The human gut microbiota, the consortium of microbial inhabitants in our distal gut, has been increasingly recognized as playing a major role in the maintenance, promotion and distortion of health. A healthy gut microbiota is involved in energy extraction from dietary components , regulation of components of the immune system , vitamin synthesis , and colonization resistance, i.e., protection against colonization by gastrointestinal pathogens . In addition, there is an increasing number of associations between a microbiome imbalance and various diseases and medical conditions . Such disturbances of the healthy microbiome composition have been found associated with infections with gastrointestinal pathogens such as Campylobacter, Salmonella and Vibrio cholerae  to more elusive imbalances found in the setting of inflammatory bowel diseases , metabolic syndrome , and irritable bowel syndrome .