| Ruminants can convert to plant polysaccharides that are difficult for humans to digest into high-quality proteins,such as meat and milk,which is of great significance for agriculture and human sustainable development.Dairy goats are one of the earliest domesticated dairy animals,with rich variety resources and vast distribution area.Goat milk is characterized by rich nutrition and easy absorption by human body,which has become one of the important sources of high-quality protein in developing countries.The digestive tract microbiota and their metabolites affect the digestion and absorption of nutrients,body health,and physiological homeostasis of ruminants.At the same time,the early life digestive tract microbiome may have long-term effects on host digestive fermentation,feed utilization efficiency,and animal productivity.However,the digestive tract microbiome features of dairy goats and their long-term microbial mechanisms in regulating gastrointestinal fermentation,body health and growth performance remain unclear.In the present study,dairy goats feeding the same diet and under the same management conditions were selected for systematic research on the gastrointestinal microbiome composition,function and microbial interactions and their long-terms effects on gastrointestinal fermentation,body health,and production performance,through large-scale sampling,tracking experiments,and multi-omics analysis,to provide theoretical basis for early regulation of the digestive tract microbiota,and improvement of feed utilization efficiency and production performance of dairy goats.Experiment 1 Rumen microbiome features and their correlation with rumen fermentation and growth performance in young dairy goatsIn order to identify the keystone rumen microbiota that affect the growth performance and rumen fermentation of young goats,young dairy goats under the same diet and management conditions were selected,and the correlation between the growth rate,rumen fermentation,and microbial community were investigated.In the present study,ninety-nine 6month-old Guanzhong dairy goats with similar birth dates and good health conditions were selected to collect rumen fluid samples before morning feeding,weigh their birth weight and sampling weight,and determine rumen fermentation parameters and rumen microbial composition by 16S rRNA gene amplicon sequencing,and the relationship between the growth performance,rumen microbial community and rumen fermentation of young goats was analyzed.The results showed that the average daily gain（ADG）of young goats was significantly positively correlated with the molar of propionate,propionate concentration,and butyrate concentration in the rumen,and significantly negatively correlated with the molar proportion of acetate and the acetate to propionate ratio in the rumen（P<0.05）.ADG of young goats was significantly positively correlated with the concentrations of His,Trp,Arg,Val,and total EAAs in the rumen,and positively correlated with some NEAAs（such as Gly and Ala,P<0.05）.Moreover,we found that ADG was significantly positively correlated with the content of C18:lcll,UFAs,and MUFAs,as well as the C18:1Δ9-desaturase index in the rumen,and significantly negatively correlated with the content of antesio-C13:0,antesioC15:0,SFAs,and OBCFAs（P<0.05）.ADG of young goats was significantly positively correlated with the relative abundance of norank F082,Candidatus Saccharimonas,Ruminococcus gauvreauii group,Streptococcus,and Succinivibrionaceae UCG-001 in the rumen,and significantly negatively correlated with Prevotella,Prevotellaceae UCG-003,unclassified Prevotellaceae,and Prevotellaceae NK3B31 group（P<0.05）.The correlation analysis between microbial abundance and rumen fermentation parameters showed that ADG positively correlated microbiota were significantly positively correlated with propionate,most AAs,and MUFAs in the rumen（P<0.05）.Moreover,rumen bacteria（such as Prevotellaceae UCG-003 and ASV800）could be used as useful biomarkers to distinguish young goats with different growth performances,with an accuracy of 80.0%.Taken together,the rumen microbial community are closely related with rumen fermentation parameters,and the growth performance of young dairy goats.Rumen specific microbiota may affect rumen fermentation parameters,thereby regulating animal growth performance.Experiment 2 Mechanism of rumen microbiome regulating growth performance in young dairy goatsIn order to reveal the mechanisms of rumen microbiome regulating the growth performance of young dairy goats,the differences in rumen microbiome function,microbial metabolism and host metabolism of young goats with different growth rate were analyze by metagenome,rumen and serum metabolome.The results showed that,compared to LADG group,four "carbohydrate metabolism" pathways（TCA cycle,pyruvate metabolism,butanoate metabolism,and propionate metabolism）,three "amino acid metabolism" pathways（Taurine and hypotaurine metabolism,Lysine degradation,and D-Arginine and D-ornithine metabolism）,and two "lipid metabolism" pathways（Linoleic acid metabolism,and alphaLinoleic acid metabolism）were enriched in HADG group（P<0.05）.The 6phosphofructokinase（EC2.7.1.11）and triose-phosphate isomerase（EC5.3.1.1）and pyruvate kinase（EC 1.2.7.1）were involved in translating 6-phosphogluconate to pyruvate were enriched in HADG group（P<0.05）.In addition,the HADG group increased the gene abundance of CAzymes that involved in the degradation of starch（GH1339）,xylan（CE2 and CE3）,and lignin（AA4）in the rumen（P<0.05）.Rumen metabolome revealed that Lhydroxyethyllysine,tyrosyl-phenylalanine,and seryl-glycine that belong to amino acids,short peptides and analogues,and maltoriose,melibiose,and 3-galactosyllactose that belongs to carbohydrates and carbohydrate conjugates,12S-HHT and 13-HpODE that belongs to lipids were significantly enriched in HADG group（P<0.05）.Correlation analysis revealed a significant positive correlation between the ADG positively correlated microbiota and microbiota function of feed degradation and their metabolites（P<0.05）.Additionally,serum metabolomics revealed that the HADG group had significantly higher levels of serum Dornithine,L-glutamine,L-arginine,hydroxylysine,creatine,LysoPC（16:1（9Z）/0:0）,and glucuronolactone（P<0.05）.In conclusion,HADG goats have a more efficient