Uncultivated bacterial symbionts of humans: an untapped resource for drug discovery. The human microbiome is composed of thousands of bacterial species; many of which remain uncultivated. Other mammals (e.g., rodents) harbor uncultivated bacterial symbionts that play a crucial role in the activation of the host's immune system and subsequently, in its ability to fight infections. In humans, however, almost nothing is known about the interactions between uncultivated members of the human microbiome and their host (microbe-host interactions) or about the interactions between uncultivated and cultivated members of the microbiome (microbe-microbe interactions). In an effort to identify possible molecular modulators of these interactions, we set out to characterize biologically active small molecules that are produced by uncultivated members of the human microbiome. Using a specialized bioinformatics workflow, we discovered dozens of biosynthetic gene clusters for small molecules in genomes of uncultivated members of the human microbiome. Surprisingly, some of these biosynthetic gene clusters resemble to a great extent biosynthetic gene clusters for known drug-like molecules, which enables the accurate prediction of their products' structures and biological activities. Following these findings, we herein propose to experimentally characterize these drug-like small molecules in four steps. A) Cloning the biosynthetic gene clusters of interest from human metagenomic DNA. B) Heterologous expression of these biosynthetic gene clusters in various bacterial hosts. C) Solving the chemical structure of these new molecules using Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS). D. Characterizing the biological activity of these microbiota-derived molecules using a combination of in vitro and in vivo assays. The studies proposed here will not only uncover important interactions between humans and their uncultivated symbionts, but will also allow access to a unique set of microbiota-derived, drug-like, new molecules that have been naturally selected for use in humans.

Public Health Relevance

Variations in the composition of the human microbiota have been correlated to several diseases; yet, little is known about the underlying details of these correlations. Here, we propose to uncover these details by studying the set of chemicals produced by common yet understudied members of the human microbiota. Unexpectedly, our preliminary data suggest that some of these chemicals resemble to a great extend therapeutic drugs that we already use, revealing a treasure trove for new pharmaceuticals hidden within our bodies.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
NIH Director’s New Innovator Awards (DP2)
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Special Emphasis Panel (ZRG1)
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Brown, Liliana L
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Princeton University
Schools of Arts and Sciences
United States
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Cervantes-Barragan, Luisa; Chai, Jiani N; Tianero, Ma Diarey et al. (2017) Lactobacillus reuteri induces gut intraepithelial CD4+CD8??+ T cells. Science 357:806-810