Microbial communities contain many evolving and interacting bacteria, which makes them complex systems that are difficult to understand and predict. We use theory – including game theory, agent-based modelling, ecological network theory and metabolic modelling – and combine this with experimental work to understand what it takes for bacteria to succeed in diverse communities. One way is to actively kill and inhibit competitors and we study the strategies that bacteria use in toxin-mediated warfare. We are now also using our approaches to understand the human gut microbiome and its key properties including ecological stability and the ability to resist invasion by pathogens (colonization resistance). Our ultimate goal is to both stabilise microbiome communities and remove problem species without the use of antibiotics.