Internal seminar - Daniel Wong (LPENS)

Abstract: Long appreciated for its ecological diversity, the gut microbiome has recently been shown to evolve within individual hosts, observed in the sweeps of genetic variants over days or weeks. These mutational signatures hint at a rich adaptive landscape shaped by concurrent environmental fluctuations, interspecies interactions, and host-to-host transmission. However, disentangling these short-term evolutionary forces from the noisy mutational dynamics inferred from whole-genome sequencing remains a challenge. Here, I will present an alternative approach – high-throughput genomic barcoding – that permits the simultaneous tracking of thousands of competing microbial lineages at high frequency resolution (<10^-5). Applying this method to mouse colonization experiments with 60,000 barcoded Bacteroides thetaiotaomicron (Bt) lineages, we show how the Bt adaptive landscape is shaped by inter-host transmission and by a co-colonizing 49-species community. Time permitting, I will connect these empirical insights to theory, demonstrating how rapid adaptation can bias the dynamics of ecological diversification in a simple class of consumer-resource models.