Characterisation and optimisation of the rumen microbiome

The rumen microbiome is arguably one of the most economically important microbiomes on the planet. Globally, there are over 1 billion cattle and other food-producing ruminants and they are of vital importance for food security, providing meat and dairy products to billions of humans. However, the current global food system fails to feed 10% of the 7 billion humans on the planet, and the population is set to exceed 9 billion in 2050 and 11 billion in 2100. As such, the FAO estimates that by 2050 meat production will need to increase by 76% and dairy production by 63%. At the same time we must reduce the impact of the food system on the environment. In short, we must produce more food using fewer resources.

Understanding how ruminants convert their food into energy, and subsequently milk and muscle protein, is therefore of obvious importance. If we can improve the efficiency of food digestion by ruminants, we may be able to produce more food while using fewer resources, a key aim of improving global food security.

The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiome. The rumen contains a microbial ecosystem in which a dense and complex mixture of bacteria, archaea, protozoa and fungi convert carbohydrates to short-chain, volatile fatty acids (VFAs).

We have discovered thousands of novel Bacterial and Archaeal species in the cattle rumen, and we are able to predict their metabolic potential using computational techniques. However, full understanding of their role and behaviour in the rumen microbial ecosystem will require bringing these novel species into culture, and studying them in vitro and in vivo.

In this PhD, you will (i) bring into culture important rumen microbial species, focusing on gaps in the current catalogue (there are an approximately 2,300 missing species; (ii) study these novel microbes in the lab in terms of their metabolic potential, and growth and behaviour on various substrates; (iii) build beneficial communities of microbes that mimic beneficial behaviour and study these communities using multi-omics techniques; (iv) test some of these communities in an animal trial to study their effect on important ruminant phenotypes