Application of meta-omics techniques to the rumen microbiome of dairy cows

The main objective of the research described in this thesis is to 1) assess the alterations in the community structure and functions of the ruminal microbiome when dairy cows were fed either a lipogenic diet or two different glucogenic corn-based diets, in which corn was subjected to contrasting processing conditions (grinding vs steam flaking), and 2) evaluate the applications of omics techniques in detecting the alterations of rumen microbiome in response to these diets. Chapter 2 reviews the identified microbes and enzymes associated with amylolytic and cellulolytic activities in the rumen and the application of metagenomics in studying rumen functioning. This chapter provides key information on candidate microbes and enzymes which is evaluated in the following chapters. Chapters 3 and 4 study the changes in ruminal fermentation when the above-mentioned lipogenic and glucogenic diets were incubated with rumen fluid using an in vitro batch-culture technique. The parameters include the microbial communities, molecular metabolites, pH values, the extent and kinetics of gas production, and other fermentation end-products such as volatile fatty acids, ammonia-nitrogen, and lactic acid. Utilising the results of the in vitro fermentation studies, an animal trial was conducted to further investigate alterations in metabolic mechanisms of ruminal microbes. In Chapter 5, responses of ruminal microbes in terms of fermentation profiles, microbial community structure, and metabolism pathways when dairy cows are fed the three diets are evaluated through a combination of 16S rRNA sequencing and metabolomics approaches. In Chapter 6, an integrated analysis of the metagenomics and metaproteomics techniques is made on the community structure, metabolic pathways, and enzymatic activities of the ruminal microbiome in dairy cows fed the experimental diets. Chapter 7 provides a discussion of the major research findings, the rumen microbial structure through the metagenomics approach, the metabolic pathways involved in VFA synthesis, and a future look of the use multi-omics techniques in rumen functioning studies.