The surfaces of the human body interact with quadrillions of microorganisms. This so-called microbiome influences processes in healthy as well as diseased humans. The microbiome consists of a number of different microorganisms including bacteria, archaea, viruses, fungi and protozoa. A change in the microbiome (dysbiosis) has been associated with a number of diseases (e.g., autoimmune and metabolic diseases, cancer). Thanks to (methodological) advances in microbiome research, it is now possible to analyze microbiome-human interactions. The emphasis is on basic research with the goal of conducting microbiome-based diagnostics and providing direct or indirect therapy for the microbiome.