Study On The Influencing Factors Of The Composition And Dynamics Of The Intestinal Microbiome Of Forest Musk Deer (Moschus Berezovskii)

There are a large number of microbial communities in the gut of mammals,which are closely related to the health of the host.Forest musk deer is the first-class protected species in China and IUCN Red List endangered species.Its breeding population is not only an important source for the recovery of wild resources,but also a necessary way to solve the source of natural musk and relieve the pressure of wild forest musk deer.The high incidence of intestinal diseases in captive forest musk deer is closely related to the composition of intestinal microbiome.However,there is no systematic study on the intestinal microbial community of forest musk deer.Therefore,this study using non-invasive sampling method,16 S rDNA high-throughput sequencing,Metagenome sequencing and Enzyme-Linked Immuno Sorbent Assay to comprehensively analyzed the composition and dynamic changes of the intestinal microbiome of forest musk deer.This research is of great significance for improving the health status of captive forest musk deer and strengthening the management of captive population.The main results of this study are as follows:1.Through the comparative study on the intestinal microbiome of captive and wild forest musk deer,the results showed that captive did change the composition of natural intestinal microbiome of forest musk deer.At the phylum level,the relative abundance of Bacteroidetes,Firmicutes,Spirochaetae and Verrucomicrobia were significantly different between the captive and wild forest musk deer;At the family level,the relative abundance of Verrucomicrobiaceae,Bacteroidaceae and Bifidobacteriaceae were significantly different between the captive and wild forest musk deer;At the genus level,the genera with significant differences between the two groups include Bacteroides,Akkermansia,Alistipes,Ruminococcus,Faecalibacterium,Bifidobacterium,etc.PICRUSt functional gene prediction showed that the function of glycan biosynthesis and metabolism,metabolism of cofactors and vitamins,nucleotide metabolism and energy metabolism of captive forest musk deer was significantly higher than that of wild forest musk deer,while the carbohydrate metabolism function was significantly higher in wild forest musk deer.In the process of captivity breeding,the composition of intestinal microbiome of captive forest musk deer can be changed to be similar to that of wild forest musk deer by changing the diet of captive forest musk deer,which lays a foundation for reintroduction.2.By analyzing the composition of the intestinal microbiome of healthy forest musk deer,mild diarrhea forest musk deer and severe diarrhea forest musk deer in captivity,the results showed that the richness and diversity of intestinal microbiome of healthy forest musk deer were significantly higher than those of mild and severe diarrhea forest musk deer,but there was no significant difference between mild and severe diarrhea forest musk deer.LEf Se analysis showed that there might be a corresponding relationship between the degree of intestinal microbiome disorder and the main pathogenic bacteria.The pathogenic bacteria Escherichia-Shigella was mainly enriched in the intestines of mild diarrhea forest musk deer;while the pathogenic bacteria Fusobacterium was mainly enriched in the intestines of severe diarrhea forest musk deer.At the same time,the abundance of cellulose decomposing bacteria Prevotellaceae＿UCG-004 and Ruminococcaceae＿UCG-005 in the intestines of individuals with diarrhea decreased,suggesting that the digestive physiological function of forest musk deer would also be affected in the case of diarrhea.This study provides an important scientific basis for the prevention and control of diarrhea in captive forest musk deer.3.Through the study of the establishment of intestinal microbiome and the dynamic changes of cortisol,triiodothyronine,immunoglobulin A levels of young forest musk deer from birth to weaning.The results showed that there was significant correlation between the predominant intestinal microbiome and its diet during the development of young forest musk deer.In this process,as the food of young forest musk deer changed from breast milk to plants,the diversity of microbial communities gradually increased and the composition tended to mature,and finally reached a stable level around 80 days after birth.The fecal cortisol level of young forest musk deer was relatively stable before the separation of mother and young,but increased significantly after separation.The change trend of triiodothyronine and immunoglobulin A was similar,with the decrease of breast milk intake,the levels of triiodothyronine and immunoglobulin A also showed a downward trend,and reached the lowest level after the separation of mother and young.Correlation network analysis showed that during the development of young forest musk deer,Ruminococcaceae＿UCG＿002,Lactobacillus,Bifidobacterium,Prevotella＿1 has the strongest relationship with other bacteria,suggesting they may play a major regulatory role in the intestine of young forest musk deer in the early stage.This study shows that the separation period is a sensitive period during the growth of young forest musk deer.In the process of captivity breeding,breeders should be able to detect these predictable changes in these parameters use non-invasive method in the further protection and management.4.In this study,the changes of cortisol hormone,intestinal microbiome abundance and function of mother and young musk deer in 80-day lactation group,90-day lactation group and 100-day lactation group were studied.The results showed that the increment of cortisol hormone level of mother forest musk deer increased with the increase of lactation time.The increment of cortisol hormone in young forest musk deer was the highest in 80-day lactation separation group,but there was no significant difference between 90-day lactation separation group and 100-day lactation separation group.With the increase of lactation time of mother musk deer,the abundance of Firmicutes and Bacteroides was significantly lower after separation.Based on the annotation results of COG,KEGG and CAZy databases,the abundance of functional groups annotated by intestinal microbiome of female and young forest musk deer in 90-day lactation separation group changed little before and after separation.Based on the above results,in captivity,the separation of mother and young forest musk deer at 90 days of lactation was less affected by stress,and the physiology was relatively stable,which was the appropriate weaning time.