Microbes, such as bacteria, fungi and viruses play a central role in human health, food production and agriculture. Understanding -- on a mechanistic level -- how individual microbes interact in communities and how they affect their surroundings is a mandatory first step in developing actionable insights that can help us develop new drugs, produce better food and increase plant efficiencies. In this talk, we will provide an overview of how causal models can be employed to solve this task. We further discuss the challenges that make it difficult to apply existing analysis techniques and highlight some potential solutions and avenues for future research.