Bacteriophage as an alternative to pharmacological-dose zinc oxide for mitigating post-weaning diarrhea in piglets: insights from integrated multi-omics analysis

The diarrhea that occurs in piglets after weaning due to Escherichia coli infection represents a critical challenge in swine production. The pharmacological dose of zinc oxide (ZnO), once widely used to prevent diarrhea in piglets, has faced restrictions or bans in animal feed. However, while the role of ZnO in modulating gut health is well documented, less is known about how phages with identical or different from those of ZnO influence the gut microbial community, its metabolites and host interactions in weaned piglets. This study investigated the potential molecular pathways and multi-omics signatures associated with bacteriophages (phages) serve as a high-dosage zinc oxide alternative to mitigate post-weaning diarrhea in piglets, utilizing microbiome, metabolomic, and proteomic analysis. The results showed that phages reduced diarrhea rate compared to ETEC K88 group. Fecal microbiome showed that phages increased Phascolarctobacterium and Faecalibacterium abundances and reduced Clostridium sensu stricto 6 abundance. Fecal metabolomics found that phages modulated bile secretion, fatty acid biosynthesis, and unsaturated fatty acid biosynthesis. Jejunal proteomic revealed that phages altered interaction between gut microbiota and host via immune network for IgA production, Fc gamma R-mediated phagocytosis, and NF-κB pathway. Integrated multi-omics revealed that phages reduced diarrhea in ETEC K88-infected pigs through modulation of bile secretion and ferroptosis pathways. This study offers novel insights into the influence of phages on the gut microbiota, their metabolites, and host interactions in weaned piglets, while providing valuable references for the application of phage-based strategies as an alternative to pharmacological-dose zinc oxide in mitigating post-weaning diarrhea.