Spatial Sequencing of Host-Microbiome Interactions

Microbe-microbe and host–microbe interactions are central to the functioning of the human microbiome, but few tools are available to measure these interactions spatially within tissues. In this talk, Dr. De Vlamink introduced multiplexed imaging and spatial RNA sequencing approaches that enable simultaneous mapping of gut microbial communities, host gene expression and host gene regulation at single-micron resolution. By applying these methods, he revealed the longitudinal stability of spatial architectures in the healthy human oral plaque microbiome, demonstrated the location-dependent organization of microbial communities in the mouse intestine, and revealed interactions within and between microbial taxa at short length scales. Dr. De Vlamink also showed how these tools reveal changes in microbial and host cell architectures at microbiome–tumor interfaces. Last, he discussed recent extensions of these methods to enable spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes. Together, these methods provide a new avenue to study host-microbiome interactions, with the potential for significant advances in microbiome science.