Spatially resolved host and microbiota RNA profiling in the mouse gut using microDBiT

Hosts and their microbiomes coexist in a shared environment, engaging in dynamic interactions that are essential to maintaining health and modulating disease processes. To fully understand these interactions, spatially resolved and unbiased approaches are needed to map gene expression from both host and microbial cells within their native tissue context. Here, we present microDBiT, a spatial transcriptomic platform that enables simultaneous, high-resolution profiling of host and bacterial RNAs, including both mRNA and rRNA. Using microDBiT, we mapped the spatial distribution of host and microbial transcripts in the ileum and colon of germ-free mice, gnotobiotic mice colonized with a defined gut microbial community, and specific pathogen-free mice treated with dextran sulfate sodium (DSS) to induce colitis. We observed location-specific transcriptomic alterations in both host and bacterial cells in response to colonization and during inflammation. These results demonstrate the utility of microDBiT for dissecting host-microbiome interactions at high resolution and provide new insights into immune responses, spatial microbial localization, and microbiome-associated disease processes. This study introduces microDBiT, a spatial transcriptomics method that maps host and bacterial RNA together in gut tissue, revealing how microbes and host responses vary across intestinal regions and during inflammation.