Adult giant pandas (Ailuropoda melanoleuca) express transitional characteristics in that they consume bamboos, despite their carnivore-like digestive tracts. Their genome contains no cellulolytic enzymes; therefore, understanding the development of the giant panda gut microbiome, especially in early life, is important for decoding the rules underlying gut microbial formation, inheritance and dietary transitions. In addition, the gut bacterial microbiota of giant panda is important in governing its health, dietary nutrient adsorption and even population evolution. Bacteriophages act as key regulators of the diversity and population of bacterial microbiota in the ecosystem. Exploring the bacteriophage dynamics in the gut ecosystem could reveal the mechanism controlling the gut bacterial microbiota. In this study, we investigated the change of the gut microbiome of giant panda during the first 9 months of growth after birth, and to identify the determining factors in shaping the gut microbiome towards that of adults. Meanwhile, we found a possible dynamic interaction between bacteria and bacteriophages in the gut microbiota of giant panda during development, in which the observation of switch of lytic form and lysogenic form of temperate phages, and dynamics of diet-related bacteria and bacteriophages, for the first, probably provide clues to the viral role of the gut microbiota of giant panda under different dietary intake. In the first section of this thesis, we investigated the gut microbiomes of two newbom giant panda brothers (22 samples) and their parents (11 samples) living in Macao, China, from 2016 to 2017, by deep metagenomic sequencing. Both giant panda cubs exhibited progressive increases in gut microbial richness during early growth and development, particularly during the first sixth months after birth. Results showed that Enterobacteriaceae dominated the gut microbial compositions in both adult giant pandas and cubs. A total of 583 co-abundance genes (CAGs) and about 79 metagenomic species (MGS) from bacteria or viruses displayed significant changes with age in the giant panda cubs. Seven genera (Shewanella, Oblitimonas, Helicobacter, Haemophilus, Aeromonas, Listeria and Fusobacterium) showed significant association with respect to gut microbial structural determination in the nursing stage of giant panda cubs. Furthermore, 10 orthologous gene functions and 44 pathways showed significant changes with the early stage of the growth. Of the significant metabolic pathways, 16 pathways from Escherichia, Klebsiella, Propionibacterium, Lactobacillus and Lactococcus displayed marked differences between parents and their cubs at birth, while 29 pathways from Escherichia, Campylobacter and Lactobacillus exhibited significant increase in cubs from 6 to 9 months of age. In addition, oxidoreductases, transferases and hydrolases dominated the significantly change of gut microbial enzymes during the growth of giant panda cubs, while few of them were involved in cellulose degradation. The findings indicated that diet determined the gut microbiome transitions and Enterobacteriaceae played an important role of in the guts of giant panda in early life. In the second section, with further in-depth bioinformatics analysis of deep metagenomics sequencing data on more fecal DNA samples (a total of 68 DNA samples: the samples from section 1; 4 and 10 new samples from cubs and their parents, respectively) collected from the giant panda family living in Macao, we found Enterobacteriaceae phage dominated the bacteriophage diversity, and presented predominantly in lysogenic form in the gut microbiota of cubs and adults. The bacteriophage diversity was supported by annotating bacteriophage genomes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers, in the assembled scaffolds of samples. Meanwhile, the gut bacteriophage diversity in giant panda cubs was much lower than that in adults, at which, among all detected bacteriophage, Enterobacteria phage phi92 and Salmonella phage Vi II-E1 exhibited the most significant enrichment. Besides, the gut bacteriophage diversity were much higher than the gut bacterial diversity at birth, and eventually decreased in subsequent development, while interestingly, it increased again and maintained higher than the gut bacterial diversity in adults. Nevertheless, we observed a higher diversity of diet-related gut bacteria than their bacteriophages in adults except Lactococcus, and also a significant enrichment of lysogenic form of their bacteriophages in adults. In addition, we detected an increase of antibiotic genes and virulent genes in the gut microbiome of giant pandas from cubs to adults. These findings suggest a fluctuating dynamics between the diversity of bacteria and bacteriophage in the gut microbiota of giant panda during early growth and development after birth, and disclose the importance of food intake on determining bacteriophage composition and switch in the gut microbiota of giant panda. In summary, this study showed gut microbiota gradually increased in richness, but reduced inheritance, during the growth of giant panda cubs after birth. Also, Enterobacteriaceae family members and their bacteriophages played vital roles in controlling the gut microbiota of giant panda cubs and adults. Cubs at 6 months old enter a significant period, during which a comprehensive and substantial increase of microbiome occurs. This increase resulted in provisionally higher bacteria diversity than bacteriophage diversity in the gut microbiota of cubs at 6—9 months of age. Furthermore, when the diet shift from milk to bamboo, the abundance of milk-digesting bacteria and their bacteriophages decreased simultaneously, at which the bacteriophages showed a faster reduction rate than bacteria. The findings suggest a dramatic dynamics between bacteria and bacteriophages, and shed light on the importance of diet in regulating the diversity of diet-related bacteriophages, in the gut microbiota of giant panda. In summary, this study showed gut microbiota gradually increased in richness, but reduced inheritance, during the growth of giant panda cubs after birth. Also, Enterobacteriaceae family members and their bacteriophages played vital roles in controlling the gut microbiota of giant panda cubs and adults. Cubs at 6 months old enter a significant period, during which a comprehensive and substantial increase of microbiome occurs. This increase resulted in provisionally higher bacteria diversity than bacteriophage diversity in the gut microbiota of cubs at 6~9 months of age. Furthermore, when the diet shift from milk to bamboo, the abundance of milk-digesting bacteria and their bacteriophages decreased simultaneously, at which the bacteriophages showed a faster reduction rate than bacteria. The findings suggest a dramatic dynamics between bacteria and bacteriophages, and shed light on the importance of diet in regulating the diversity of diet-related bacteriophages, in the gut microbiota of giant panda.