Our body is inhabited by an enormous number of microbes which are crucial for our health. The bacteria in our gut for example help us to digest food but can also make us sick in case of an infection. The overall composition and function of those communities are strongly shaped by the interactions of the microbes within them e.g. how the microbes influence each others growth. These interactions are especially important in the case of microbial infections. Since pathogens have to interact with the microbial communities that already inhabit the host, the native microbes can repel or support the pathogens and thus protect the host from diseases or even facilitate them. Although microbial assemblages are pivotal for our health we have currently no satisfying way to get a mechanistic understanding of them which would be crucial to specifically manipulate these communities e.g. for therapeutic interventions. The aim of this proposal is to develop a microscopy method that allows to obtain interaction networks within complex communities. Since bacteria can only share the same space if they tolerate each other but avoid each other in case of competition, interaction networks of complex communities can be derived from the spatial co-occurence of the bacteria that form them. With this technology I especially want to investigate how pathogens embed into the native gut microbial community of the model organism Caenorhabditis elegans. I want to understand how interactions between pathogens and native gut microbiota can protect a host from infections. Finally, I want to use this technology to identify bacteria in the native gut community that can outcompete pathogens and work as specific probiotic against microbial infections. This approach could revolutionize the usage of probiotics and offer completely new ways to prevent and treat infectious diseases, which are especially valuable in times where we see more and more pathogens become resistant against antibiotics.
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