Studying the UnderstudiedHyper Ammonia Producing Bacteria And Bacteriophages in the Rumen Microbiome
Student thesis: Doctoral Thesis › Doctor of Philosophy
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Greenhouse gas emissions and feed efficiency in ruminant livestock are pertinent and important topics, ones which have not suffered from lack of attention as ample research has endeavoured to further our understanding of the complex rumen microbial ecosystem. Despite this, some populations remain understudied. This is the key motivation behind the studies herein, which contribute to the understanding of the niche bacterial population of hyper ammonia producers (HAP) and bacteriophages (viruses that infect bacteria). HAP species degrade amino acids and peptides for energy, in the process producing hydrogen, carbon dioxide, and excessive amounts of ammonia. Hydrogen and carbon dioxide feed into methane production by archaea present in the rumen, whilst excess ammonia is removed from the animal host. This makes the HAPs an ideal target for potential population control, but firstly it was imperative to better understand them. This study first characterised the ammonia production phenotypes of bacterial cultures, then compared their genomes and transcriptomes to identify a signature that indicates the HAP phenotype. The work presented here has demonstrated the complexity and variability underlying the seemingly simple HAP phenotype, warranting further investigation in future work and isolation of novel HAPs in order to better understand this group before controlling the population. Phage therapy is one approach to population control that has been relatively little explored to date in the rumen. Despite phages being abundant in the rumen, there were only five genomes available of phages isolated from rumen-associated samples. This study isolated and characterised a further five novel phages that infect Butyrivibrio fibrisolvens. While the work presented here did not identify phages active against HAPs, these five Butyrivibrio phages contribute valuable information about the structure and function of the rumen ecosystem. It is suggested that continuation of this line of enquiry in future work would complement ongoing research utilising metagenomics, metatranscriptomics and metaproteomics aimed at understanding and improving rumen efficiency
Thesis, 11.6 MB, PDF
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Thesis, 11.6 MB, PDF
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