How bacteriocins can impact the gut microbiome
The human gut microbiome is a complex place, one that is populated by a wide range of microorganisms, many of which have a direct impact on our health and overall well-being. “This clear link between the microbiome and health has led to an urgent need to develop tools that could be used to predictably shape the gut microbiota,” says Natalia Ríos Colombo, a researcher at University College Cork and Marie Skłodowska-Curie fellow. One such tool is the introduction of bacteriocins, antimicrobial peptides produced by many bacteria that kill other types of bacteria. “Bacteriocins are natural modulators of the human microbiome, which is one reason they are gaining interest as potential microbiome-editing tools,” explains Colin Hill, a professor of Microbial Food Safety at University College Cork’s School of Microbiology. With the support of the EU-funded BIOMA project, Colombo, under the supervision of Hill, set out to better understand the role bacteriocins play in deciding the overall composition and functionality of the gut microbiome.
The impact of bacteriocins
To start, Colombo created otherwise identical strains of bacteria that either do or do not produce bacteriocins, which she then added to synthetic stable communities. “From here, we sat back and waited to see the impact, if any, and whether we could predict what that impact might be,” adds Hill. What the researchers found was that introducing bacteriocin-producing strains did indeed have an impact on overall microbiome composition. According to Colombo, the most obvious effect was on the microbes that are sensitive to the bacteriocin. However, she also noted some off-target effects, such as when a newly introduced bacteriocin kills bacterium strain A, which was already producing a different bacteriocin that targeted bacterium strain B. “In this case, the introduced bacteriocin resulted in an expected decrease in strain A, but also an increase in strain B that would be unexpected if you didn’t know about the second bacteriocin,” remarks Colombo.
Mathematical models predict bacteriocin’s impact on microbiome composition
Not only did the project confirm the bacteriocin’s impact on microbiome composition, researchers also discovered that it is possible to predict this impact using simple mathematical models. While such mathematical modelling was not originally part of the BIOMA project plan, it turned out to be one of the project’s key outcomes. “Natalia sought the advice of mathematicians and introduced the model herself, which gave us the ability to predict the result of a complex experiment and then see it play out in reality,” notes Hill. This ability to predict results is important given the fact that whenever you introduce something in an attempt to kill a target strain there will always be consequences. “With enough fundamental information, we should be able to predict any secondary, unexpected effects and take steps to make sure we don’t do more harm than good,” says Colombo.
Tuning microbiome composition
While the BIOMA project is now finished, the need to further understand the forces that shape microbiomes and their functionality is not. That’s why the research team is currently exploring the possibility of designing interventions capable of deliberately manipulating microbiomes to provide health benefits. “We need ways to deliberately shape microbiomes, and the BIOMA project has certainly given us some interesting tools for doing so,” concludes Hill.
Keywords
BIOMA, gut microbiome, health, bacteriocins, microbiota, bacteria, mathematical models
