3D-printed pill samples gut microbiome to assess bacterial profile

A research team led by Tufts University engineers has developed a 3D-printed pill that samples bacteria found in the gut microbiome as it passes through the gastrointestinal tract (GI). The ability to profile bacterial species inhabiting the gut could have important implications for the diagnosis and treatment of conditions that are affected by the microbiome, according to the researchers, who published their findings in Advanced Intelligent Systems.

The pill is more sophisticated than just a sponge. It is manufactured in a 3D printer with microfluidic channels that can sample different stages of the GI tract. The surface of the pill is covered with a pH sensitive coating, so that it does not absorb any samples until it enters the small intestine, bypassing the stomach, where the coating dissolves. A semi-permeable membrane separates two chambers in the pill, one containing helical channels that take up the bacteria and the other containing a calcium salt-filled chamber. The salt chamber helps create an osmotic flow across the membrane which pulls the bacteria into the helical channels. A small magnet in the pill enables one to hold it at certain locations in the gut for more spatially targeted sampling using a magnet outside the body. A fluorescent dye in the salt chamber helps locate the pill after it exits the GI tract.

The 3D-printed pill is the first non-invasive diagnostic tool capable of providing a profile of microbiome populations throughout the entire GI tract, researchers said. Current methods of sampling the microbiome involve analysis of fecal DNA and metabolites, but that approach provides little information of the environment upstream of the distal colon, where bacterial species can vary significantly.

The pill has been studied and found to provide accurate identification of bacterial populations and their relative abundance in both in vitro and in vivo applications, said researchers. It has been tested in pigs and primates, yet clinical trials will be needed to determine if the pill can be used routinely in humans for clinical care.

More than 1,000 species of bacteria can inhabit the gut. Most of these bacteria have a beneficial, supportive role in digestion and protection against disease. When the natural balance of the microbiome is skewed, a condition called dysbiosis occurs, which can be associated with inflammation, susceptibility to infections, and exacerbation of diseases such as cancer. Research is increasingly unveiling specific microbiome metabolites that have beneficial or protective effects for the host against disease.

The researchers see this technology as bridging an important gap in gastrointestinal diagnosis, according to Sameer Sonkusale, PhD, professor of electrical and computer engineering at Tufts University's School of Engineering and corresponding author of the study.

"We are learning quite a lot about the role of gut microbiome in health and disease,” said Sonkusale. “However, we know very little about its biogeography. The pill will improve our understanding of the role of spatial distribution in the microbiome profile to advance novel treatments and therapies for a number of diseases and conditions."