It is increasingly apparent that human health is reliant on our fellow travellers, the innumerable microorganisms that inhabit our bodies. This realization has led to the concept of the superorganism, which suggests that shared metabolic and signalling pathways are crucial for optimal existence of both host and commensal microflora. This commentary focuses on implications of this paradigm for personalized medicine and therapeutics. Study of the microbiome, the collection of microorganisms inhabiting the body, may identify disease-associated microbial profiles with pathophysiological and diagnostic value. As with genomics, companies will emerge offering direct to consumer microbiome analysis. Probiotics can potentially modulate the superorganism for therapeutic benefit. However, the probiotics industry will need to undergo a transformation, with increased focus on stringent manufacturing guidelines and high-quality clinical trials. Ultimately, we suggest that healthcare will move beyond its prevailing focus on human physiology, and embrace the superorganism as a paradigm to understand disease.