Computational metagenomics and analysis
Team Leader and Senior Scientist
rdf [at] ebi.ac.uk
ORCID: 0000-0001-8626-2148
EditWe explore the entire microbiome, including the important yet understudied viral and eukaryotic (single-cell) fractions, to elucidate the functions of microbial communities, as well as their complex interplay and dynamics.
In doing this, we also consider the genomic plasticity and diversity generated by mobile genetic elements (MGE), which can create opportunistic pathogens and/or drug resistant microbes.
Finally, we constantly evaluate and adopt new technologies (e.g. long-read sequencing) to overcome technical and analytical challenges, such as capturing microbial diversity from complex samples, obtaining high-quality genomes from low-yield environments, and reducing the computational overheads to achieve in-field, real-time surveillance.
Our large-scale studies have identified thousands of novel species, which are now driving new developments in the MGnify microbiome resource. We have:
Our overarching goal is to decode the role of microbial communities in health and disease. We will exploit these new and expanding genomic resources to elucidate compositional changes and to address key knowledge gaps, including uncharacterised human microbiomes from under-represented geographical regions.
We will study the functional repertoire encoded by these newly discovered genomes to identify those with key roles in microbial adaptation to a particular ecological niche.
We will also focus efforts on the detection, prevalence, and impact of MGE (e.g. plasmids, phages, and transposons) to facilitate insights into their roles in community function, and exploit their functions in applied settings, for example fuelling new greener approaches to industrial biotechnology.
Finally, we will pursue real-world applications of metagenomics techniques, such as pathogen surveillance or the study of complex symbionts.
