Our basic research focuses on the bioinformatic and computational analysis of large-scale human population cohort datasets that include a microbial component, typically metagenomic sequences from the gut or other body sites. We address a range of clinical, biological and ecological questions on host-microbe association, interaction and function as well as the influence of microbes (commensals or pathogens) and the gut microbiota on health and disease, including metabolic and cardiovascular diseases.

Our scientific interests are generalist and fundamental at heart, but a few topics are of particular current interest, through led projects in the lab or collaborations:

– Can past infections (foodborne pathogens and other) influence our future health? The ecology of asymptomatically carried pathogens in the human gut and links with non-communicable diseases.
– Characterizing the human gut archaeome and its associations with health and disease.
– Genetic basis of microbial pathogenic variation and its association with human or animal disease.
– Effect of antibiotic and non-antibiotic medication on the gut microbiome and gut resistome dynamics.

Please see the Publications page for more information.