Identifying ecological factors that drive the evolution of innate versus adaptive immunity in bacteria

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How are we going to deal with bacterial infections if pathogens are resistant to antibiotics? And how do we protect bacteria that are useful for industrial production of cheese and yoghurt against their parasites (bacteriophages, the viruses of bacteria)? These are questions of great societal and economic importance that need to be addressed in the near future. The answer to the first question may well lie in the application of parasites that cause the economic problems in industry that is referred to in the second question. Like all organisms bacteria face infectious diseases caused by parasites (bacteriophages) that abuse host resources for their own benefit. These bacteriophages sometimes cause severe problems in food industry, but can perhaps also be applied to fight bacterial infections in humans, or bacterial infections of crops in agriculture. However, bacteria evolved several mechanisms to acquire immunity against bacteriophages. Understanding how bacteriophage immunity evolves in bacteria is one of the key objectives of my research. I am particularly interested in the evolution of two distinct immune mechanisms: bacterial innate and adaptive immunity. I will test how environmental variables impact on the evolution of either immunity mechanism. This will hopefully lead us to conditions where both immune systems of the bacterial host are ineffective, which will aid the use of bacteriophages to combat bacterial infections. On the other hand, my research will likely also identify conditions where the immune system of bacteria is highly effective, which can then be used in food industry to avoid that bacteria that produce our food (e.g. yoghurt) become infected with bacteriophage, which results in severe economic losses. Hence, my research will reveal how, when and why ecological factors drive the evolution of bacterial immunity against bacteriophages. This information is only one step away from applications in industry, where bacteria need to be protected from bacteriophages. Bioreactors could be designed in such a way that bacterial immunity levels are optimal, which would strongly reduce the frequency of bacteriophage infections and the concomitant economic losses. For the purpose of treating patients that are infected with antibiotic resistant bacterial pathogens, phages can be used as an alternative treatment (phage therapy). In this context, my research will provide clues what the optimal treatment method may be in order to avoid or at least reduce the evolution of bacterial immunity against the bacteriophages. Although phage therapy is not yet used on patients, many believe this to be the medicine of the future and a promising alternative for antibiotics. Nevertheless, phage therapy is already being applied in agriculture, to protect crops from bacterial infections, and in food preservations, for example to avoid contamination of food with pathogenic bacteria. Hence, the knowledge gained from my research can be directly implemented to optimize the procedures of applying bacteriophages to combat unwanted bacteria. Apart from these important applications, my research will also provide fundamental insights into the evolution of immunity mechanisms and how their evolution is affected by ecological factors. This may provide general insights that are also applicable to other systems. For example, it will help us to understand how immune systems evolve in nature and what their importance is in controlling diseases and how they influence the evolution and spread of parasites.