Biological, Computational and Mathematical characterisation of microbial dark matter from the rumen.

Supervisors: Dr. Chris Creevey ([Email Address Removed]), Dr. Amanda Clare (IMPACS) & Dr. Kim Kenobi (IMPACS).

Gut microbes are vitally important to the health, efficiency and environmental impact of their animal hosts and especially for ruminants as they allow access to the nutrients in forage that would otherwise be inaccessible to the animal. However, as only a small percentage of the predicted numbers of microbes in the rumen have been successfully cultured, most of the genomic information collected so far has come from culture-independent techniques, such as metagenomics. The genomic information retrieved from the “unknown” organisms, termed “microbial dark matter”, can constitute 40% of all the sequencing data and its characterisation is one of the greatest challenges to fully understanding the gut microbiome. We are looking for a talented and motivated scientist to take on this challenge.

This Ph.D. project will utilise the vast amount of experience and data produced in IBERS from the rumen microbiome, coupled with expertise from the departments of computer science and mathematics to address this pressing issue. This will involve analysing the biological signatures from the available genomes and metagenomes from rumen microbes, linking metabolic processes across taxonomically divergent organisms in the system and identifying the processes they carry out. This information will be used to generate models to characterise the functions of the microbial dark matter.

This PhD studentship provides an opportunity to gain world-class expertise in microbial genomics and bioinformatics, particularly as they are applied to gut microbial ecosystems. The successful candidate will be a member of the ecological and evolutionary genomics lab (http://www.creeveylab.org) under the direct supervision of Dr. Chris Creevey (http://www.aber.ac.uk/en/ibers/staff/chc30/), and be a member of a thriving team of researchers in the BBSRC-funded herbivore gut ecosystem group in IBERS.