Study On Gastro-intestinal Microbial Flora And Its Response To Diet In Cashmere Goat

The gastrointestinal tract?GIT?of goats is a complex microecosystem,whose stability plays a vital role in the health of the animal body and has an influence on the production performance of goats.During the whole growth stage from birth to adulthood,the development of goat GIT and the establishment of microorganisms are mutually influencing and coordinated.However,there are still few systematic studies on the establishment of gastrointestinal microflora at the whole stage of"birth-weaning-adulthood"in goat,especially in shed-fed cashmere goats which live in desert and semi-desert ecologically fragile areas.The purpose of this study was to study the dynamics change of bacterial community in different parts of GIT of pre-weaning Shanbei white cashmere goats at different ages,so as to provide the basis for early appropriate dietary intervention or early weaning.We also studied the colonizing process of the bacterial community in digesta and mucosa sample in rumen,cecum,and colon of the cashmere goat from birth to adulthood to compare its spatiotemporal specificity.Through investigating the response of the rumen microecosystem to different nutrient levels in the diet,we preliminarily revealed the interaction between the microorganisms and the host and laid a foundation for healthy rearing of cashmere goats.In this study,high-throughput sequencing technology was adopted to study the dynamics of microflora in GIT at different age.The main results of this study are as follows:1.In the preweaning cashmere goat from the day 0 to 56,results showed that the composition of bacteria in GIT showed the corresponding age specificity except in jejunum and ileum.The composition of bacteria in the rumen was relatively stable from the 28^th day,while the bacteria in the reticulum,omasum,abomasum,duodenum,cecum and colon accessed to the relatively stable period from the 42^nd day.With the increase of age,the composition of the bacterial community in stomach,small intestine and hindgut was gradually distinguished.2.A total of 41 phyla and 1049 genera were detected in GIT.The dominant bacteria in the stomach was Bacteroidetes,while Firmicutes occupied dominantly in the intestine.From day 0 to 56,the dominant bacteria in the rumen changed from Firmicutes to Bacteroidetes,while Proteobacteria converted to Firmicutes in the intestine.Among all the GIT,there were26 dominant genera,which showed obvious temporal and spatial changes in the process of colonization.3.In the whole growth stage from 0 to 1.5 years old of the cashmere goat,results showed that the number of OTU,Chao and Shannon in the digesta and mucosa sample of rumen,cecum and colon were lower at day 14,and then increased significantly with the goats aged?P<0.05?.Whatever in digesta or mucosa,with the goats aged,the similarity between each age group increased,and the composition of bacteria gradually developed toward matured.The composition of bacterial community was significantly different between in digesta and in mucosa,and this showed a spatiotemporal specificity.In the rumen,there was a significant difference in the composition of bacteria between in digesta and mucosal sample.However,in the hindgut,there was a high similarity of bacterial composition between the digesta and mucosa sample at each age group before weaning,while there was a significant difference in the bacterial community structure between the two types of samples after weaning.4.In digesta,Bacteroidetes mainly existed in the rumen,and Firmicutes and Proteobacteria mainly existed in the cecum and colon.With the goats aged,the first dominant bacteria in rumen changed from Firmicute to Bacteroidetes,while in cecum and colon,there was a transform from the phylum Proteobacteria to Firmicute.With the increase of age,Proteobacteria in the mucosa sample was replaced by Firmicutes and Bacteroidetes.There were a total of 25 core bacterial genera in the digesta sample of rumen,cecum and colon.A total of 21 core bacteria was found in the mucosal sample of the three regions.The core bacteria of the two types of samples can be divided into three categories:the leading bacteria,the transitional bacteria and the mature bacteria.The results showed that bacterial genera such as Prevotella 1,Rikenellaceae RC9,Bacillus,Lactobacillus,Butyricicoccus,Faecalibacterium,unclassified Ruminococcaceae and Ruminococcaceae UCG-005 mainly enriched in the digesta.However,the genera including Butyrivibrio 2,Prevotellaceae UCG-001,norank?f?Neisseriaceae and Treponema 2 mainly existed in mucosal.5.As for the functional metabolic pathway,the genes associated with amino acid metabolism,energy metabolism,Translation and vitamin cofactor metabolism mainly enriched in rumen,while genes related to carbohydrate metabolism and Membrane transport were mainly abundant in the hindgut.In rumen,the bacteria in digesta may be more involved in carbohydrate degradation,while the bacteria in mucosa