I am based at Aberystwyth University whilst I finish writing up my thesis, with supervisors Prof Chris Creevey (now at Queen's univeristy, Belfast) and Prof Alison Kingston-Smith. I was funded by KESS II and the European Social Fund, and this scholarship was partnered with Dynamic Extractions. I was also employed as a research assistant with Chris at Queen's university for 6 months to further expand and explore some interesting phage-related outcomes from my PhD work.
Bacteriophages are viruses that infect bacteria. They are ubiquitous, and the most abundant thing (they're not technically organisms!) in the biosphere. They are highly specific, each phage infecting only one bacterial species or even strain. They are therefore highly diverse. A phage generally consists of a proteinaceous shell containing its genetic material in the form of double or single stranded RNA or DNA. Some have tails, tail fibers, and baseplates (often looking like spiders). Phages undergo one of two lifecycles, either injecting its DNA for incorporation into the host cell to become a prophage, which will propogate with future bacterial cell generations until cell stress causes phage formation. Lytic phages lyse the bacterial cells by hijecking cell machinery to make many viral progeny which burst out the bacterial cell. The latter bacteriophages are of interest in phage therapy, and those lytic phages that lyse particular rumen bacteria could have an implication in livestock husbandry. This is where I want to focus my future work.
Hyper Ammonia Producers
Hyper Ammonia Producers (HAPs) are a group of bacteria forming a niche within the microbiome, and have been found in the rumen, as well as swine manure and some human gut microbiomes. They are (generally) asaccharorlytic obligate amino acid fermenters, breaking down peptides and amino acids to produce energy, and in the process hydrogen and/or carbon dioxide, and a significant amount of ammonia. In the rumen, hydrogen and carbon dioxide are further metabolised by archaea, entering the methanogenesis pathway which produces methane, a greenhouse gas that contributes to global warming. The excess ammonia produced is removed from the ruminant host as urinary urea, and is a loss of potentially useful nitrogen form the animal. The contribution of HAPs to inefficiency in the rumen as well as indirectly methane emissions, HAPs are an interesting target for bacteriophages as a novel mitigation strategy for methane mitigation and increase of feed efficiency. They are relatively understudied, with only very few species known in the rumen, and it is unknown if all HAPs share any commonalities that could be used to discover more. Since they make such appealing targets, their role in the rumen must first be well characterised and understood. Filling in these gaps is one of the aims of my research.