Age-stratified human GUT-on-a-chip model to study microbiome-mediated epithelial aging

The National Institute on Aging awarded The Jackson Laboratory $506,000 on September 1, 2026, under the Aging Research program (CFDA 93.866) to develop an age-stratified human gut-on-chip model that integrates organoid-derived young and old colon epithelia with patient-derived microbiomes within a dynamically perfused, oxygen-controlled microphysiological environment. The recipient will establish the first such platform capable of sustaining obligate anaerobes and examining how aging-related changes in host epithelium and microbiome composition individually and in concert shape barrier function and inflammatory signaling. The project benchmarks molecular and functional hallmarks of colon epithelial aging—including barrier loss, lineage imbalance, mitochondrial dysfunction, and senescence-associated secretory phenotype—by comparing young and old organoid-derived tissue across controlled apical-basal oxygen gradients. The work addresses the mechanistic connection between microbiome aging and epithelial decline, with implications for understanding age-associated infection risk, frailty, cognitive decline, metabolic disorders, and cardiovascular disease. Performance occurs in Farmington, Connecticut, with a period of performance ending August 31, 2028. The assistance type is Project Grant.

Abstract

Aging of the human GUT is accompanied by impaired barrier integrity, mitochondrial dysfunction, reduced regenerative capacity, and chronic low-grade inflammation ("inflammaging"), driven by both intrinsic changes in epithelial cells and parallel shifts in the GUT microbiome. Mounting evidence links these changes, and age- associated shifts in the GUT microbiome, to heightened infection risk, frailty, cognitive decline, and metabolic and cardiovascular disorders. The need to understand the causal mechanisms connecting microbiome aging with epithelial decline is of great public health significance. Despite mounting clinical and experimental evidence that aged microbiomes exacerbate epithelial dysfunction and that young microbiomes can restore resilience, mechanistic insight has been limited by the lack of human models capable of CO-culturing complex, strictly anaerobic microbiomes with patient-derived epithelial tissues under physiological oxygen gradients. We have developed a human GUT-on-chip that sustains obligate anaerobes and organoid-derived colon epithelium across a controlled apical-basal oxygen gradient. We will leverage our GUT chip platform to establish the first age- stratified, human GUT-on-chip platform that integrates organoid-derived young and old colon epithelia and microbiomes within a dynamically perfused, oxygen-controlled microphysiological environment. The long-term objective is to elucidate how aging-related changes in host epithelium and microbiome composition, individually and in concert, shape barrier function and inflammatory signaling, driving vulnerability to age-associated disease. We will first benchmark molecular and functional hallmarks of colon epithelial aging, including barrier loss, lineage imbalance, mitochondrial dysfunction, and increased senescence-associated secretory phenotype, by comparing young and old organoid-derived epithelia cultured under physiologic oxygen. We will then dissect whether age-associated microbial communities accelerate epithelial decline or whether intrinsic epithelial aging predominates, using a cross-age experimental design and rigorous multi-omics profiling in the GUT-on-chip. By resolving the directionality and mechanisms of GUT microbiome-epithelium crosstalk in aging, this work will produce the first human-relevant reference standards for epithelial aging phenotypes, reveal actionable targets for intervention, and lay the groundwork for microbiome-based therapeutics, precision medicine, and prevention strategies to promote health span in aging populations.