Bacteria with recording function capture intestinal health status

Our gut is home to countless bacteria that help us digest food. But what exactly do microorganisms do inside the body? What enzymes do they produce and when? And how do bacteria metabolize healthy foods that help us ward off disease?

To get answers to these questions, researchers from the Department of Biosystems Science and Engineering at ETH Zurich in Basel have modified bacteria to function as data loggers to obtain information about the gene activity. Together with scientists from the University Hospital of Bern and the University of Bern, they have now tested these bacteria on mice. This is an important step towards the future use of sensory bacteria in medicine for applications such as diagnosing malnutrition and understanding diets suitable for an individual.

The immune system becomes a data logger

The data logging feature was developed over the past few years by researchers led by Randall Platt, professor of biological engineering at ETH Zurich. To do this, they used the CRISPR-Cas mechanism, which is a type of immune system found naturally in many bacterial species. If bacteria are attacked by viruses, they can incorporate fragments of viral DNA or RNA into a section of their own genome called the CRISPR matrix. This allows the bacteria to “remember” the viruses they have come into contact with, allowing them to fight off a future viral attack more quickly.

To use this mechanism as a data logger, the researchers did not concern themselves with extracts of DNA from viral intruders, but focused on something else: the mechanism can be exploited in such a way that bacteria incorporate extracts of their own Messenger RNA (mRNA). in the CRISPR network. mRNA molecules are the blueprint that cells use to make proteins. As such, mRNA extracts can reveal which genes are used to build proteins to perform cellular functions.

To make the method effective, the scientists introduced the CRISPR network of the bacterial species Fusicatenibacter saccharivorans in a strain of gut bacteria Escherichia coli, which is considered safe for humans and available as a probiotic. The transfer included the blueprint for an enzyme called reverse transcriptase, which can transcribe RNA into DNA. This enzyme also transcribes the information contained in mRNA into DNA, which, along with CRISPR-associated proteins, is necessary to incorporate the DNA extract into the CRISPR network.

Get information without disturbing the body

Then, researchers from Bern University Hospital and the University of Bern, led by Andrew Macpherson, administered these modified gut bacteria to mice in the laboratory. They collected fecal samples from the animals and isolated bacterial DNA, which they then analyzed using high-throughput DNA sequencing. Through subsequent bioinformatics assessment, performed and evaluated collaboratively, they were able to work through the mass of data and reconstruct the genetic information from the mRNA extracts. This allowed scientists to determine by non-invasive means how often gut bacteria made a given mRNA molecule while in the body, and therefore which genes are active.

“This new method allows us to obtain information directly from the intestine, without having to disturb the intestinal functions”, explains Andrew Macpherson, professor and director of gastroenterology at the University Hospital of Bern. As such, the method has major advantages over endoscopies, which can be unpleasant for patients and always involve disruption of bowel function, as the bowels must be empty for the examination.

Determination of food status

“Bacteria are very good at registering environmental conditions and adapting their metabolism to new circumstances such as dietary changes,” says Macpherson. In experiments with mice given different foods, the researchers were able to show how the bacteria adapt their metabolism to the respective nutrient supply. A report of the findings was published in the latest issue of the journal Science.

The researchers would like to develop the method further, so that one day they can study human patients to see how diet influences the gut ecosystem and how this affects health. In the future, they hope to use the method to determine the dietary status of children or adults. Armed with this information, doctors will be able to diagnose malnutrition or decide if a patient needs nutritional supplements.

Additionally, the researchers were able to recognize inflammatory responses in the gut. The researchers administered the sensor bacteria to mice with intestinal inflammation as well as to healthy mice. This way, they could identify the specific mRNA profile of gut bacteria that go into inflammation mode.

Distinguish different bacteria

Current research published in the journal Science includes a scientific development that allows researchers to distinguish two strains of bacteria from each other based on individual genetic “barcodes”. In the future, this will make it possible to study the function of genetic mutations in bacteria in laboratory animals. This will allow scientists to compare the mRNA profile of different bacteria, such as normal versus mutant bacteria. Thanks to the molecular data logger, it is possible for the first time to determine this profile, because they pass through the intestine and not only when the bacteria reach the feces, so the information shows what happened when the bacteria still lived in the gut.

Another possible avenue would be to further develop the system to distinguish the RNA profiles of bacteria in the small intestine and the large intestine. In addition, the data logger function could be integrated with other types of bacteria. This would open the door to applications in the field of environmental monitoring. An analysis of the bacteria in the soil of a cultivated field, for example, would make it possible to establish whether herbicides have been used.

Safe application possible

The researchers have filed patent applications for the method itself and for characteristic RNA profiles that are signatures of certain nutritional molecules and indicators of gut health.

Before the sensor bacteria can be used outside the lab – including in human patients – scientists still need to clarify various safety and legal issues, as the bacteria have been genetically modified. “In principle, there are ways to use living genetically modified microorganisms as diagnostic or therapeutic agents in medicine, provided certain conditions are met,” says Platt. It is possible, for example, to modify the bacteria in the sensor so that they need certain nutrients and can therefore only survive in the intestine of a patient. As soon as these particular bacteria leave the intestine, they will die. The integration of appropriate security mechanisms is the next step towards the application of the method in medicine.

This research was supported by ERC grants awarded to Randall Platt and Andrew Macpherson, and by a grant from the Botnar Research Center for Child Health. The studies involving mice were carried out at the Clean Mouse Facility at the University of Bern, which is supported by the Genaxen research foundation.

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