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.