Gut microbes and their activity are crucial factors for our well-being. It has become evident that there are considerable differences in individual composition of the microbiota, and first attempts towards stratification led to the definition of three main consensus profiles, the so-called enterotypes (Arumugam et al., 2011). Stratification of microbiota according to composition, such as by enterotypes, showed that those different microbial steady states were strongly associated with long-term dietary habits (Wu et al., 2011), and certain enterotypes have shown higher frequencies in Irritable Bowel Syndrome (IBS ) patients or obese subjects with higher risk for metabolic syndrome (Rajilic – Stojanovic et al., 2011; LeChatelier et al., 2013). Although the presence of enterotypes has been disputed (Knights et al., 2014), it is possible that there may be specific microbial stratifications or some key signature microbes involved in the generation of particular metabolites, which in turn might be related to host health. There are multiple studies that reported that healthy subjects and patients differ in microbiota composition. However, a general consensus or causal associations with host parameters are largely lacking.