Microbes with a mission
With superbugs on the rise, researchers are searching for new ways to fight bacterial infections to save lives. Now, scientists from UC Berkeley and UC San Diego are working on a system that uses probiotics and prebiotics to suppress harmful bacteria.
Focusing on the lung microbiome, the researchers aim to identify probiotic strains that can combat Pseudomonas aeruginosa and Staphylococcus aureus — two deadly pathogens that often infect people with cystic fibrosis or pneumonia. Basically, they’re looking for good bacteria that are hungry for a fight.
“The concept is that we can assemble and differentially feed a set of natural ‘healthy’ lung microbes and cause them to essentially ‘eat the lunch’ of any invading pathogen,” said Adam Arkin, professor of bioengineering. “That is, they literally eat all the metabolites that a pathogen needs to either establish itself or propagate in that environment.”
He credits former Ph.D. student Kelsey Hern with the idea of enabling good bacteria to outcompete bad bacteria. Hern described the strategy as ecological rather than combative — like crowding out weeds in a garden. By selectively feeding beneficial microbes, it closes the nutrient buffet that pathogens need to survive. Genome analysis guides the selection of strains that eat specific foods, ensuring they compete with the target pathogen, not each other.
“We wanted to use our understanding of lung microbiome ecology to design communities that would work together to inhibit the pathogen,” said Hern.
To create a probiotic, researchers take bacteria from healthy patients and test them for safety and performance. Strains that grow well together and compete with pathogens are combined into a formulation, which is delivered to the lung via a nebulizer.
Next steps include designing a “backpack” that supplies prebiotics to sustain the bacteria until suitable food is available. The team is also developing patient-friendly ways to gauge dosing needs — key to turning engineered bacteria into reliable, real-world therapy.
Learn more: Using the microbiome to combat lung pathogens