Gut Microbial Metagenomics And Intestinal Mucosal Transcriptomics In Landrace Pigs With Different Feed Efficiency

Feed conversion efficiency of livestock is an important indicator to measure growth traits,which affects a large proportion of economic benefit of breeding.The feed conversion efficiency of pigs is closely related to intestinal health and physiological status,which are affected by a large number of microorganisms living in the gut.And the host's diet and genetic background and other factors affect the composition of the intestinal microbiota.The gut microbiota and host exist complicated and close interaction.In this study,the relationship between pig feed efficiency and intestinal microbial community and gene expression in intestinal mucosa were investigated by metagenome and transcriptome sequencing.The fattening stage of Landrace sows were raised in the same environment,and grouped according to the difference in feed conversion efficiency,feces samples and intestinal segments(duodenum,jejunum,ileum,cecum,colon,rectum)were collected,and performed the 16S rDNA sequence V3+V4 region high-throughput sequencing.The results showed that the fecal microbial structure of high and low feed efficiency pigs was similar,and the main dominant bacteria were Firmicutes,Bacteroidetes,Spirochaetes and Proteobacteria,took over 95%of all bacteria.At the genus level,there were differences among the two groups,for example,Prevotella was significantly enriched in the lower group,and the relative abundance of Treponema,Lactobacillus,etc,were higher in the high group.There were differences in the types and proportions of predominant bacteria in different segments of the intestine,and a clear difference in the microbial clustering between the small intestine(duodenum,jejunum,ileum)and large intestine(cecum,colon,rectum)and fecal samples.The differential bacteria in the high and low groups in each section of the intestine were different and could be distinguished by biomarkers(differential genus).Metagenomic de novo sequencing of the cecum and colon digesta microbial genome,different microbes were mainly involved in carbohydrate metabolism and might affect the growth of the host.The high feed efficiency groups contained more probiotics,such as some lactic acid bacteria,both in the cecum and colon.The lower feed efficiency groups enriched higher proportion of Prevotella.The results of functional annotation showed that the different pathways in the high feed efficiency group of cecal microbes were mainly related to the pyruvate metabolic pathway,which affects the host's absorption of energy.Many of the differential pathways in colon microbes were associated with coenzyme factors and vitamin metabolism.The cecal and colon mucosal tissues were analyzed by transcriptome sequencing.138(high FCR group cecal mucosa versus low group),64(high FCR group colonic mucosa versus low group)and 165(cecal mucosa versus colonic mucosa)genes were differentially expressed and annotated.The up regulated genes in comparison of high and low groups in both cecal and colonic mucosa were related to starch loss,some nucleotides and drug metabolism,and involved in short chain fatty acid metabolism,gastrointestinal motility and biotransformation.The down regulated genes were mainly involved in immune and disease related metabolism.Preliminary screened the feed efficiency related candidate genes,such as GUCA2A,GUCA2B,HSP70.2,NOS2,PCK1,SLCs,and CYPs.Correlation analysis revealed that differentially expressed genes that were significantly associated with differential bacteria,such as S100G,TMEM200A,etc.Except for Prevotella,the up regulated genes were positively correlated with the significantly related microorganisms,and the down regulated genes were negatively correlated with the significantly related microorganisms.With variant feed efficiency,the fecal and intestinal microbes existed differences of the same pig species,and the microbes were different in different gut locations.The functional differences of the cecal and colonic microbes were revealed by metagenomic sequencing analysis between two groups,respectively.By differentially expressed genes analyzed corresponding intestinal locations,a small number of differentially expressed genes related to nutritional metabolism in intestinal mucosa were influenced by microbial structural differences.In addition,there were significant correlations between differentially expressed genes and different microbes.Because only 4 pairs of individuals were used as samples in this study,the results of the study were better able to be verified in the larger pigs in the future.