Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus

Gut microbial dysbiosis and its derived-metabolites changes have been evidenced to participant in diarrhea piglets; little is known underlying the crosstalk between gut microbiota and metabolites in pregnant sow diarrhea induced with PEDV. In this study, we performed fecal metagenomic and metabolomic profiling in diarrheic pregnant sows infected with PEDV to evaluate the functional characteristics of gut microbiota and metabolites. Microbiome analysis revealed the alterations in composition and diversity of gut microbiota in diarrheic pregnant sows compared with non-diarrheic. The relative abundances of the genera Prevotella, Treponema and Bacteroides were significantly lower and the abundant of Lactobacillus and Ruminococcus were increased in diarrheic pregnant sows. In addition, we found that the increase of Ruminococcus_sp_CAG563, Mycoplasma_sp_CAG472, Prevotella_sp_CAG520, Candidatus_Melainabacteria_bacterium and Eubacterium_coprostanoligenes was the important characteristics in diarrheic pregnant sows. In addition, metabolomic analysis showed a distinct metabolic profile in diarrheic pregnant sows infected with PEDV and the differential metabolites were associated with secondary bile acid biosynthesis, protein digestion and absorption, amino acid biosynthesis. Moreover, our multi-omics data integration analysis indicated that the significant dominant bacteria in diarrheic pregnant sows were positively correlated with 5-aminovaleric acid, pantothenate, 8,4-oxyneolignan-4-xyloside and xanthine, while the predominant coexistence of Treponema, Bacteroides, and Fibrobacter promoted the production of dodecanedioic acid, sesamol and sebacic acid in non-diarrheic pregnant sows infected with PEDV. Taken together, our findings revealed the dynamic changes in the microbiota and metabolites of diarrheic pregnant sows during PEDV infection, identifying microbiota‑derived metabolites associated with host resistance, providing novel insight into the host–gut microbiota interaction.