Main areas of my research:
Describing novel taxa: Automated system for description of novel taxa
A large portion of the gut microbiome remains uncultured, termed the "dark matter". I have contributed to the valid naming of >100 bacterial species. To help others, I have produced Protologger, a tool designed to simplify the process of describing novel taxa. Protologger provides multiple lines of evidence for taxonomic placement as well as functional profiling and the ecological occurrence of the input novel taxa. Protologger can now be installed locally via Conda or used via the website; protologger.de
Functional protein ecology: Changing the focus of microbiome research from species to proteins
Microbiome research has focused on studying species, and then inferring their functionality. Given the data we can generate from shotgun metagenomes and metatranscriptomics, we can instead focus directly on the functions. We proposed the term 'functional protein ecology' for this shift in focus. InvestiGUT is a tool we have developed to allow the distribution of proteins to be studied across ~10,000 human gut metagenome samples, and the prevalence with human health conditions and geography to be studied.
Designing functionally representative synthetic communities
Microbiome samples of an ecosystem vary greatly, making mechanistic understanding difficult due to a lack of consistantly and reproducability. A solution for this is to generate communities of isolated bacteria, where the members are know, and therefore the can be maniplated or kept consistant for reproducability. These communities are called synthetic communities (SynComs), and should capture the functionaity of the ecosystem they aim to represent. We have designed a tool, MiMiC2, for the creation of SynComs based on metagenomic data.