Region‐Specific Profiling of the Gut Microbiome and Metabolite Landscape in Response to Dietary Intervention Using Electronics‐Free Ingestible Smart Sampling Capsules

ABSTRACT

The composition and functional activity of the gut microbiome are profoundly influenced by external interventions, including dietary modification, probiotic supplementation, antibiotic treatment, and pharmacotherapy, with consequent effects on metabolic, inflammatory, and immune homeostasis. Dysbiosis arising from or persisting despite such interventions has been linked to the pathogenesis of inflammatory bowel disease, colorectal cancer, metabolic syndrome, and type 2 diabetes, underscoring the clinical importance of accurately characterizing intervention‐driven microbiome changes. The prevailing methodology for assessing these changes — analysis of fecal samples — captures only a distal, composite signal that does not reliably represent the microbial populations or metabolic activity of upstream intestinal regions. Mounting evidence from comparative sampling studies demonstrates poor correlation between fecal microbial profiles and those of the small and proximal large intestine, and it is well established that the majority of short‐chain fatty acids (SCFAs) produced through intestinal fermentation are absorbed prior to excretion, rendering stool‐based metabolite measurements an incomplete surrogate for luminal fermentative activity. Accordingly, robust assessment of how interventions reshape the gut microbiome necessitates direct, non‐invasive, and temporally resolved sampling from discrete intestinal sites. Herein, the first application of electronics‐free ingestible sampling capsules to the investigation of region‐specific microbiome and metabolite responses to a defined dietary intervention is reported. Two capsule variants — a small‐intestinal sampling (SIS) capsule activated by the elevated luminal pH of the proximal small intestine, and a large‐intestinal sampling (LIS) capsule activated by microbiota‐mediated acidification in the colon — were deployed in a cannulated porcine model in which animals received either a low‐fiber (LF) or high‐fiber (HF) diet. Capsule‐derived microbiome and metabolite profiles were validated against concurrently collected intestinal digesta and fecal samples. 16S rRNA gene sequencing revealed spatially distinct, diet‐dependent shifts in microbial community composition — including marked enrichment of Lactobacillus , Bifidobacterium , Prevotella , and Faecalibacterium under the HF diet — that differed substantially between the small and large intestine and were largely undetectable in paired fecal samples. Targeted metabolomic analysis demonstrated that propionate and butyrate concentrations in colonic capsule samples were approximately doubled under the HF diet relative to LF, differences that were absent from matched stool data. These findings establish ingestible capsule technology as a validated, non‐invasive platform for spatially resolved characterization of the intestinal microbiome and metabolome, with direct relevance to the design and interpretation of dietary and therapeutic intervention studies.