About
I work in metatranscriptomics, microbiome research, and clinical diagnostics. I focus on improving how we detect infections and track pathogens.
In the INTEGRATE study, I analysed over 1,000 stool samples from patients with diarrhoea. This is the UK’s largest study comparing traditional lab tests to next-generation sequencing (Cunningham-Oakes et al., 2025). We used DNA (metagenomics) and RNA (metatranscriptomics) to detect pathogens directly from a patient sample (no culturing needed). This approach found infections that standard tests missed and revealed which genes were active during infection. RNA stayed stable in older, unpreserved samples and improved detection of pathogens like Cryptosporidium, Salmonella, and Adenovirus compared to clinical tests. This makes it a powerful tool for tracking outbreaks. By combining RNA and DNA, we got the clearest view yet of what causes gut infections and how microbes behave inside the gut.