Spatial metagenomic characterization of microbial biogeography in the gut

Spatial structuring is important for the maintenance of natural ecological systems(1,2). Many microbial communities, including the gut microbiome, display intricate spatial organization(3–9). Mapping the biogeography of bacteria can shed light on interactions that underlie community functions(10–12), but existing methods cannot accommodate hundreds of species found in natural microbiomes(13–17). Here we describe metagenomic plot-sampling by sequencing (MaP-Seq), a culture-independent method to characterize the spatial organization of a microbiome at micron-scale resolution. Intact microbiome samples are immobilized in a gel matrix and cryo-fractured into particles. Neighboring microbial taxa in the particles are then identified by droplet-based encapsulation, barcoded 16S rRNA amplification and deep sequencing. Analysis of three regions of the mouse intestine revealed heterogeneous microbial distributions with positive and negative co-associations between specific taxa. We identified robust associations between Bacteroidales taxa in all gut compartments and showed that phylogenetically clustered local regions of bacteria were associated with a dietary perturbation. Spatial metagenomics could be used to study microbial biogeography in complex habitats.