Exploring the microbial ecosystem that spans the human digestive tract can, at times, feel similar to searching for life on Mars. Unlike the microbiota that populate the lower digestive tract, the inhabitants present in the small intestine are shrouded in mystery, existing just beyond the reach of modern technology. However, equipped with a three-dimensional (3D) printer, an osmotic engine, and a semipermeable membrane, Hojatollah Nejad and Sameer Sonkusale—engineers at Tufts University—have built an ingestible pill that may help to characterize the biogeographical layout along the intestine.

Studying the gut microbiome has mostly involved cataloging of fecal matter which is rich in colonic microbiota. While informative, such methods result in a biased understanding of a complex ecosystem. The human intestinal tract is long, typically extending beyond 13 feet, and possesses both acidic and basic environmental conditions.

Many have hypothesized that the microbial composition will differ among these environments as well. According to Sonkusale, “the gut microbiome is a very dynamic community that inhabits different areas of the gut, so there is still a lot of research to be done in figuring out [its] entire biogeography.”

Such research could have far-reaching effects. Lawrence David of the Duke University School of Medicine says that “many people suspect that if you had better sampling [of the gut microbiome], the accuracy with which we diagnose or predict disease would be higher.” However, methods for sampling of the small intestine are currently limited to invasive surgery or extrapolation of data gathered from fecal matter.

To address this, Sonkusale’s team used stereolithography (SLA) 3D printing technology to build an ingestible pill for targeted microbiome sampling. The pill has two chambers separated by a semipermeable membrane consisting of interwoven cellulose acetate fibers, leaving 5 µm holes for water—but not bacteria—to pass through. A helical entryway in the first chamber allows for entry of fluid and microbiota while making the passive back-flow of samples out of the chamber difficult.

Beyond the membrane lies a second chamber with an osmotic engine—a highly concentrated salt solution that is capable of pulling water from the first chamber through the semipermeable membrane via osmotic pressure. A 100 µm hole at the bottom of the pill enables expulsion of this water at great enough speeds so as to prevent environmental material from entering the second chamber directly.

Through in vitro testing, Nejad demonstrated that this osmotic engine could pull fluid and solid material into the collection chamber from the pill’s immediate environment. This, coupled with an enteric-hydrogel coating whose chemical makeup renders it stable under acidic conditions but soluble in a basic environment, enables sample collection to be targeted to the basic conditions of the small intestine, while remaining sealed off from the acidic environment of the stomach.

Nejad then used two model organisms for in vivo testing: the pig, which is commonly used in microbiome studies; and rhesus macaques, whose intestines more closely resemble humans’. After collecting the pills, DNA sequencing technology was used to identify the microbial species that were present.

The research team found notable differences between fecal samples and those collected in the pills, showing that the pills may be successfully sampling a part of the intestine that has long eluded researchers. However, “there is no reference point given for what the upstream gut microbiome actually looks like,” says Nicole Narayan, a bioinformatics scientist specializing in microbial studies at Second Genome. Sam Westreich, a microbiome scientist at DNAnexus, says that without this reference to compare against, “it’s hard to know if the pill is providing a targeted sample of the small intestine or a more longitudinal picture of the gut as a whole.” Both Narayan and Westreich concluded, though, that this study is a nice first step and that the technology is very promising.

David agrees, “These types of technical details aside, I’m still enthusiastic about the concept. I think it’d be really interesting to take these sampling techniques and revisit previous studies trying to link the microbiome to health and disease.”

To Nejad and Sonkusale this was the first of many studies. According to Sonkusale, “The pill is on a discovery mission like the Mars pathfinder.”

Read the article in Advanced Intelligent Systems.