Bacteria with recording function capture gut health status

Numerous bacteria that reside in our stomach aid in food digestion. But what precisely do the microbes in the body perform? When do they create certain enzymes? And how do the bacteria break down meals that promote health and keep us healthy?

Researchers at the Department of Biosystems Science and Engineering at ETH Zurich in Basel modified bacteria such that they serve as data recorders for information on gene activity in order to address these concerns. They have now examined these bacteria in mice in collaboration with researchers from the University Hospital of Bern and the University of Bern. This is a crucial step toward employing sensor bacteria in medicine for future uses like identifying an individual's ideal diet and detecting malnutrition.

Researchers working under the direction of Randall Platt, professor of biological engineering at ETH Zurich, created the data logger function during the previous few years. They used the CRISPR-Cas mechanism, a form of immune system found naturally in many bacterial species, to do this. Bacteria have the ability to integrate bits of viral DNA or RNA into a region of their genome known as the CRISPR array in the event that they are attacked by viruses. This enables the bacteria to "remember" viruses with which they have interacted, enhancing their ability to quickly fend off subsequent viral attacks.

The technique may be exploited such that the bacteria insert snippets of their own messenger RNA (mRNA) into the CRISPR array, which is what the researchers focused on in order to employ this method as a data logger rather than viral invader DNA snippets. Cells employ mRNA molecules as their blueprint while making proteins. As a result, mRNA fragments can show which genes are employed to create proteins that carry out biological activities.

The scientists modified a strain of the intestinal bacterium Escherichia coli, known to be harmless for humans and sold as a probiotic, by inserting the CRISPR array of the bacterial species Fusicatenibacter saccharivorans into it. The transfer contained the reverse transcriptase enzyme's blueprint, which can convert RNA into DNA. Along with other CRISPR-associated proteins, this enzyme also converts the information in the mRNA into DNA, which is required for integrating the DNA fragment into the CRISPR array.

Then, under the direction of Andrew Macpherson, researchers from University Hospital of Bern and the University of Bern gave these altered gut bacteria to mice in a laboratory setting. They took samples of the animals' feces, separated the bacteria's DNA, and then used high-throughput DNA sequencing to analyze it. They were able to go through the vast amount of data and recreate the genetic information contained in the mRNA snippets with the help of a later bioinformatic assessment, carried out and evaluated in partnership. This allowed the researchers to ascertain which genes are activated and how frequently the gut bacteria produced a particular mRNA molecule while they were in the body.

According to Andrew Macpherson, Professor and Director of Gastroenterology at University Hospital Bern, "this novel approach allows us to receive information straight from the gut, without needing to perturb intestinal functioning." Because the bowels must be empty for the inspection, the approach offers a number of benefits over endoscopies, which can be uncomfortable for patients and invariably cause disruptions in intestinal function.

Bacteria are adept in detecting environmental changes and adjusting their metabolism to novel situations, such as nutritional alterations, according to Macpherson. The researchers were able to demonstrate how the bacteria modified their metabolism to the various nutrition supplies through tests with mice that were fed various meals. The most recent edition of the journal Science has a report on the findings.

The technology has to be improved further so that researchers may one day analyze human patients to see how nutrition affects the gut environment and how this impacts health. They want to employ the technique in the future to assess an adult's or child's food status. With this knowledge, medical professionals will be better equipped to identify malnutrition or determine whether a patient requires nutritional supplements.

The researchers were also able to identify gastrointestinal inflammatory reactions. Both healthy mice and animals with intestinal inflammation received the sensor bacteria from the researchers. They were able to pinpoint the precise mRNA profile of gut bacteria that transition to an inflammatory state in this way.

The most recent study, which was published in the journal Science, makes use of a technological innovation that enables researchers to identify between two bacterial strains using unique genetic "barcodes." This will eventually allow for the investigation of the role of bacterial gene alterations in laboratory animals. Scientists will be able to compare the mRNA profiles of various bacteria, such as normal vs mutant bacteria, as a result. The molecular data logger makes it feasible to identify this profile for the first time as the bacteria move through the intestine rather than only when they end up in the feces. This allows the information to reveal what transpired while the bacteria were still present in the gut.

Another option is to improve the method for separating the RNA profiles of the bacteria in the small and large intestine. Additionally, additional varieties of bacteria might integrate the data logger function. Applications in environmental monitoring might result from this. It may be determined if herbicides had been applied, for instance, by analyzing soil microbes from an agricultural field.

The researchers have submitted patent applications for both the approach itself as well as the distinctive RNA profiles that serve as both the hallmarks of certain dietary components and measures of intestinal health.

Because the sensor bacteria have been genetically altered, there are still several safety and legal issues that need to be resolved before they can be utilized outside of the lab, including in people. As long as specific requirements are met, living genetically altered microbes can be used as diagnostic or therapeutic agents in medicine, according to Platt. It is conceivable, for example, to alter the sensor bacteria such that they can only live within a patient's gut because they require specific nutrients. These specific bacteria will expire as soon as they exit the intestine. The next step in using the approach in medicine is to incorporate appropriate safety precautions.