High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing

Inter–microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome–host interactions in the gut at one micron resolution. This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA–sequencing. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong inter–microbial interactions at short length scales, shaping of local microbiome niches by the host, and tumor–associated changes in the architecture of the host–microbiome interface. This method is compatible with broadly available commercial platforms for spatial RNA–sequencing, and can therefore be readily adopted to broadly study the role of short–range, bidirectional host–microbe interactions in microbiome health and disease.