Ecology of the human early life microbiome

We know we get colonized with trillions of microbes as soon as we are born, but how does this happen? Is there an evolutionarily conserved sequence of events, and if so, which ecological process(es) drive this? Given that modern humans live very different now than only 100 years ago, how does modern lifestyle influence this pattern of colonization during early life? We are trying to answer these questions using birth cohort studies in industrialized and non-industrialized countries.

The early-life microbiome in asthma development

Asthma is the chronic disease that affects most children around the world. What's even more worrisome is that its incidence continues to increase rapidly, and cases are becoming more severe. Research from Drs. Arrieta, Finlay and collaborators has shown that changes in the gut microbiome very in early in life can increase a baby's risk to develop asthma. Our lab is currently interested in finding more bacteria and fungi involved in this interesting association, exploring the immune mechanisms behind it, and finding ways to correct it. We are answering these questions using data from our human studies and modeling it in mouse models of airway inflammation.

It's not just bacteria, is it?

We are colonized with a complex mix of bacteria, fungi, protozoans, helminths and viruses, yet the vast majority of the microbiome studies around the world only include bacteria. In the big picture of our relationship with our gut microbiome, what influence do non-bacterial microbes have? How do these microbes effect bacterial communities? How to they interact with our immune system? We are currently applying ecological theory concepts to explore the relationships between microbial eukaryotes and prokaryotes, using bioinformatic and mouse model strategies.