The microbiome: what it means for medicine.

surge in human microbiome research currently underway around the world. For the past decade, new molecular methods have started to unlock the secrets of this unseen universe, and suddenly it is dawning on us that human individuals are not the dominant life-form in the symbiosis of our existence. It is often quoted that humans are 10% human and 90% microbial when a comparative count of cell numbers is taken into consideration, 1 but perhaps more astonishingly, it is now clear that our human microbiome, the collection of genes encoded by our microbial passengers, is at least one hundred-fold greater than our own genome. The diversity of the human 'microbiota' is enormous, with approximately 500–1000 species existing in our gastrointestinal tracts alone. We are the vessels for this community of microbes (including bacteria, viruses, and yeasts) living on us and in us, and as we start to unravel the multitude of roles that this microbiota fulfils, it is becoming clear that our microbes play a far more relevant and important role in the maintenance of our health than we have ever stopped to consider before. 2 Therefore, it stands to reason that we are at a pivotal point in our attitude towards microbes in a medical context. adjusting our perception of 'germs' From an early age most of us are taught that 'germs are bad' and that we need to avoid them wherever possible. For clinicians, there is further reinforcement of this concept, from the threat of the relatively small but significant number of microbes that are pathogenic to us. Infectious disease continues to be a major threat to health despite the medical advances we have made in the past few decades. The success of antibiotic therapy heralded a new era in our collective consciousness that, in the words of the US Surgeon General, William Stewart, in 1967, boldly suggested that it was time to 'close the book on infectious disease'. 3 The medical over-confidence that followed saw the use of antibiotics spread from the treatment of life-threatening infections to the treatment of less serious disease, from mild otitis media to acne. Now in 2014 we have realised the error of our ways, as we witness the widespread and increasing emergence of antibiotic-resistant microbes. Quite rightly, this is forcing a re-examination of the circumstances of antibiotic administration in both medical as well as environmental practices (for example, farming, where the Food …