Spatial structure can functionally determine ecological interactions and evolution of microbial communities. The gut microbiota is known to be spatially structured longitudinally along the gastrointestinal tract, but micro-scale structure in the gut lumen has not been extensively explored. Here, we show that bacteria cluster within species in the cecum of gnotobiotic mice. We find that clustering is not driven by active swimming, antibody-mediated aggregation, or factors exclusive to the host, but likely due to bacterial growth in the matrix of gut content. In samples from mice and humans, we show that upper large-intestinal content behaves as a nonNewtonian fluid that changes its viscoelastic properties under the force of gut contractions. We argue that microbial growth in the gel-like structure of cecum content can lead to micro-scale bacterial clustering, which is periodically disrupted by peristalsis-driven shear thinning and clearance. Our study shows mechanistically how spatial structure in the gut emerges through the interplay between microbial and host physiology and highlights the possibility of host control over gut microbiota distribution through gut contractions.