A Small Pill‐Like Ingestible Microdevice for Site‐Specific Microbiome Sampling in the Upper GI Tract

The gut microbiota varies along the length and cross‐section of the gastrointestinal (GI) tract, influencing diseases. Direct sampling from the upper GI tract remains challenging due to anatomical constraints and low‐volume genomic sequencing. Here, we report an ingestible, pill‐like microdevice (7 × 2.7 mm) that enables in vivo microbiome and biomarker sampling in Sprague–Dawley rats – demonstrating, for the first time, successful autonomous pyloric transit of a microdevice via oral gavage. The device comprises an enteric‐coated gelatin cap that protects it in gastric pH (1–1.5) and disintegrates at intestinal pH (3–5), allowing luminal fluid via an inlet connected to activation and sampling chambers. A polyacrylate hydrogel in the activation chamber swells to seal the inlet to prevent cross‐contamination. In vivo studies ( n = 5) confirmed successful pyloric transit in 4/5 rats without tissue injury or inflammation. Each retrieved device yielded 13.48 ± 4.66 ng genomic DNA, enabling 16S rRNA sequencing of site‐specific microbiota distinct from fecal profiles. Concurrent detection of intestinal alkaline phosphatase (≈6.5 µg mL −1 ) confirmed dual microbiome–protein biomarker capability. We demonstrate species‐level microbiota identification via nanopore sequencing using an orally ingestible platform technology for longitudinal gut microbiome profiling, paving way for studies in large animals and humans.