Microbes with sophisticated storage technology: Researchers have equipped bacteria with a genetic recording function and thus gained insights into processes in the intestines of mice. The sensor microbes recorded their own gene activity as they traveled through the digestive system. This reflected their experiences related to the nutrient supply or disease processes in the rodent gut. The researchers say that the concept could lead to the development of a non-invasive diagnostic procedure.
Be it human, animal, plant or microbe – whether a living being is confronted with certain challenges is reflected in the activity of certain genes in its body. Messenger RNA (mRNA) is formed, which forms the basis for the genetic control of functions in cells and the entire organism. This relationship is already being used to demonstrate biological processes. However, there is a disadvantage: mRNA is not stable – cells quickly break down these molecules again. However, researchers led by Randall Platt from ETH Zurich have developed a sophisticated molecular storage system in recent years that can record transcription events, at least in bacteria, and then make this data accessible.
The recording function is based on the Crispr/Cas system. Naturally, bacteria can use it as a simple immune memory that stores genetic information about pathogens: if the bacteria are attacked by viruses, they can incorporate pieces of the viral genome into their own genome carriers, known as Crispr arrays. In it, short DNA fragments from pathogens are archived. The genetic snippets of different pathogens are separated from each other by short, identical DNA sequences. The information on the Crispr arrays can then help bacteria defend themselves if they are attacked again by a known pathogen.
Refined recording function
In order to be able to use this concept as a data logger, the researchers manipulated the system in such a way that the bacteria incorporated snippets of their own messenger RNA into the Crispr arrays instead of viral DNA fragments. An enzyme becomes active that translates RNA information back into DNA information. These pieces are then built into the Crispr arrays. The converted messenger RNA snippets thus store information about which genes were active in the bacteria. The researchers can then collect this data by sequencing.
Platt and his colleagues have now explored the possibility of using this method for medical diagnostics. They administered a strain of the intestinal bacterium Escherichia coli equipped with the storage function to mice. These microbes then passed through the test animals’ digestive systems. The researchers isolated the bacterial DNA from fecal samples and analyzed it. In this way, they were also able to specifically reconstruct the genetic information of the stored messenger RNA snippets.
Microbial data collection in the gut
In this way, the scientists report, they were actually able to capture information about the gene activity in the bacteria that had occurred during the journey through the digestive system. This also reflected certain aspects of the environment. “With the new method, we can obtain information directly from the intestine without having to disturb the intestinal function,” says co-author Andrew Macpherson from Inselspital Bern. In concrete terms, the researchers were able to show, through experiments with mice that were fed differently, how the bacteria adapted their metabolism to the respective nutrient supply. “Bacteria are very good at sensing environmental conditions and adapting their metabolism to changing conditions such as food,” explains Macpherson.
Further experiments also showed that the system can provide information about which other bacteria the sensor microbes in the gut came into contact with. The researchers were also able to identify indications of inflammatory reactions: when they administered the sensor bacteria to mice with intestinal inflammation and healthy comparison animals, they were then able to identify certain differences in the messenger RNA profile of the storage system.
The results now form an important basis for the further development of the system for use in medicine, say the scientists. For example, the sensor bacteria could be used to diagnose certain inflammatory bowel diseases, to determine malnutrition or to clarify which diet is right for a patient. Before the instrumented microbes can be used in humans, however, safety issues must first be clarified, the researchers point out. They are currently working on changes in their sensor bacteria that mean that they cannot survive outside the intestine. “Basically, there are ways to use living genetically modified microorganisms as diagnostics or therapeutics in medicine, if certain conditions are met,” says Platt.
Source: Swiss Federal Institute of Technology Zurich (ETH Zurich), specialist article: Science, doi: 10.1126/science.abm6038