated oxidative phosphorylation, whereas GS pigs showed a profile focused on lipid metabolism and a shift toward energy storage as an adaptation. In contrast, the housing system was the main driver of microbial composition, with ECO housing enriching fermentative taxa such as Lactobacillus and Campylobacter , presumably due to outdoor exposure, while CON housing enriched fewer Lactobacillus but more Clostridium . Breed–Housing combinations analysis revealed distinct adaptive strategies: the modern GL breed responded strongly to housing conditions at both the transcriptional and microbial levels, whereas the traditional GS breed, while also transcriptionally responsive, maintained a more stable microbial community phenotype across environments. Integrated host-microbiome analysis identified a core set of host genes (e.g., PCSK9 and SCD ) that were strongly correlated with housing-specific microbes, defining a lipid–inflammation axis. Conclusion Breed and rearing environment jointly shape the porcine jejunal transcriptome and microbiota through distinct strategies. Together, these data provide molecular insight into how traditional and modern breeds differentially respond and potentially adapt to divergent husbandry systems, with implications for health and productivity. Clinical trial number Not applicable.