I am part of a team based at Aberystwyth University who are leading the Wales' research effort to eradicate bovine tuberculosis. We are led by Prof. Glyn Hewinson, and backed by Sêr Cymru II and the Welsh Government, and more about the funding of this project can be found here. I am working closely with the Animal and Plant Health Agency (APHA) and epidemiologists in the Welsh Government to study and define the population structure of Mycobacterium bovis in Wales using whole bacterial genome sequencing to further advise the better targeting of bovine tuberculosis control strategies across Wales. I am also employing bioinformatic analyses to further delve into the genomes to determine whether there are phenotypic differences between clones of M. bovis. Read more about the teams' aims here. My day to day work revolves around computational analysis, using Python, R, Bash and the Unix command line to do this. You can keep an eye on my GitHub for publically available code, but note that it is not the most up to date, and some code is kept private until suitable to share, usually after publicaton.
I completed my viva in December 2020, and successfully defended my thesis titled "Hyper Ammonia Producing Bacteria And Bacteriophages in the Rumen Microbiome". I was based at Aberystwyth University for my PhD studies, 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 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 hijacking 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.