Metagenomics is an approach to investigate the combined genetic material of an entire microbial community at once, and has completely changed the way we view the (microbial) world. For example, the human body is a complex super-organism where bacteria are about ten times more abundant than human cells, and viruses are another ten times more abundant than the bacteria. This ratio holds for other (host-associated) environments as well, and most of these microbes and viruses remain poorly explored. We develop innovative bioinformatic tools to study metagenomes, and apply them to investigate the microbes in various natural habitats, including their influence on the health and disease of the host.
Powered by advances in next-generation sequencing technology, metagenomics has the potential to discover new microbes and viruses at an unprecedented scale and resolution. As such, metagenomics has changed the face of virus discovery. In most environments, unknown DNA sequences are a significant, if not dominant component of the metagenome, also known as biological “dark matter”. These unknowns can be mined for genome sequences of novel species, including viruses. Viruses are the least well-characterized, and at the same time the most genetically diverse superkingdom, and are enriched in the unknown fraction of metagenomes. We employ metagenomics for (virus) discovery in natural environments, and in samples related to diseases of unknown origin.