
doi: 10.7488/era/7181
Ruminants including cattle, sheep, and goats are globally important farmed animals defined by their complex digestive system. They possess a non-glandular forestomach composed of three sections followed by one ‘true’ secretory stomach. The rumen is one of the sections of the forestomach and acts as a fermentation chamber, breaking down complex plant matter into products including volatile fatty acids (VFAs) that are easily absorbed and utilised by the host. As the mammalian host is unable to produce enzymes to ferment and digest this plant matter directly, they rely on a community of microorganisms in the rumen, that work in symbiosis with each other and the host, to carry this out for them. A by-product of this fermentation is hydrogen which is quickly removed in a thermodynamically favourable reaction through conversion to methane. This gas is then exhaled and represents energy lost to the atmosphere that the host can no longer use. To increase the productivity of the host and reduce the negative effects of ruminants on global warming, the conversion of plant matter to VFAs needs to be optimised, with the production of methane avoided as much as possible. This can be achieved by learning more about the bacteria, archaea, fungi, protozoa, and viruses present in the rumen through culture-dependent and culture-independent methods, which work best when used together. In this thesis, a range of rumen microbes were cultured on a range of commonly used rumen culture media, to determine which of the main rumen microbes could be cultured using this method and which medium/media they were enriched on, if any. Next, using these co-cultures, pure cultures of rumen microbes were obtained using dilution-to-extinction and streak plating, and included Xylanibacter (Prevotella), Butyrivibrio, and Anaeroplasma. These were characterised using whole-genome sequencing (WGS) and compared to the current collection of cultured rumen microbes. Metagenome-assembled genomes (MAGs) were also generated from rumen contents and compared to the isolates obtained and to existing rumen MAG databases. The functions of these rumen microbes predicted from their genome sequences were compared to their observed characteristics in vitro, to determine their likely role in the rumen microbial ecosystem and to see how accurately the WGS data could be at predicting actual function. An in-depth RNA analysis of the growth of three novel Butyrivibrio spp. isolated in this thesis was also carried out to determine to what extent differential gene expression was seen when grown on a range of substrates. Finally, an in vitro fermentation experiment was carried out, adding a high dose of a native rumen Xylanibacter (Prevotella) to see if the fermentation profile of rumen fluid could be shifted away from methane production and towards VFA production. These results support the need for both culture-dependent and culture-independent exploration into the rumen microbiota in order to increase host productivity and decrease methane production. This is particularly important to fully define the rumen fermentation profile, identify novel pathways or microbes that could be important in mitigating methane emission and increase productivity, and mitigate the effect of livestock on the environment while ensuring the livestock sector is a successful and productive component of the food chain for years to come.
culture-independent methods, VFAs, Rumen microbiome, Fermentation, Volatile fatty acids, Culture-dependent methods, Methane production
culture-independent methods, VFAs, Rumen microbiome, Fermentation, Volatile fatty acids, Culture-dependent methods, Methane production
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