Ingestible device reveals insights into human gut microbiome and metabolome

A study employing an ingestible device to sample the human intestinal tract during normal digestion has identified differences in microbial, proteomic, and bile acid profiles between various intestinal regions and stool. The research, conducted by Dari Shalon, Jacob Folz, among others, was published on May 10, 2023 by Nature.

According to the study, the human gut is a complex and diverse ecosystem that plays a critical role in numerous aspects of our health, including digestion, immune function, and disease prevention. Traditional studies on the gut microbiome have predominantly relied on stool samples. These samples provide only a partial understanding of this intricate system. The study suggests that stool samples fail to capture the regional heterogeneity of the gut which is crucial for understanding unique microbial communities, metabolomes, and proteomes across different intestinal regions. As such, Shalon et al. assert there's a need for more direct and localized sampling methods to gain deeper insight into how gut microorganisms impact human physiology and health.

The study states that accurately sampling the human intestinal tract without causing disturbance has been a longstanding challenge. Previous methods like using organ donors or endoscopic procedures either offer limited information due to post-mortem changes or contamination risks or are invasive and unable to capture the gut's natural state. Furthermore, most research on bile acids—essential for understanding the gut's signaling properties—has relied on incomplete data from stool or blood samples according to Folz et al. This gap in methodology has reportedly hindered a comprehensive understanding of the gut microbiome's role in human health and underlines the need for an innovative approach to sample the gut more effectively.

To address these challenges as stated in their research paper, Shalon et al. developed a novel ingestible device for sampling the human intestinal tract during normal digestion. They claim that this device allows for collection of luminal contents from various parts of the small intestine and ascending colon thus enabling detailed multi-omic analyses. The study revealed significant differences in microbiome composition, gene class abundance, and host proteome between the intestines and stool. It also identified gradients of microbially transformed bile acids along the intestinal tract, providing new insights into the gut microbiome's influence on human physiology. Researchers concluded that this advancement in sampling technology opens avenues for more accurate and comprehensive studies of the human gut microbiome and its impact on health and disease.

Springer Nature: Dari Shalon, Jacob Folz, et al., Profiling the human intestinal environment under physiological conditions, Nature (2023). https://doi.org/10.1038/s41586-023-05989-7