Harnessing the Microbiome for Health

May 14, 2014
Cover of Nature

Cover graphics by Steven H. Lee/ Studio Graphiko

In recent years, microbes have moved from public enemy number one to a critical ally in the fight against illness. After a century marked by a “shock-and-awe” relationship with the 100 trillion microbes that live in or on our bodies, a new crop of entrepreneurs believes that the next generation of therapies may come from identifying the friendly microbes among us, and harnessing their power for good. In so doing we will be starting to unwind the revolution that started in the late 1800′s, when the English surgeon Sir Joseph Lister demonstrated that sterilizing operating rooms with carbolic acid could be a critical tool in the prevention of hospital-acquired infections. From then to now we have seen the ubiquitous use of products that seek to control the microbes on our skin, in our mouths, on our clothes and on the surfaces of our world. In parallel, the use of antibiotics has saved countless lives … while their misuse in agriculture and the clinic has begun to wreak havoc. Like much else in medicine, it was the advent of next-generation sequencing that began to open our eyes to the value of changing this relationship. Through the Human Microbiome Project, a two-year study, we now have the genetic sequence of bacteria harvested from more than 240 individuals, which identified more than five million genes that could play an important role in strategies for improving health.

Human Microbiome Project

Human Microbiome Project:
C Huttenhower et al. Nature 486, 207-214 (2012) doi:10.1038/nature11234.

Next-generation sequencing is powering a new understanding of this population diversity by making it easier to catalog individual microorganisms within large pooled samples, and by helping to identify individual microorganisms without the difficult and time-consuming step of growing them in culture. As a result, we have a more rapid, accurate and accessible way of readily distinguishing friend from foe in the microbial world. As followed the sequencing of the human genome more than a decade ago, the innovation rush to the microbiome is approaching full gallop. Top-tier publications are coming at an increasingly rapid clip. Innovative new companies have moved in with dreams of creating an entirely new class of therapeutic products, including first movers Second Genome, Vedanta (both partners with Johnson & Johnson Innovation), the Flagship Ventures spinout Seres Health and others. Initially researchers began with diseases of the gastro-intestinal (GI) tract, an early and obvious place to start to look for illness correlations, and the use by some physicians of crude fecal transplants for treating c. difficile has amply demonstrated the impact that harnessing the microbiome can have. But with conditions ranging from obesity to cancer to allergy now under intense investigation, it is clear that GI diseases are only the start. We know from the mapping of the genome more than a decade ago that there is still a lot of work to do to turn these new discoveries and insights into viable new medicines. The first step in this process – moving from shock and awe to disarmament – has already begun.