The human microbiome is the community of bacteria and microorganisms that lives in association with the human body. Outnumbering human cells, the microbiota resides on human tissue or in body fluids, and grows with particular density in the gastrointestinal tract.

The microbiome’s association with health and disease

The human microbiome has been linked to a wide range of serious diseases, from infectious etiologies like Clostridium difficile to complex chronic conditions like obesity and Crohn’s disease. Recent discoveries have demonstrated a compelling and previously underappreciated link between human health and the trillions of microbes that live within us.

Yet, it is unclear from these associative studies whether microbial dysbiosis causes disease or whether disease causes microbial dysbiosis. Although observational work is intriguing, it can only show correlation, not causation.

Solving the puzzle of causality

Interventional studies that intentionally manipulate the microbiome can illuminate the causal relationships between these organisms and disease. Fecal microbiota transplantation (FMT) for the treatment of recurrent C. difficile infections (rCDI) provides a well-known example of how engineering the microbiome can produce desirable clinical outcomes. The data from these interventional experiences provide a unique window into the specific microbes that drive clinical phenotypes.