Identification Of Microorganisms Associated With Residual Feed Intake In Qinchuan Cattle And Their Correlation With Host-expressed Genes Based On Macrogenome

In beef cattle production,feed costs account for the highest proportion of input costs,accounting for about 65%to 70%,and with the rising prices of feed materials in recent years,feed costs will also increasingly increase.Therefore,improving feed utilization efficiency of beef cattle not only can make full use of forage resources,reduce the feed input cost of beef cattle breeding and improve the economic benefits of beef cattle breeding,but also has extremely important practical significance for protecting ecological environment and achieving sustainable development.Residual feed intake(RFI)is one of the ideal indicators to weigh the efficiency of forage utilization.In this study,we combined macro-genome and transcriptome sequencing technologies to investigate the microbial characteristics associated with RFI in beef cattle and its relationship with host gene expression.The main results are as follows.1.macrogenomic analysis of rumen fluid and fecal microorganisms in cattle with different RFI in Qinchuan cattleIn order to investigate the differences in gastrointestinal microorganisms among different RFI Qinchuan cattle,rumen fluid and fecal samples were sequenced using macrogenomic sequencing methods.The results showed that the rumen and fecal microorganisms of different RFI individuals had similarities and differences,and the differences were mainly in the biological functions of the microorganisms.The results of taxonomic annotation showed that the abundance of Bacteroidetes was higher in the LRFI group than in the HRFI group and lower in the Firmicutes group at the gate level in rumen fluid;in feces,the abundance of Bacteroidetes was higher in the HRFI group than in the LRFI group at the gate level.At the genus level,Prevotella abundance was higher in the LRFI group than in the HRFI group in the rumen;KEGG functional annotation showed that the relative abundance of carbohydrate metabolism,translation,nucleotide metabolism,amino acid metabolism,signaling,replication and repair,energy metabolism,cofactor and vitamin metabolism,transport and catabolic pathways were increased in the LRFI group;CAZy functional annotation The analysis showed that compared with the HRFI group,the LRFI group showed an increasing trend in abundance,except for the decrease in the abundance of Auxiliary Activities.2.Association analysis of the duodenal transcriptome and rumen microbial macrogenome associated with RFI in Qinchuan cattleThe gut flora,as a second set of genomes in the organism,is involved in the regulation of important host phenotypes,while the host genetic background is also involved in gut microbial colonization.To investigate the relationship between host gene expression characteristics and gut microbes,we performed a correlation analysis between them.The results showed a significant positive correlation between FAM3D gene expression and Prevotella and Paraprevotella abundance(P<0.05);a positive correlation between Treponema and Muribaculum abundance and PRDX4 and HPD gene expression(P<0.05);a positive correlation between CDH26 gene expression and Prevotella abundance showed positive correlation(P<0.05);while CCR4 gene expression showed negative correlation(P<0.05)with Oscillibacter and CDH26 gene expression with Phascolarctobacterium,Chlamydia and Bacillus abundance,suggesting that gastrointestinal flora and host gene expression may have potential reciprocal effects in terms of RFI phenotype.3.Association analysis of rumen differentially expressed genes with rumen microorganismsIn this study,correlation analysis between RFI-related gene expression and microbial abundance was conducted using public data to provide a basis for subsequent manual regulation of beef cattle feed intake.The results showed that a total of 26 differential genes were identified in both datasets,among which eight genes were consistently up-and down-regulated,and the other seven genes were up-regulated in the HRFI group,except for the GABRP gene.The correlation results showed that differential gene FAM171A2 expression was positively correlated with the abundance of Treponema(P<0.05).Despite the different sources of differential genes,differential gene expression genes FAM171A2,PRDX4 and HPD base identified in duodenum and rumen based on RFI phenotype were all positively correlated with the abundance of Treponema(P<0.05),suggesting that gastrointestinal flora colonization is conserved in different beef cattle groups and Treponema may be one of the RFI-related Treponema may be one of the potential microbial markers associated with RFI in beef cattle.