Application of Molecular Techniques to Overcome challenges of Ruminant Nutrition in the Tropics

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Student thesis: Doctoral ThesisDoctor of Philosophy

Original languageEnglish
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Award date2020
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Livestock farmers in many parts of sub-Saharan Africa contend with low production caused by shortage of feed, low quality forages or both. Fibrous feeds and crop residues of low digestibility constitute the major proportion of feeds available to most ruminants under smallholder situations in developing countries. The characteristic feature of tropical forages is their slow rate of microbial breakdown in the rumen with the result that much of the nutrients of the feed are voided in the faeces. The slow rate of breakdown reduces the outflow rate from the rumen and depresses feed intake. This dissertation is organised into seven chapters aimed at understanding the degradation of low-quality feeds in the rumen with a goal of improving it. Chapter one is comprises of a literature review with background information regarding ruminants, rumen microbiology, molecular techniques, tropical fodder trees and crop residues. The chapter also outlines the aims and objectives of the dissertation. Chapter two details the materials and methods used for the experiments. Chapter three details the evaluation of the chemical composition, in vitro degradation, and effect on composition on rumen bacteria of leaves of seven African fodder tree species to determine their suitability for ruminant nutrition. The results showed that the leaves of the trees could be a source of highly nutritious feed to supplement bulk feeds. However, also contained
secondary metabolites which had a significant in vitro effect on rumen microbes. Advances in sequencing technologies have facilitated the study of the rumen microbial community composition with higher accuracy and greater throughput than was previously achievable. In Chapter four, a new entrant into the sequencing platforms, the Oxford Nanopore MinION, was evaluated. The results showed that the platform had potential as a cheaper, faster, and more accurate alternative for taxonomic investigation of the rumen microbial ecosystem. Crop residues form an important part of ruminant feedstuff in many developing countries. Chapters five and six investigated rice straw as a representative of these residues. The results showed that the effect of the chemical composition in vitro degradation was as a result of a complex interaction between the various components of the straw rather than their absolute measurements. Colonisation of newly ingested plant material by rumen microbes is a prerequisite for ruminal degradation of plant biomass. The in vitro colonisation of the rice straw samples was investigated via 16S sequencing of attached bacteria. Results in Chapter five showed that the colonisation dynamic with two distinct phases. Further, Chapter six demonstrated that there are interactions between the chemical composition of the substrate and the colonising bacteria. The studies showed that understanding the dynamics of colonisation could enable interventions to improving ruminant fermentation efficiency. Chapter seven is a summary of the conclusions and recommendations from the studies