Multi-Omics Systems Biology Studies of the Gut Microbiome of Herbivorous Mammals

• Main Authors: Po-Yu Liu, 劉勃佑
• Other Authors: Hon-Tsen Yu
• Format: Others
• Language: en_US
• Published: 2019
• Online Access: http://ndltd.ncl.edu.tw/handle/mjfbj2

博士 === 國立臺灣大學 === 基因體與系統生物學學位學程 === 107 === The gut microbiota coevolve and coadapt with their mammalian hosts in response to changes in hosts’ physiological status (e.g. thermal regulation) and external environments (e.g. food sources) over the evolutionary history. In small herbivorous mammals, the gut microbiota helps in efficiently acquiring energy in response to the rapid loss of body heat. Additionally, the gut microbiota of wild mammals is altered according to the food availability per season. Leaf-eating (folivorous) flying squirrels are among the smallest arboreal herbivorous mammals, which occupying the specialized evolutionary and ecological niches; however, little is known about the interactions of the wild folivorous flying squirrels and their gut microbiota. Therefore, in this study, we used the wild folivorous flying squirrels as study models and integrate multi-omics approaches (metagenome, metatranscriptome, and metabolome) based on the central dogma of molecular biology to investigate the gut microbiome of flying squirrels. Chapter 2 was conducted a comparison for the gut microbial compositions and carbohydrate metabolic potentials of four species folivorous flying squirrels with different body sizes and mass-specific metabolic rates based on Kleiber’s law. Chapter 3 described the seasonal dynamics of flying squirrels’ (Siberian flying squirrels) gut microbiota and the landscape phenology of their forest habitats. Chapter 4 provided functional profiles (nutrient extraction and phytotoxin degradation) of the white-faced flying squirrels’ cecal microbiota by using multi-omics tools. In addition, in order to realize the microbial individual interactions within the community, we isolated a cellulolytic microbial consortium from rat cecum to be a model community. Chapter 5 aimed to decipher the metabolically and ecologically sympatric mechanisms among consortium members. The gut microbiota comparison of four flying squirrels revealed that the Firmicutes was the predominant taxa of all the flying squirrel gut microbiota, while the Bacteroidetes was the secondary predominant gut microbial taxa of the small and medium flying squirrels. However, the Bacteroidetes was absent in large flying squirrels. In addition, metagenome prediction demonstrated that small flying squirrels harbored the most carbohydrate metabolic potentials (adjusted by body mass). The gut microbiota of the Siberian flying squirrels were altered along with seasonal temperature and vegetation changes. The 20°C was the turning point of gut microbiota shifting; more diverse gut microbial compositions were found at the lower temperature. The gut metabolomics profile of white-faced flying squirrels demonstrated that the transits of chemical environments along with the digestive process, including more than 600 phytochemicals degraded with this path. Parallel metagenomic and metatranscriptomic analyses revealed that systems of flagella, chemotaxis, and ABC (ATP-binding cassette) transporters were the keys for nutrient extraction and phytotoxin degradation of the cecal microbiota. Metagenomic analysis for cellulolytic consortium revealed that metabolic complementarity occurred within the sympatric consortium. The time-serial analysis and competition model provided the evidence for the steady state of consortium mutualism.