High-throughput sequencing-based metagenomic and transcriptomic analysis of intestine in piglets infected with salmonella .

enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of infection are at high risk of non-typhoidal gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by infection causes proliferation of and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.