Ingestible sampling devices have enabled profiling of the intestinal environment and the metabolome at multiple locations along the intestinal tract in research published in Nature and Nature Metabolism. The capsules were designed to collect fluid at four different pH levels, enabling collection at sites in the duodenum, ileum and colon. Analysis revealed that the bacteria, phages, host proteins and metabolites present at intestinal sites differed from those in stool samples. The approach also enabled sampling over time during digestion, revealing associations between diet and host and microbial metabolism. The devices enable simple, non-invasive sampling of previously difficult to access regions of the intestinal tract.