Spatial metagenomic characterization of microbial biogeography in the gut

Spatial structuring promotes biodiversity and is important to the maintenance of natural ecological systems. Many microbial communities, including the mammalian gut microbiome, display intricate spatial organization. Mapping spatial distributions of bacterial species enables the detailed delineation of fundamental ecological processes and interactions that underlie community-wide behaviors. However, current approaches have a limited capacity to measure the spatial organization of natural microbiomes with hundreds of species. Here, we describe spatial metagenomics, a framework to dissect the organization of a microbiome at micron-scale spatial resolution and metagenomic depth through nucleic acid “plot sampling”. Intact microbiome samples are immobilized within a gel matrix and subjected to cryo-fracturing to generate clusters of co-localized cells, and the identities and abundances of taxa present in these clusters are determined via droplet-based encapsulation and deep sequencing. Analysis of thousands of microbiome clusters from the mouse intestine across three distinct regions revealed heterogeneous microbial distributions with positive and negative co-associations between specific taxa. While the murine intestinal microbiome mostly exhibited regionally distinct spatial organizations, robust associations between Bacteroidales taxa were observed across gut compartments. Analysis of a dietary perturbation revealed phylogenetically clustered regions suggesting local habitat filtering that may be important to maintenance of diversity observed on plant-polysaccharide diets, and enabled identification of spatial niches that may be shared across distinct diets. Spatial metagenomics constitutes a powerful new culture-independent technique to mechanistically study microbial biogeography in complex habitats.