Comparison Of Transcriptome And Metabolome And Microflora In Cecum Of New Zealand Rabbits In SPF And Usual Breeding Environment

The traits of animal are influenced by both genetic and environmental factors.In this study,New Zealand rabbits from America were bred in the usual environment(UE)and SPF environment(SE)respectively for 10 consecutive years so as to study the environmental impact in the breeding process.And 6 New Zealand rabbits were selected from each of the two groups.We studied the differences in gut microbiota,metabolic,growth and immunity between two groups of New Zealand rabbits.At the same time,the relationship between the gene expression,metabolites,gut microbiota,growth and immunity in two breeding environments was also studied.The influence of breeding environment on character formation was analyzed finally.The differences of growth,immunity and other traits of two groups of New Zealand rabbits were compared firstly in this study.Then the differences between microbiome,metabolome and transcriptome were compared.Finally,the relative quantitative method is used to verify.The main results are as follows:(1)In terms of slaughter indicators,the New Zealand rabbits of group SE grew faster than group UE,but the organ weight was lower than group UE as a whole.Combined with the previous measurement of blood physiological and biochemical indexes of New Zealand rabbits under two different environments in our laboratory.It can be obtained although the growth rate of New Zealand rabbits in group SE was faster than that in group UE,their immunity was lower than that in group UE.(2)According to the results of 16 SrRNA,the gut microbial diversity of New Zealand rabbits in group UE was significantly higher than that in group SE.By comparing the diversity in phylum and genus in two groups,it can be seen that bacteroidetes,firmicutes,cyanobacteria,bacteroides,clostridium and ruminococcus have significant differences and higher abundance between the two groups.At the phylum level,the firmicutes of New Zealand rabbits in group UE were significantly higher than those in group SE,so more short-chain fatty acids(SCFAs)were produced,which was beneficial to enhance the immunity of New Zealand rabbits;At the genus level,the Numbers of bacteroidetes in group SE were significantly higher than those in group UE,so they could produce more bile acids,which was not conducive to the enhancement of immunity.(3)According to the sequencing results of untargeted metabolomics,we found that the main pathways enriched by differential metabolites were Bile secretion,Cysteine and methionine metabolism,Arachidonic acid metabolism,Galactose metabolism,Starch and sucrose metabolism,Metabolic pathways,ABC transporters,Glucagon signaling pathways,Alpha-linolenic acid metabolism,etc.According to the specific fitting model and screening conditions(VIP>1,P<0.05),18 differentially metabolized compounds were screened in this experiment.It can be seen that the differential metabolic compounds mainly involve the amino acids,carbohydrates lipid and lipid-like molecules.In the differential expressed metabolites,cholesterol,vitamin D3,prostaglandin E2,Fumaric acid,Maleic acid,Manninotriose,Glycogen,Stachyose and Chitobiosewas significantly higher in the group SE than in the group UE.Arachidonic acid,Linoleic acid,Nervonicacid,tyrosine,L-phenylalanine,FMLP and epinephrine in the group SE was significantly lower than that in the group UE.(4)According to the results of transcriptome,1678 differentially expressed genes in the two groups were enriched in 44 pathways.Through GO enrichment analysis,it can be known that the physiological and biochemical processes mainly involved in the differential genes include the immune response to intestinal smooth muscle contraction defense response,positive regulation of white blood cell migration,positive regulation of lymphocyte migration,and stimulation response.The results of KEGG pathway enrichment analysis showed that the enrichment pathways(P<0.05)mainly included signal molecules and interaction immune diseases,viral infectious diseases,bacterial infectious diseases,immune system and signal transduction pathways.Through GO analysis and KEGG pathway enrichment analysis,13 differentially expressed genes including IL18,CRYAB,HTR1 D,ITGB8,CLU,CCL21,PTGER3,IL1 A,CCL4,IRF1,DDX58,IFIT2 and OAS2 were selected.The first 7 were upregulated genes and the last 6 were down-regulated genes.Through relative quantitative verification,the differentially expressed genes were significantly different between the two groups.In conclusion,the quantity and abundance of gut microbiota in the group UE were significantly higher than those in the group SE.In addition,the function of immune response and regulation was better than that of group SE.The difference between the growth and immune traits of two groups of New Zealand rabbits can be partly attributed to the different gut microbiota structure,which is realized by regulating the synthesis of short chain fatty acid bile acids and other substances and their effects on glucose and lipid metabolism.