Tech start-up seeks to address ‘data blind spot’ in small intestine sampling

The Massachusetts-based startup will be presenting its work on how its ingestible, pH-responsive capsule enables direct collection of small-intestinal luminal fluid for sequencing and multi-omics analysis at the upcoming IPA World Congress + Probiota 2026.

“Without direct sampling from the small intestine, we’re missing crucial information—not just for diagnostics, but for clinical trials and therapeutic development as well,” said Zoe Watson, co-founder and CEO of Microvitality.

Developing ingestible gut health capsule technology

Microvitality was born from the Tufts University Gordon Institute, where Watson and business co-founder Sofia Paschenti met in an innovation management program.

Drawing on personal experiences with friends and family struggling with unresolved gut health issues, they set out to address a gap in clarity and effective solutions, working with the university’s technology transfer office to identify an ingestible capsule technology.

The duo began collaborating with Dr. Sonkusale’s lab in the School of Engineering, and what started as an academic effort quickly gained momentum through strong user interest and evident commercial viability. After several years of development within the university, the team spun the project out into what is now Microvitality. The company has been in operation since September 2023 and secured exclusive rights to the technology in April 2025.

Research exposes small intestine ‘data blind spot’ in stool-based microbiome analysis

The founders identified that most of the microbiome industry often relies on stool sampling, which reflects only the colon microbiome, and while it is a widely used approach in research and translational work, it overlooks the small intestine.

“This isn’t new knowledge; there’s extensive literature showing that the small intestine plays a critical role,” Watson told NI. “Yet decisions about small-intestine biology are still being made using indirect proxies, such as breath tests or stool samples.”

In Microvitality’s research, subjects with identical diets and lifestyles showed no significant differences in stool microbiome profiles, despite clear physiological differences.

However, when sampling from the small intestine, they observed significant differences in microbial diversity and abundance.

“We refer to this as a ‘data blind spot’,” Watson said.

It is not to say that stool sampling should be discounted, Watson noted, adding that for a comprehensive understanding of the gut ecosystem, multiple data sources are still valuable.

“Ideally, we see a future where data from across the entire GI tract can be integrated to strengthen clinical insight,” she said.

Contamination-minimised small intestine sampling for multi-omics analysis

The ingestible capsule is swallowed like a standard pill and travels through the oesophagus and stomach, withstanding the acidic environment, and once it reaches the small intestine, the outer coating dissolves based on pH conditions, Watson explained.

“This exposes inlets that allow natural peristaltic motion to draw in fluid, so the capsule passively collects luminal fluid, which expands an inner chamber containing a micro-valve mechanism,” she said.

“Once full, the capsule self-seals, continues through the digestive tract, and is later recovered, and from the collected sample, we can perform sequencing and full multi-omics analysis.”

While there are a handful of sampling capsules on the market, Watson says that Microvitality differs in that it is able to minimise contamination from the large intestine, as well as offering a scalable capsule size which can be designed for use in adults, paediatrics, and even small animals.

“This opens up significant opportunities—not only for diagnostics but also for clinical trials,” she said. “In paediatrics, for example, this could reduce the need for invasive endoscopies, which are extremely challenging for children.”

Small intestine sampling to improve SIBO diagnosis and personalised treatment

Microvitality has first focused on Small Intestinal Bacterial Overgrowth (SIBO), a condition where there’s an abnormal increase in bacteria in the small intestine, leading to digestive issues like bloating, pain, diarrhea, gas and poor nutrient absorption.

“SIBO has both personal relevance for us and enormous clinical significance,” she said. “It’s estimated to affect one in four adults globally, yet diagnosis remains imprecise.

“The colon is incredibly dense, like a rainforest, while the small intestine is more like a desert, but in SIBO patients, that balance is disrupted.”

She noted that current diagnostic approaches are largely binary, relying on threshold cutoffs, whereas direct sampling enables far deeper insight. By sequencing microbial diversity and abundance, identifying disease-associated taxa, and supporting multi-omics analysis, the approach allows for a more nuanced and informative understanding of gut health.

“Many biomarkers are diluted or transformed by the time they reach the colon,” she said. “By sampling at the source, we can access data that simply hasn’t been available before.”

Furthermore, the team see SIBO as a strong ‘proof-of-concept’ indication, Watson explained, noting that demonstrating accurate, direct sampling and analysis validates the platform, and helps them to then expand into additional indications over time.

“We’re interested in areas such as gut–brain health, longevity, cardiometabolic disorders, and personalised wellness. There’s also a major public health angle—particularly around antimicrobial resistance. Many patients are prescribed antibiotics without truly personalised data,” she said.

“By understanding the small-intestine microbiome directly, we can help move away from trial-and-error treatment and toward more targeted, effective interventions.”