Microbes can now be found in nearly every niche the human body offers. However, the complexity of the microbiota of a given site depends on the particular environmental condition thereof. Only microbes which are able to grow under these conditions, will prevail. Recent publications imply that the microorganisms do not only have multiple, critical consequences for host physiological processes such as postnatal development, immunomodulation and energy supply, but also effects on neurodevelopment, behavior and cognition. Within this book we will focus on the techniques behind these developments, epigenomics and on the various parts of the human body which are inhabited by microorganism such as the mouth, the gut, the skin and the vagina. In addition, chapters are dedicated to the possible manipulations of the microbiota by probiotics, prebiotics and faecal transplantation.