rumen microbiome composition and function,which can improve rumen feed utilization efficiency,provide more energy and nutrients to the host and thereby improve host metabolism and growth performance.Experiment 3 Effects of rumen keystone microbiome on rumen fermentation,microbial community,and lactation performance in dairy goatsIn the experiment,a tracking study were conducted to reveal the long-term effects of rumen keystone microbiota on the rumen microbial community,rumen fermentation and lactation performance of dairy goats.Base on the above experiments,the experiment tracked the HADG and LADG group,collected rumen fluid samples and milk samples during lactation period,recorded milk production and analyzed rumen fermentation parameters,rumen microbiome and milk composition.The results showed a significant positive correlation between ADG of young goats and their milk production during first lactation（P=0.04）.Compared with LAL group,the milk yield,the lactose,milk fat,and milk protein yields were significantly higher in HAL group,and the molar of rumen acetate and A:P were significantly decreased in HAL group（P<0.05）.Compared with the LAL group,the abundance of Oscillospiraceae NK4A214 group,Ruminococcus,Christenesenellaceae R-7 group,and Lachnospiraceae NK3A20 group were significantly higher in the rumen of HAL group,while the abundance of Prevotella,Prevotellaceae UCG-003,Prevotellaceae UCG-001,Succiniclasticum,and unclassified f Prevotellaceae were significantly decreased in HAL group.Microbial co-occurrence network analysis of rumen microbial communities showed that rumen keystone microbiota such as Prevotella,played important roles in the interaction network of rumen microbial communities in young and lactating goats.Moreover,these keystones bacteria of young goats were significantly correlated with some important rumen microbiota of lactation goats（P<0.05）.The rumen of the HADG and HAL groups had more microbial modules that were positively correlated with rumen propionate fermentation,while the rumen of the LADG and LAL groups had more microbial modules that were positively correlated with rumen acetate fermentation（P<0.05）.Additionally,machine learning analysis found that rumen bacteria in young goats,such as Streptococcus,could serve as useful biomarkers for predicting lactation performance in dairy goats,with an accuracy of 91.7%.In conclusion,the keystone rumen microbiota of young goats had long-term effects on rumen microbial succession and composition,rumen function,and lactation performance by regulating the microbe-microbe interaction,microbial community structure,and rumen function.Experiment 4 Mechanism of the rectum keystone microbiota in modulating the microbial community and growth performance in dairy goatsSimilar to rumen microbiome,gut microbiome of ruminants are involved in the digestion and absorption of nutrients,maintenance of intestinal homeostasis and body health.However,the mechanisms by which gut microbiota and their metabolites regulate host health and growth performance remain unclear.In the present study,rectal contents and blood samples of goats with different growth performances were collected to determine gut fermentation parameters,microbiota and blood immune indexes at young and adult periods.Results showed that the ADG of young goats was significantly positively correlated with the total concentration of short-chain fatty acids（SCFAs）,acetate,propionate,and butyrate concentrations in rectal contents（P<0.05）.Compared to the LADG group,the content of serum albumin（ALB）and albumin-globulin ratio（AGR）were significantly increased in the HADG group,the content of globulin（GLB）and immunoglobulin G（IgG）were significantly reduced in the HADG group（P<0.05）.The analysis of Spearman correlation and microbial co-occurrence network found that some rectal microbiota,such as Succinivibrio,Prevotellaceae UCG-003,Oscillibacter,Streptococcus,and Faecalibacterium,were significantly positively correlated with the ADG of young goats,while Christensenellaceae R-7 group,Turicibacter,Romboutsia,and Clostridium sensu stricto 1 were significantly negatively correlated with the ADG of young goats（P<0.05）.Moreover,rectal Faecalibacterium,Succinivibrio,and Christensenellaceae R-7 group played important roles in the microbial interaction network.Correlation analysis of keystone rectal microbiota with gut SCFAs and serum immune indicators found that ADG-positive microbiota were significantly positively correlated with rectal SCFAs,while ADG-positive microbiota and the total concentration of rectal SCFAs were significantly negatively correlated with serum IgG content（P<0.05）.In addition,six rectal bacterial taxa（Colidextribacter,Prevotella,Prevotellaceae NK3B31 group,Lachnospiraceae UCG-001,Oscillibacter,and Prevotellaceae UCG-003）could be used as potential biomarkers for differentiating high or low growth rate goats,with 98.3%accuracy of prediction.Furthermore,compared to young goats,SCFAs producing bacteria,such as unclassified Prevotellaceae,Succinivibrio,Prevotellaceae NK3B31 group,and Oscillibacter were significantly decreased in lactation goats（P<0.05）.PICRUSt2 analysis showed that the functions of carbohydrate,polysaccharide,and amino acid metabolism in the rectal microbiota of adult goats were significantly downregulated compared to those in young goats（P<0.05）.This study demonstrated that some keystone rectal microbiota play important roles in gut microbiota structure and gut fermentation.These microbiota and their metabolites（such as SCFAs）contribute to improving host health and growth performance,and can be used as biomarkers to accurately classify young goats with different growth performances.Additionally,as the maturation of rumen and foregut,the contribution of the changes of those microbiota to feed degradation and energy supply decreased in adult goats.In summary,the digestive tract keystone microbiota play important roles in the microbial composition,structure,metabolic function and microbial interaction in young dairy goats.These keystone microbiota and their metabolites contribute to improving animal health and growth performance,and could be used as effective biological markers to classify or predict the growth performance and lactation performance of dairy goats.Moreover,rumen keystone microbiota. |
