Giant pandas are unique animals because of their digestive system is similar to carnivores but they have in fact adapted to a plant diet with bamboo as their main food source. According to fossils records, giant pandas were omnivorous approximately 7 million years ago, becoming almost vegetarian after 4.6 to 5 million years of evolution. However, their genome and anatomical structure do not favor bamboo digestion. For more than a decade, researchers have been questioning the underlying mechanism of their ability to digest bamboo. In 2010, the genome of giant panda was completed, which confirmed that their genome had no gene encoding for cellulolytic enzymes. Thus, the gut microbiota of giant panda, which has been hypothesized to play a key role in bamboo digestion, has garnered unprecedented attention. Researchers are also interested in the giant panda’s gut microbes due to their potential application in biomass conversion. In Chapters 2 and 3 of this thesis, the microbial catalog of the giant panda’s gut microbiota was characterized, showing possible age-related microbial dysbiosis. Moreover, the microbiota, both bacterial and fungal was highly individualized because very few operational taxonomic units were shared among the four pandas in this study. Novel homoacetogens were also identified in the giant panda using functional gene clone-library sequencing. Using metagenomic sequencing, I uncovered the first evidence of human and animal related viruses in the giant panda’s gut. In addition to the community structure, I also determined the metabolic pathways of the microbiome. From KEGG annotation, a metabolic pathway for both cellulose and hemicellulose metabolism was identified. Comparative metagenomic analysis indicated that the giant panda’s gut microbiome was taxonomically and functionally distinct from those in mammals. In Chapters 4 and 5, a total of 97 species of bacteria were isolated and identified using biochemical assays. Four of these bacteria showed powerful cellulolytic and hemicellulolytic activities on solid media. The gram-positive bacteria (HKUOP_BS) and the gram-negative bacteria (HKUOP_A14) were found to be rod shaped, facultative anaerobes that had the ability to powerfully hydrolyze both cellulose and hemicellulose using intracellular and extracellular enzymes respectively. In Chapter 6, I determined the complete genome of a cellulolytic bacterium, Klebsiella oxytoca HKUOPL1, from giant panda and further described the annotated virulence, drug resistant, functional and potential horizontal transferring genes. The phylogenomic tree indicated that K. oxytoca HKUOPL1 closely resembled the K. oxytoca KCTC 1686 strain commonly used in 2,3-butanediol production. In captive giant pandas, a mucous excretion episode usually occurs with mild to severe colic. To understand the host-microbial interactions during this episode, bacterial communities were compared between mucous excreta and normal feces. The shifts in community abundance (especially flooding of Clostridia) may be associated with the mucous excretion episode. This study provides a better understanding of the microbial community structure and function in the giant panda’s gut. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy