Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa

Abstract

Significance Many human diseases are causally linked to the gut microbiota, yet the field still lacks mechanistic understanding of the underlying complex interactions, because existing tools cannot simultaneously quantify microbial communities and their native context. In this work, we provide an approach to tissue clearing and preservation that enables 3D visualization of the biogeography of the host–microbiota interface. We combine this tool with sequencing and multiplexed microbial labeling to provide the field with a platform on which to discover patterns in the spatial distribution of microbes. We validated this platform by quantifying bacterial distribution in cecal mucosa at different stages of antibiotic exposure. This approach may enable researchers to formulate and test new hypotheses about host–microbe and microbe–microbe interactions.