Minimally invasive capsule-string device enables spatially resolved microbiome profiling across the upper gastrointestinal tract.

Regional variation in the human gastrointestinal microbiome remains difficult to characterize because existing sampling methods either rely on invasive endoscopy or stool, which poorly reflects the upper gut. We evaluated a minimally invasive capsule-string device capable of collecting luminal and mucosal material from the esophagus, stomach, duodenum, and jejunum during natural transit. In healthy adults, compartment-level samples were anatomically localized using pH, bile staining, and string length, and microbial communities were profiled by 16S rRNA gene sequencing. The device was well tolerated and consistently recovered sufficient biomass from all upper GI regions. Distinct microbial signatures were evident across compartments, with the strongest differences observed between proximal (esophageal and gastric) and small-intestinal communities. Although the individual host exerted the dominant influence on the overall community structure, a reproducible regional signal persisted after accounting for between-person variation. These findings demonstrate that capsule-string sampling provides reliable access to spatially resolved upper GI microbiota without endoscopy. This approach enables more precise mapping of gut microbial organization in vivo and creates new opportunities for longitudinal, mechanistic, and disease-focused studies of host‒microbiome interactions in regions that have historically been inaccessible.