Researchers have equipped gut bacteria with data logger functionality as a way of monitoring which genes are active in the bacteria.

Our gut is home to countless bacteria, which help us to digest food, but its function produces countless (well, numerous) questions, too. Exactly what do the microorganisms do inside the body? Which enzymes do they produce? When? How do the bacteria metabolise health-promoting foods that help us avoid disease?

Longevity.Technology: Researchers at the Department of Biosystems Science and Engineering at ETH Zurich in Basel had these questions too, so they modified bacteria to get some answers. The modified bacteria were able to function as data loggers for information on gene activity and the Basel researchers teamed up with scientists from University Hospital of Bern and the University of Bern to test these bacteria in mice. This research represents an important step towards using sensor bacteria in medicine in the future for applications such as diagnosing malnutrition and understanding which diets are optimal for an individual.

Immune system becomes data logger

The data logger function has been developed over the past few years by researchers led by Randall Platt, Professor of Biological Engineering at ETH Zurich. To do this, they employed the CRISPR-Cas mechanism which leverages a type of immune system present naturally in many bacterial species. If the bacteria are attacked by viruses, they can incorporate snippets of the viral DNA or RNA into a section of their own genome called the CRISPR array; this lets the bacteria “remember” viruses with which they have had contact, allowing them to fight off a future viral attack with greater speed.

To put this mechanism to use as a data logger, rather than focus on DNA snippets of viral intruders, the researchers concentrated on something else: exploiting the mechanism so that the bacteria incorporate snippets of their own messenger RNA (mRNA) into the CRISPR array. These mRNA molecules are the blueprint that cells use to manufacture proteins, and as such, mRNA snippets can reveal which genes are being used to build proteins for executing cellular functions.

To make the method effective, the scientists introduced the CRISPR array of the (fun to say) bacterial species Fusicatenibacter saccharivorans into a strain of the intestinal bacterium Escherichia coli, which is regarded as safe in humans and available as a probiotic. This transfer included the blueprint of an enzyme called reverse transcriptase, which is able to transcribe RNA into DNA. Transcription is the process by which the information in a strand of DNA is copied into a new molecule of mRNA, and reverse transcriptase also transcribes the information in the mRNA into DNA form, which along with accompanying CRISPR-associated proteins, is necessary for incorporating the DNA snippet into the CRISPR array [1].

Do not disturb

Next, researchers from University Hospital of Bern and the University of Bern, led by Andrew Macpherson, administered these modified gut bacteria to mice in the lab. Having collected faecal samples from the animals and isolated the bacterial DNA, the team analysed the samples using high-throughput DNA sequencing. A subsequent bioinformatic evaluation was performed and assessed in collaboration which enabled the team to work through the mass of data and reconstruct the genetic information of the mRNA snippets. This allowed the scientists to determine by noninvasive means how often the gut bacteria manufactured a given mRNA molecule during their time in the body – and therefore which genes are active.

“This new method lets us obtain information directly from the gut, without having to disturb intestinal functions,” says Andrew Macpherson, Professor and Director of Gastroenterology at University Hospital Bern [2]. This means that this method has significant advantages over endoscopies, which can be intrusive and uncomfortable for patients and always involves disturbing intestinal function, as a patient’s bowels need to be empty for the examination.

Determining dietary status

“Bacteria are very good at registering environmental conditions and adapting their metabolism to new circumstances such as dietary changes,” Macpherson says [2]. In experiments with mice that were given different foods, the researchers were able to show how the bacteria adapted their metabolism to the respective nutrient supply. A report of the findings has been published in the latest issue of the journal Science.

To build on the research, the team would like to further develop the method in order to be able to 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 and doctors, armed with this information, will be able to diagnose malnutrition or decide whether a patient needs nutritional supplements.

In addition, the researchers were able to recognise inflammatory responses in the gut. The researchers administered the sensor bacteria to mice with intestinal inflammation as well as to healthy mice; in this way, they could identify the specific mRNA profile of gut bacteria that switch to inflammation mode [1].

Distinguishing different bacteria

The current research published in the journal Science includes a scientific development that enables the researchers to distinguish two strains of bacteria from each other based on individual genetic “barcodes” [1]. In the future, this should make it possible to investigate the function of gene mutations in bacteria, allowing scientists to compare the mRNA profile of different bacteria, such as normal compared with mutant bacteria. Thanks to the molecular data logger, it is possible for the first time to determine this profile as they pass through the intestine, rather than just when the bacteria reach the faeces – this means the information shows what was happening when the bacteria were still living in the gut and is therefore more useful.

Another conceivable avenue would be to further develop the system to distinguish RNA profiles of bacteria in the small and large intestine. In addition, the data logger function could be incorporated into other types of bacteria, which would open the door to applications in environmental monitoring. An analysis of soil bacteria from a crop field, for example, would establish whether herbicides had been used or make for more effective farming practices.

Safe application possible

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

Before the sensor bacteria can be used outside the lab – including in human patients – the scientists still have to clarify various safety and legal questions, as the bacteria have been genetically modified.

“In principle, there are ways of using live genetically engineered microorganisms as diagnostic or therapeutic agents in medicine, provided that certain conditions are fulfilled,” Platt explains [2]. It is possible, for instance, to modify the sensor bacteria so that they need certain nutrients and therefore can survive only inside the gut of a patient, which would mean that as soon as these particular bacteria leave the gut, they would die. Integrating suitable safety mechanisms is the next step towards application of the method in medicine.

[1] https://www.science.org/doi/10.1126/science.abm6038
[2] https://ethz.ch/news/2022/05/bacteria-with-recording-function