The world is about to run out of antibiotics that are effective against the most resistant bacteria. This has led a Danish research group to adopt alternative methods in the search for new antibiotics. They have developed a veritable battlefield between bacteria that are harmful to humans and other more helpful types. After the battle is over, the researchers try to find the weapons used by the winner to examine whether these may also help people defeat the bad bacteria.
Antibiotics are a product of nature, and researchers have sought and found many new antibiotics in fungi and bacteria since penicillin was first discovered in 1928. The overuse of most antibiotics in animal feed and antibacterial treatment has led to a massive increase in antibiotic resistance. This has led researchers to seek completely new types of antibiotics – using novel methods.
“In nature, microorganisms naturally compete and develop weapons to defeat each other. We have therefore developed a method to reveal how natural bacterial enemies can defeat the bacteria harmful to people. When the battle is over, we can then screen the good bacteria to see what weapons they used to defeat the bad bacteria. We then end up with several new candidate molecules and can test whether they are suitable to be developed into antibiotic drugs,” explains Tilmann Weber, Senior Researcher, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark.
Genome mining
The researchers have named this bacterial battlefield competition-based adaptive laboratory evolution (co-ALE). They subject bacteria to an evolutionary process at a highly accelerated tempo, with robots helping them to perform many assays in parallel.
“Researchers could not carry out all these tests manually. Another major benefit of the co-ALE method is that the researchers do not usually need to know which exact genes to switch on or off to achieve the required results because natural selection and evolution take care of this.”
Instead of having to isolate and purify the compounds produced by the bacteria one by one, the researchers can test many compounds and cells simultaneously through co-ALE. Further, natural selection only produces positive answers if the bacteria’s chemical weapons have succeeded against their opponents.
“The next step in the process is just as important: we need to determine exactly which bacterial weapons worked and how they are built into the bacteria. For this, we use a technology called “genome mining”. When we find a bacterium that can combat the pathogen, we can easily determine its DNA sequence and identify which genes were responsible for the antibacterial activity using the computer programs we develop.
Nature does it best
Once this information has been obtained, the researchers can knock out the genes to see whether this changes the outcome of the bacterial battle.
“This is the ultimate test that determines whether we have discovered the right weapon: if the good bacteria now lose to the bad ones, this must be because we removed this essential weapon. We then can subsequently engineer bacteria that can produce these exact compounds in larger amounts in cell factories.”
The goal for the next 6 years is to identify and produce at least 50 candidates for new antibiotics to combat the gram-negative bacteria that represent a massive challenge to health systems worldwide.
“We believe that allowing nature and evolution to help us in identifying promising compounds and combining this screening method with state-of-the-art metabolic engineering and bioinformatics approaches to produce these compounds biotechnologically provide an excellent basis to reach our ambitious goals.”
“The evolution of genome mining in microbes – a review” has been published in Natural Product Reports. In 2017, the Novo Nordisk Foundation awarded a Challenge Programme grant to Tilmann Weber for the project Integration of Informatics and Metabolic Engineering for the Discovery of Novel Antibiotics (IIMENA).
