A central aspect of life sciences is to explore the symbiotic cohabitation of animals, plants and humans with their specific bacterial communities. Scientists refer to the full set of microorganisms living on and inside a host organism as the microbiome. Over the past years, evidence has accumulated that the composition and balance of this microbiome contributes to the organism’s health. For instance, alterations in the composition of the bacterial community are implicated in the origin of various so-called environmental diseases. However, it is still largely unknown just how the cooperation between organism and bacteria works at the molecular level and how the microbiome and body exactly act as a functional unit.