2023 Theses Doctoral

Spatial Analysis of Microbial Communities from Macro to Micron Scales

Richardson, Miles Philip Zilli

The microbial world is a rich tapestry of communities experienced at the micron scale, but often studied at the macro scale. The methods commonly used to study microbial communities are unable to capture this heterogeneity, limiting insight into the processes that create them. High resolution methods have been applied to the human gut, but not at sufficient scale to sufficiently characterize the spatial structure of the community.

Here, we examine the methods we use to study microbial communities, their limitations, and present SAMPL-seq, a method that allows for micron-scale interrogation of human and murine gut communities. In this we discover novel and consistent colocalization of microbial taxa across people. Further, we use many of the methods discussed to explore spatial heterogeneity of the microbes of hospital rooms and fusobacterial strains in the gut, revealing before unseen natural diversity.