There has been a bit of popular press recently about an article published in Cell by a group of scientists at UCSF. The research team that published this article had previously developed an algorithm to look at microbial genetic data and identify genes that were coding for natural products (small molecules that have some, usually unknown, purpose). Natural products are generally produced in low amounts, or only produced under certain conditions, so they are difficult to discover and isolate. Throughout pharmaceutical industry history, natural products have been a great source for antibiotic and other pharmaceutical development, because several of their functions mediate microbe to microbe interactions.
When the researchers tested the microbiome genes in the Human Microbiome Project's database using this algorithm, they discovered tens of thousands of new, natural products, including over 3000 that are found in the average individual's microbiome. Of these 3000 they even found a vaginal microbe from a bacteria, Lactobacillus gasseri, that created a molecule that was similar to an antibiotic that is currently in clinical trials. When the molecule's antibiotic efficacy was tested in the laboratory, the scientists discovered that it was a potent antibiotic towards common gram-positive pathogens.
The microbiome is an extraordinarily complex system which is one of the primary reasons it has taken so long to properly investigate. This complexity however, could lead to a gold mine of new compounds and molecules to discover, especially in a system where competition, cooperation, and communication between bugs is so high. Based on this research, I don't think it will be long before a molecule originally discovered in the microbiome is commercialized.