played a important role in energy metabolism.In cecum,compared with bacteria in mucosa,the bacteria in digesta are more involved in amino acid metabolism.6.In study of microflora response to diet,results showed that compared with 85%,100%and 115%diet,130%nutritional level dietary group,the bacterial abundance and diversity in digesta and the bacterial diversity in mucosa decreased significantly under 130%diet.The proportion of Bacteroidetes in both digesta and mucosa decreased with the increase of nutrient level in diet.The proportion of Rikenellaceae RC9 gut group,Ruminococcus 1 and Ruminococcaceae UCG-014 in the rumen digesta significantly reduced in 115%and 130%dietary group while the abundance of Succiniclasticum,norank?f?Muribaculaceae and Selenomonas 1 were higher in these groups?P<0.05?.In mucosa,compared with standard diet group,the proportion of Prevotella 1 significantly decreased in 115%and 130%dietary group,while the proportion of Butyrivibrio 2,Desulfovibrio and Mogibacterium significantly increased?P<0.05?.Low?85%?or high?130%?dietary nutritional level also inhabited the colonization of archaea in rumen digesta.Compared with the standard diet group,the nutrient level of 130%diet significantly reduced the diversity of fungi and the abundance of protozoa in rumen digesta?P<0.05?.7.With the increase of dietary nutrition level,the concentration of acetic acid decreased significantly,while the concentration of propionic acid,butyric acid,isobutyric acid and valeric acid increased significantly,and the ratio of acetic acid/propionic acid also significantly decreased.The high nutrient level diet lead to the significantly decrease of the p H,increase of the concentration of LPS,and the up-regulation of mucosal inflammatory factors?such as IL-1?,TNF-?and IL-10?.The expression of Claudin-1,Claudin-4,Occludin and ZO-1 proteins in the mucosa decreased continuously.8.Results showed that the genus Ruminococcaceae NK4A214 group was significantly positively related to acetic acid and butyrate,while the genus Prevotellaceae NK3B31 group was significantly negatively correlated with LPS?P<0.05?.In addition,Desulfovibrio and Campylobacter in the mucosa were positively related to IL-1?and TNF-?,respectively,and Butyrivibrio 2 was positively related to IL-10.Furthermore,Desulfovibrio was negatively significantly correlated to the expression of Claudin-1,Occluding and ZO-1?P<0.05?.9.In the study on the bacterial accumulation effect of soil in the natural grazing area around sheep farm,PCo A results showed that the bacterial community composition in sheep feces?YF?was significantly different from that in the natural grazing area?ZF?at different distances,and the bacterial community composition similarity between ZF0 and ZF500-2000was relatively low,while that between ZF500-2000 was relatively high.Combined with Venn diagram and Adonis analysis,it can be seen that compared with other distances,the bacterial similarity of YF and ZF0 was relatively high,that is,the cashmere goat had the most important influence on bacreial community of soil in the farm,but had a minor impactl on that within a distance of 500?2000 m around the farm.In summarize,combined with the gastrointestinal development and bacterial colonization in preweaning goats,the study suggested that the Shanbei white cashmere goats could be weaned after the age of 42 days.During the whole growth stage from birth to adulthood of cashmere goats,whether in digesta or in the mucosa,with the increase of age,the similarity of bacteria groups within or between each day age group increased continuously,and the composition of bacteria was gradually stable.The bacterial community of each GIT could be basically divided into three categories:lead bacteria,transitional bacteria and mature bacteria.The composition of bacterial community was significantly different between in digesta and in mucosa,and this showed a spatiotemporal specificity.In rumen,there was a significant difference on bacterial community composition between in digesta and mucosa at each age group.But in hindgut,with the increase of age,the difference of bacterial community between these two sites was gradually obvious and showed different metabolic function.In study on the response of microflora to diet,it had been found that the dietary nutrition level not only significantly altered the composition of the microflora in the ruminal digesta,but also had a certain influence on the bacteria in the mucosa of rumen.The dietary nutrition level altered the composition of VFA,decreasd p H in rumen,and further had an influence on the expression of inflammatory factors and TJ proteins in ruminal mucosa of cashmere goats.The activity of cashmere goats had a great influence on the composition of the soil bacterial community in the farm,but the influence was small within the distance of 500?2000 m around the farm.With the increase of distance,the influence of cashmere goats on bacterial community in the natural soil of grazing area decreased gradually.