The gut microbiome is made up of trillions of cells of bacterial and archaea, as well as fungi, other eukaryotes and viruses. This assemblage of microbiota is adapted to life in the intestine, where together they perform services for the host ranging from food digestion to protection against pathogens. The microbiome is assembled from birth onwards and shaped by the diet, lifestyle and health of the host, as well as by the genetic make-up of the host. By adulthood each of us harbors a unique, individualized microbiome that performs similar tasks across individuals. However the differences in microbiome composition and function are emerging as important for differences in various health and disease states, raising questions about how the microbiome interacts with its host to impact health and other aspects of host biology.

In the Department of Microbiome Science we ask fundamental questions about the evolutionary origins of the human gut microbiome and how it influences host physiology and evolution. We have three main area of research: (1) evolution of the human gut microbiome and interplay with host genetics, (2) lipids in host-microbiome symbiosis, and (3) microbiota-innate immune interactions. Please read the subsections for more on these topics along with representative papers from the lab in these areas.

We remain firmly rooted in the microbial ecology of the human gut microbiome. Because a large component of our work involves the analysis of gut metagenomes we encounter novel microbial diversity first through sequence analysis. We have delved into the biology of particular groups that caught our attention: you can check these out in the Bestiary. We also contribute to method development in the field of metagenome analysis.