New Non-Invasive Method Developed for Studying the Gut and Microbiome

New Non-Invasive Method Developed for Studying the Gut and Microbiome

The gut and the microbiome play a huge role in overall health and the influence microbes have on health is becoming better understood; however, there are challenges to overcome when studying the gut and microbiota. It is possible to conduct investigations of fecal matter and the blood, but these provide indirect measurements of what is happening in the gut. Endoscopy can be used to examine the health of the gut, but since fasting and purging are required, this method has severe limitations.

A team of scientists has developed a novel way of investigating gut health that involves the use of genetically engineered E. coli sentinel cells. These cells can pass through the gut safely and have been engineered to record changes in gene expression on their journey. Bacteria in the gut respond to each other and the host’s diet and immune system, so when the E. coli cells are excreted, they can be analyzed to reveal information about the intestinal tract and the microbes that colonize it.

“Deep sequencing of these DNA recordings revealed characteristic signatures based on dietary, host, and microbiota contents at different levels of the intestine. This work provides additional perspectives on how diet, inflammation, and microbial interactions in the body shape the health of mammalian hosts,” explained the researchers in the paper.

To record transcriptional changes, the researchers developed a recording method called Record-seq. The CRISPR-Cas system is used by bacteria to incorporate genetic material from viruses into their own genomes – in CRISPR arrays -which gives the bacteria a memory of the viruses they have encountered in the past and allows them to attack them again when they are encountered. This system was harnessed to create a recording mechanism. The researchers incorporated DNA into spacer sequences in CRISPR arrays within the genomes of the cells, which reveal which genes are activated as the bacteria pass through the gut. That information can be obtained by analyzing the excreted E. coli cells.

In this study, the researchers added the CRISPR array of Fusicatenibacter saccharivorans into an E. coli strain, and included a reverse transcriptase that transcribes RNA into DNA, as well as the CRISPR-associated proteins necessary for incorporating the DNA fragment into the CRISPR array. The researchers analyzed the bacterial DNA to discover how often a specific mRNA molecule is manufactured during the journey through the gut, and which genes were activated. The researchers were also able to show how the sentinel bacteria adapted their metabolism to the nutrient supply in the gut.

“Transcriptional recording sentinel cells open avenues in basic research and medicine. We now have a tool that can reveal host and microbial physiology within the intact and unperturbed intestine,” said Randall Platt, PhD, a professor of biological engineering at ETH Zurich, and senior author of the study.

The study was conducted on mice and would need to be adapted for use in humans, as the system only works with E. Coli, which is far from ideal. Platt and the team are now conducting experiments to identify other bacteria that could be used that do not survive in open environments and would be safe to use in humans.

You can read more about the study in the paper – Noninvasive assessment of gut function using transcriptional recording sentinel cells – which was recently published in Science. DOI: 10.1126/science.abm6038