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

Inter-microbial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here, we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA-sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. 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, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA-sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease. Overall design: Spatial transcriptomics Cryosections were obtained from the ileum of two 13 weeks old mice (male and female). For spatial total RNA sequencing, tissue sections (10 µm thick) were processed with a modified Stereoseq (STOmics) protocol.