Microbial communities play pivotal roles in human, animal and environmental health. With the help of next generation sequencing technology it has become feasible to decipher how they work and untangle how they influence each other, their hosts and the environment. In this thesis, different microbiomes were explored with mainly the help of metatranscriptomics. This has led to insights on how human intestinal microbes cooperate to degrade complex carbohydrates, and how dietary interventions in dairy cows can lead to a decreased output of methane gas produced by rumen microbes. With these and similar studies, the relevance of the microbiome will become even more acknowledged, not only by scientists, but also by the general public.