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Spatially resolved profiling of host and bacteria RNAs in mammalian tissue

ABSTRACT: The host and microbiome coexist in the natural environment, engaging in constant and dynamic interactions that are fundamental to human health. Understanding these interactions requires unbiased, spatially resolved techniques capable of mapping gene expression in both the host and microbiome within their native microenvironment. In this study, we introduce microDBiT, a spatial sequencing technology that enables simultaneous, high-resolution profiling of both host and bacterial RNAs (mRNA and rRNA). By applying microDBiT, we successfully mapped the spatial distribution of host and bacterial RNAs in the intestines, colon, and tongue of germ-free (GF) mice colonized with bacteria. Furthermore, we utilized this approach in a dextran sulfate sodium (DSS)-induced colitis model, uncovering key mRNA-level changes in both host and microbial cells. This study demonstrates the power of microDBiT in resolving host-microbiome interactions at the transcriptomic level, providing critical insights into host-pathogen dynamics, immune responses, and microbiome-driven disease mechanisms.

ORGANISM(S): Mus musculus

PROVIDER: GSE294814 | GEO | 2026/04/01

REPOSITORIES: GEO

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