First Post

   Sam Nicholls    No Comments yet    AU-PhD

Having spent quite some time ruminating over the contents of this inaugural blog post to a point beyond that of analysis paralysis, I have managed to avoid writing entirely.

Thus I’ll remove this pedestal of preclusion and begin with an uninspiringly titled First Post.

Hello, I’m Sam Nicholls; one of the latest PhD students to appear on the roster at Aberystwyth University, enrolled jointly between the Department of Computer Science and the Institute of Biological, Environmental and Rural Sciences (colloquially known as IBERS).

This inter-departmental, inter-institute collaboration has me well placed for a project that sits on the boundaries of both computing and biology and whilst doubling the supervisor count and the administrative paperwork, I have two different coffee rooms to hide in and get my name on two distinct doors.

The project, provisionally entitled Metagenomics of the Rumen Microbiome — which I’ll get to in a moment — is still being defined. Initially this was somewhat concerning but I quickly garnered from my admittedly short interactions with other PhD students that this is very much the norm at such an early stage. Phew.

I hope to provide a better overview of the project in a future post but suffice to say for now we’re looking for “interesting” micro-organisms that live in the rumen: the first stop of the four-chambered stomach that grass and feed will take on their tour through the digestive system of a cow (or other ruminant animals like sheep, goats and giraffes).

The rumen is a complex and diverse ecosystem inhabited by bacteria (Earth’s first life, abundant simple single celled micro-organisms found everywhere in their millions), archaea (micro-organisms that were initially thought to thrive only in extreme environments — with an evolution influenced by an early Earth — but more recently discovered in non-extreme environments too, play a similar role to bacteria ecologically), fungi (a broad class including single-celled yeasts, moulds and complex multi-cellular forms such as mushrooms), protozoa (single celled micro-organisms that feed from their direct surroundings and have the capacity for controlled movement with a tendency to thrive in moist environments) and viruses (the smallest of the microbes, which can only survive inside the cells of other living things). An unsuspecting cow yields anything from 20 to 50 billion bacteria in the volume of a raindrop alone.

But why is what goes on in a cow’s stomach of any interest at all? These rumen residents are adapted to efficiently break down biomass for their host’s continuing survival. The cell walls of grasses and other green plants for example, feature cellulose — long chains of glucose molecules which are difficult to digest — as a major structural component. Yet species of bacteria found in the rumen produce enzymes (catalysts for biochemical reactions) capable of breaking up these long chains in to smaller chains that are more easily further broken apart and used for energy. If we could isolate such enzymes we may be able to leverage them to improve the efficiency of biofuels like cellulosic ethanol.

This diverse and densely populated environment necessitates strong competition from its denizens to fight for their own survival. Under times of stress and competition for resources, microbes release potent antimicrobial peptides (very short proteins) to destroy their rivals.

Antibiotics are essential medicines for the treatment of bacterial infections in humans and animals. Bacteria presenting resistance to available antibiotics pose a serious problem in the world of medicine and the appearance of highly resistant and life threatening “superbugs” like MRSA are becoming increasingly commonplace in hospitals the world over. Discoveries of antimicrobials have dwindled over the past decade despite a clear medical need to synthesize new drugs to fight resistant bacteria. Yet in our unsuspecting cow’s paunch, a puzzle of peptides that could potentially lead to humanity’s next generation of antibiotics is ripe for exploration.

Another interesting possibility for analysis is working to lower methane emissions from cattle. Livestock are a significant global contributor to greenhouse gases, more so than transportation. The average cow will belch out around 500 litres of methane per day — a greenhouse gas which traps almost 30 times more heat than carbon dioxide — due to its biomass diet. By investigating the effects of various crops and feed on the rumen and the resulting interactions between the various microbes within, it might be possible to make a more environmentally friendly cow.

Finally, a methodology (both in terms of knowledge and software) for understanding the processes of such a complex biome could be applied and scaled to other microbiosystems such as that of our own gut, a world we know quite little about despite its considerable influence on our health and wellbeing.

This of course is all quite far off and currently I’m just finding my feet and when not occupied by compulsory soft-skills training, trying to absorb as much new biology terminology and techniques as possible — especially having had such little prior experience with biology coming from my computer science and statistics background.

I hope to go in to more detail shortly about what I’ve been doing so far and why trying to answer these questions pose a difficult computational problem — hopefully validating why we can make a PhD of it — as it would certainly make for a full post of its own.

In the mean time, there’s lots to be getting on with!