Effect Of Milk Replacer On Rumen Microbial Function And Rumen Epithelial Transcriptome Of Tibet Goat Kids

Rumen microbial colonization is very important to the rumen development and host health of young ruminants.The lactation dysfunction of the female goat in the disease state will affect the survival rate,increased mortality of the goat kids.In Qinghai-Tibet Plateau,irregular goat management strategies will reduce the reproductive efficiency of female goats and increase breeding costs.There is very important application value to explore the influence of milk replacer feed on the rumen microbial composition and function of goat kids.In this study,36 Tibetan female goats were selected for estrus and breeding at the same time in the Lhasa goat farm.When the goat kids to be born,and 10 goat kids were selected to feed with breast milk for 3 days.After,they were randomly divided into 2 groups according to the principle of similar body weight.The goat kids of breast milk group used breast milk to feed,and the milk replacer group（MR;n=5）used milk replacer to feed in all experiment period.All goat kids were raised for 28 days.The goat kids were slaughtered in29^th day,rumen fluid and rumen abdominal sac epithelial tissue were collected,and samples were analyzed through metagenomics and transcriptomes,respectively.The main results are as follows:1.Analysis of rumen microbial composition,we found that some microbes were significantly enriched in the MR group,including Fibrobacter_succinogenes,Lachnospiraceae_bacterium_P6A3,Sunxiuqinia_dokdonensis,methanogenic_archaeon_mixed_culture_ISO4-G1,Clostridium_sp._CAG:302,uncultured_bacterium_Ad₁43_D13_contig1,uncultured_bacterium_fosmid_p JB95A1,delta_proteobacterium_PSCGC₅296,Clostridium_sp._CAG:575,Clostridium_sp._CAG:762,Clostridium_sp._CAG:253,uncultured_Termite_group_1bacterium,uncultured_bacterium_fosmid_p JB84D8,andSubdoligranulum_variabileand Parabacteroides_sp._D13 were significantly enriched in the Con group.2.At pathway level 3,Novobiocin biosynthesis and steroid biosynthesis pathway were significantly enriched in the MR group.At the Family level of CAZy database,there are total of 14 enzyme genes significantly difference in two groups,total 12 genes were significantly enriched in the MR group,including GT94,endoglucanase（GH45）,CBM48,GH11,glycoside hydrolase 43（GH43₂7）,glycoside hydrolase 5（GH5₃9）,GH5₁0,CBM11,CBM59,chitosanase（GH46）,GT50 and PL21.Total of 2 genes were significantly enriched in the Con group,including cleave chitin or peptidoglycan（GH2）and GT20.At antibiotic resistance genes level,the antimicrobial peptide-undecene Propyl pyrophosphate phosphatase（ZP₀3930663）and antimicrobial peptide-undecallyl pyrophosphate phosphatase（ABS75156）were significantly enriched in the MR group.At the VFDB level,there are 11 virulence Factors significant differences in two groups,among then,phosphomannose mutase（LOS）,acyl-Co A transferase（Capsule I）,（Dev R/S）,type IV pili biosynthesis（Type IV pili biosynthesis）,（Mce3）,type III secretion system ATPase Eight virulence factors such as Vsc N2（T3SS2）,Accessory colonization factor（Accessory colonization factor）and Yad A were significantly enriched in the MR group,and fluorescent siderophore（pyoverdine）,ABC transporter ATP binding protein（Pyochelin）and catechol siderophore（vulnibactin）was significantly enriched in the Con group.3.Transcriptome analysis was performed on the rumen tissues of goat kids fed with milk substitutes and breast milk.Compared with the Con group,623 DGEs were significantly down-regulated in the MR group,including PNP,LOC108635488,ATR,IGSF6,GP2 LOC102175311,SDS and AKAP5,et.Total of 166 DGEs were significantly up-regulated in the MR group,mainly including PIGR,GDF5,FGF5,TPO,GAL,EPGN and TTPA.The GO enrichment analysis found that the up-regulated genes are enriching in phospholipase inhibitor activity and lipase inhibitor activity,and down-regulated genes are enriching in the immune effector process and spindle pole（spindle pole）.The spindle pole is closely related to chromosome separation,indicating that the milk replacer inhibited the fat synthesis and metabolism of the rumen epithelial tissue and weakened the immune system and the development of rumen cells of goat kids.In the KEGG enrichment analysis,we found that the all down-regulated genes of MR group are involved in the top 20 KEGG pathways,mainly including amino acid metabolism,antibiotic synthesis,carbohydrate metabolism,pathogenic bacteria infection and cellular processes.In summary,there are not significantly effect on the rumen microbial composition of goat kids using the feeding of milk replacer.For rumen microbial functions,the milk replacer promoted the effects of individual strains related to carbohydrate metabolism,and played a positive role for the growth and development of goat kids.However,it will increase the abundance of antibiotic resistance in goat kids.Feeding of milk replacer will lead to weakening of fat anabolism,amino acid synthesis and carbohydrate metabolism in the rumen epithelial tissue of goat kids,and the abundance of pathogenic bacteria infection and antibiotics synthesis were reduced.