On the sizes of gut bacterial aggregates

The spatial organization of the gut microbiota influences microbial abundances, inter-microbial competition, and host-microbe interactions. The rules relating bacterial dynamics to large-scale structure remain unclear, however. We therefore studied experimentally and theoretically the formation of three-dimensional bacterial clusters, known to influence susceptibility to intestinal transport and access to the epithelium. Analyzing imaging data for eight different bacterial strains examined in isolation in the larval zebrafish gut, we find a common family of cluster size distributions that decay approximately as power laws with exponents close to -2, becoming shallower for large clusters in a strain-dependent manner. This type of distribution arises naturally from a Yule-Simon-type process in which bacteria grow within clusters and can escape from them, coupled to aggregation that drives the system toward a single massive cluster, reminiscent of gelation in soft-matter systems. We further show that power-law distributions can persist in multi-species gut communities. These results point to biophysical principles governing gut microbiome spatial organization that may be useful for inferring dynamics in experimentally intractable systems, such as humans.