Systems Biology of Microbial Communities

Microbes usually don’t live isolated but together with myriads of other microbes in large communities. Such microbial communities also live on and in our bodies – like our gut – and are therefore crucial for our health. Despite the enormous importance of microbial assemblages for our well-being we have very limited understanding of how these communities form and function. Our lab aims to reveal basic principles of microbial communities with a combination of lab experiments and mathematical modeling. We are especially interested in how we can understand, describe and predict interactions between microbes (1), how these interactions shape complex microbial communities (2) and finally how we can use ecological forces within microbial communities for medical purposes (3).

1) What determines microbial interactions?

1) What determines microbial interactions?

Microbes strongly influence each other's growth — they interact. These interactions can be driven in many different ways: microbes can compete for resources, produce toxins or supply each other with nutrients. Despite this diversity interactions have very often one thing in common: they are mediated through the environment. The outcome of an interaction is determined by how microbes change their environment and how this change affects their own and others’ growth. With this basic idea we could show that beneficial modifications of the environment can cause spatial self-organization of microbes (Ratzke and Gore, Nature Microbiology, 2016). We could further show that microbes can also change the environment in such detrimental ways, that whole populations can wipe themselves out (Ratzke et al., Nature Ecology and Evolution, 2018). Finally, we were able to understand and predict interactions between different microbes (Ratzke and Gore, PLOS Biology, 2018). Our lab wants to extend this direction in the future to develop a more basic and general understanding of what determines microbial interactions and how we can predict them.

2) What shapes complex microbial communities?

Interactions between microbes are basic building blocks of microbial ecosystems. They influence who is present or absent in the community and therefore set the overall composition, stability and biodiversity of microbial ecosystems. However, how all these microbial interactions work together to shape the overall community remains unresolved. Can we therefore gain insight into complex communities from studying simple microbial interactions at all? We could currently show that it is indeed possible. Thus, we found that the interaction strength can set the biodiversity and stability of complex microbial communities (Ratzke et al., Nature Ecology and Evolution, 2020). Encouraged by these findings we want to further explore what features of complex communities we can predict from knowing the average interaction forces within them.

2) What shapes complex microbial communities?

3) Can we use microbial interactions to treat infections?

We carry a vast number of microbes on our body. Accordingly, pathogenic microbes that try to infect us have to interact with the native microbes. These interactions can facilitate or repel the pathogen and therefore decide whether we get sick or not. With C. elegans as a model organism we want to study how interactions within the gut microbiota influence the course of an infection and how they can protect us from getting sick. Understanding how interactions between microbes can prevent microbial infections may open new ways to treat them.