On the heels of the International Human Microbiome Congress that took place in Paris this past month, there has been much talk about the human microbiome and the effect that studying it will have on our abilities to diagnose and treat human diseases. Indeed since international efforts aimed to better understand the human microbiome began not more than 4 years ago[1, 2, 3], there have been some great discoveries. Studies have revealed differences between lean and obese twin microbiotas, and have predicted the existence of a “core microbiome” shared by us all. Additionally, it has been shown that our bacterial symbionts can influence diseases as diverse as type 1 diabetes, inflammatory bowel disease, autism, and atherosclerosis. And to sum it all up, great new tools have been developed or proposed such as Jonathon Eisen’s Microbe Field Guide, which would provide microbiologists with a taxonomic identification tool similar to those field biologists and hobby naturalists have been using for years.
But are we getting ahead of ourselves? Differences between our actual bacterial community and that which we infer are present due to mistakes or inherent biases during the collecting, processing, amplification and sequencing of microbiome samples. While the tools and techniques available at each of these steps have improved greatly over the years since this effort began, there is still a potentially high loss of accuracy in how we model our bacterial partners. Additionally, things such as strain differences, lateral gene transfer, quorum sensing, and biofilms complicate when a specific bacteria acts as a commensal friend or a pathogenic foe.
As Ed Yong explained recently in Nature News, we’ve seen this before: in 2001, the completion of the Human Genome Project promised the ability to cure human disease by uncovering the genetic factors responsible for our illnesses; ten years later, it is obvious that this has not panned out. Now with the sequencing of the human microbiome, the expectation is the same. Whether the next 10 years prove to be different than the last remains to be seen.