Spatial transcriptomics maps host–gut microbiome biogeography at high resolution

Overview

This study presents a spatial transcriptomic methodology for high-resolution mapping of host-microbiome interactions within the gut ecosystem. The approach integrates enzymatic in situ polyadenylation of bacterial and host RNA with spatial RNA sequencing, enabling simultaneous characterization of microbial and epithelial transcriptomes at single-micrometer resolution. The method addresses a critical gap in microbiome research by providing tools to measure intermicrobial and host-microbial interactions directly within their native tissue microenvironment, overcoming limitations of conventional culture-dependent and non-spatial omics approaches.

Methods and approach

The methodology combines enzymatic in situ polyadenylation of both bacterial and host RNA transcripts with spatial RNA sequencing workflows. Enzymatic polyadenylation enhances recovery of bacterial RNA molecules, which typically lack poly(A) tails, thereby improving detection sensitivity for low-abundance and spatially restricted microbial taxa. The approach is compatible with existing commercial spatial transcriptomic platforms, eliminating the need for specialized instrumentation. Validation involved benchmarking against established spatial transcriptomic workflows to quantify improvements in sensitivity and spatial resolution.

Key Findings

Application in a mouse model of intestinal neoplasia identified the spatial organization of the gut microbiota along the intestinal axis, demonstrating location-dependent variation in microbial community composition and transcriptional activity. Strong intermicrobial interactions were frequently observed at submicron to few-micrometer length scales, indicating that microbial community structure is shaped by spatially localized cross-feeding, competition, or signaling. Neoplastic transformation was associated with detectable changes in the architecture of the host-microbiome interface, including alterations in epithelial gene expression patterns and the spatial organization of microbial taxa relative to neoplastic lesions.

Implications

This methodological advance enables mechanistic investigation of the spatial basis of host-microbiome interactions in health and disease. The high-resolution mapping of intermicrobial interactions at short length scales provides a framework for understanding how local microbial community structure influences metabolic cross-talk, nutrient availability, and pathogen resistance within distinct intestinal microdomains. The compatibility with commercial platforms facilitates rapid adoption across research institutions and supports systematic investigation of spatial microbial ecology in diverse pathological contexts including inflammatory bowel disease, colorectal cancer, and infectious enterocolitis.