To date, our understanding of the organisms which constitute the microbiomes of humans and our domesticated species has been limited by the technologies available to study them. Progress from culture to species-based DNA approaches has allowed us to appreciate the scale of animal microbiomes and the changes which can occur over time and space. However, in order to design and validate rational approaches to manipulating microbiomes to optimise health, welfare and productivity, we need to begin to understand them as ecosystems, in which the host and a complex mixture of micro-organisms are continuously engaged both in co-operation to produce resources from food and in competition for those resources. The application of ecological principles can guide this understanding, but we need to validate the concepts we use, since they may not all be as applicable as they might seem.