We all encounter new microbes every day, but only a tiny fraction of introduced microbes become long-term residents of the human gut microbiome. Why do some microbes successfully establish, even though the vast majority fail to do so? How do microbes evolve as they transmit between hosts and communities?
In the Xue lab, we combine a wide range of experimental and computational approaches to investigate the ecological factors and microbial interactions that determine when new species can establish in existing microbial communities and to identify the selective pressures that act on gut microbes as they evolve within and between hosts.
What microbial interactions shape the outcomes of species introductions?
Microbes can interact through mechanisms like resource competition, cross-feeding, and interbacterial antagonism, but it remains unclear how these interactions counteract and reinforce one another in complex communities to determine the outcomes of species introductions.
To answer these questions, we build in vitro gut microbial communities and perform controlled species introductions to map microbial interactions at high throughput across varied community contexts. We also investigate the ecological factors that shape strain and species dynamics in longitudinal, in vivo gut microbiome datasets.
What selective pressures drive the evolution of gut microbes within and between hosts?
Microbes encounter variable, fluctuating environments as they propagate within hosts and transmit between hosts. These changing interactions with the host and other microbes provide opportunities for adaptive evolution, but it remains unclear what selective pressures drive the evolution of gut microbes and how these selective pressures vary between human hosts.
To investigate these questions, we develop methods to identify and interpret ongoing evolution in the human gut microbiome using longitudinal, in vivo gut microbiome datasets. We also perform evolution experiments using in vitro gut microbial communities to study how evolutionary dynamics are shaped by community context.
Xue lab at UC Irvine 