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Researchers from NYU Abu Dhabi have developed an ingestible capsule that can collect samples of bacteria from the small intestine, offering a clearer picture of the gut microbiome than stool tests alone.
Named CORAL, the capsule is built to reach areas of the digestive tract that are usually difficult to study without invasive procedures. Measuring 2.1 mm in diameter and 8.2 mm in length, CORAL is structured around a repeating lattice inspired by coral reefs.
Published in Device, this lattice was produced in a single step using projection micro stereolithography (PµSL) on equipment from Boston Micro Fabrication (BMF), containing pores about 80–100 µm wide. As the capsule moves through the gut, these pores act as traps, collecting bacteria and fluids without the need for electronics or moving parts.
Coral-inspired pill traps microbes
Led by Aashish R. Jha and Khalil B. Ramadi, the team engineered the device to hold roughly 25 µL of material in its outer shell and 4 µL in its core. Computer modeling showed that a gyroid-shaped lattice produced the right balance of flow and retention, generating a pressure drop of about 30 Pa. This was enough to pull microbes inside while preventing them from being washed away.
When tested in rats, the capsules were coated to dissolve only after reaching the small intestine. Animals could swallow up to six capsules without obstruction, and all were recovered intact after excretion using magnets. Examination of gut tissue showed that passage of the device caused no visible damage.
DNA sequencing of the samples confirmed that CORAL captures microbial communities from the small intestine that are not well represented in stool. These samples contained more Firmicutes and Lactobacillus, which thrive in the acidic environment of the upper gut, while stool contained more Bacteroidetes and genera such as Ruminococcus, common in the large intestine. The findings underline how much information is missed when studies rely on stool alone.
By isolating microbes from otherwise inaccessible regions, CORAL offers a safer and more direct way to study the upper gut. Its design, based entirely on structure rather than electronics, means it can be manufactured at scale and adapted for human use. A human-sized version would be similar to a standard capsule pill, with the same pore size but a larger capacity.
The researchers say the technology could help clarify how bacteria in the small intestine influence health, disease, and even mental well-being. While further work is needed to test the capsule in people, the study shows how a simple, passive design can open up a part of the microbiome that has been difficult to reach.
Non-invasive ingestible capsules for gut microbiome sampling
The human gut hosts trillions of microbes essential for digestion, immunity, and overall health. Disruptions in these communities are linked to diseases from bowel disorders to diabetes, obesity, and mental illness. Yet most studies rely on stool samples, which mainly reflect the lower intestine and overlook the small intestine, where distinct populations live.
To address this gap, researchers have been developing ingestible devices that can capture bacteria directly as they move through the gut. One effort Tufts University developed a 3D printed pill to sample gut bacteria described in Advanced Intelligent Systems. The pill measured microbes more accurately than stool analysis by using microfluidic helical channels and a semipermeable membrane, with calcium salt driving uptake through osmosis.
A pH-sensitive coating ensured sampling began only after the stomach, and an internal magnet allowed external control for targeted collection. Tested in pigs and primates, the pill identified bacterial populations and relative abundance, offering a potential diagnostic tool pending human trials.
In another study, Purdue University researchers developed a 3D printed capsule to sample gut bacteria non-invasively throughout the gastrointestinal (GI) tract. Each capsule measured 9 mm in diameter and 15 mm in length, with a 3D printed housing, biodegradable enteric coating, gas-permeable PDMS membrane, and an absorbent hydrogel core.
Printed on a Formlabs Form 2 system with a biocompatible polymer, the capsule activated once the coating dissolved, allowing the hydrogel to swell, absorb fluids, and seal the device. In vitro tests showed the capsule effectively captured bacteria such as E. coli while preventing leaks, suggesting potential for clinical diagnostics pending animal studies.
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Featured image shows in vivo evaluation of CORAL capsule. Image via NYU Abu Dhabi.
