Microorganisms play a crucial role for the health and well-being of higher organisms. Host-specific microbial communities of varying complexity form the so-called microbiota. It can consist of several thousand microbial species and includes bacteria, archaea and fungi. These microorganisms exchange a plethora of metabolites with their hosts and can modulate their functioning. Such interactions equally affect humans, animals and plants. This provides us with novel strategies to counteract various diseases and increase the resistance of higher organisms towards abiotic and biotic stresses by modulating the microbiota.