The development of therapies inspired by the human microbiome is at least in part limited by our lack of understanding of how human associated (HA-) bacteria communicate with their human host and affect pathogens. Human microbiome sequencing studies show strong correlations between changes in bacterial populations and human health. Despite these correlations and the evidence linking HA-bacteria to disease in mice, the mechanistic details of how HA-bacteria specifically affect mammalian physiology remain largely unknown. In other environments, bacteria are known to rely heavily on low molecular weight compounds (small molecules or natural products) to interact with other organisms. Similarly, we expect that HA-bacteria are likely to use small molecules to interact with their human hosts and pathogens. Mounting evidence suggests that, although each human microbiome is composed of a complex collection of bacteria, a much smaller number of species is highly prevalent across the majority of individuals. While we don?t know exactly which HA-bacteria are responsible for maintaining human health or causing disease, we hypothesize that small molecules produced by these commonly encountered HA-bacteria are likely to play an important role in these processes. The central aim of this proposal is to screen metabolites produced by the most commonly observed HA-bacteria in high-throughput bioactivity screening to identify GPCR and SARS-CoV-2-active small molecules and their producing biosynthetic gene clusters (BGCs). GPCRs constitute the largest family of eukaryotic trans-membrane receptors. They are known to play diverse and profound roles in human biology and are prone to regulation by small molecules. Based on the fact that GPCRs play such an extensive role in transforming chemical information from the environment into biological signals in eukaryotic cells, I believe that HA-bacteria likely affect host physiology through the production of small molecules that interact with GPCRs. The emergence of the SARS-CoV-2 virus represents a worldwide pandemic with no therapeutic drug treatments. The two Aims of this proposal will result in (1) the identification, isolation, and structure elucidation of HA-bacteria-encoded metabolites that either interact with diverse GPCRs or inhibit SARS-CoV-2, (2) the characterization of the gene clusters for these metabolites, and (3) the validation of their production by colonizing bacteria. These studies will help to illuminate the mechanistic details of how HA-bacteria shape human health. The human microbiome is reported to influence complex pathophysiological processes ranging from the regulation of the immune system to the development of the brain and the central nervous system. Changes in HA-bacterial populations are associated with diseases that affect over 200 million Americans including obesity, diabetes, inflammatory bowel disease, autism, irritable bowel syndrome, and cirrhosis among many others. Therapies derived from HA-bacteria have potential utility in controlling diverse basic biological processes and human diseases.

Public Health Relevance

This proposal is designed to identify ligands produced by human commensal bacteria that either activate specific human receptor proteins or inhibit SARS-CoV-2. This work will provide a number of important biomedically relevant outcomes. These include: 1) the elucidation of key pathways through which human microbiota affects host physiology, 2) the discovery of novel small molecules that modulate biomedically relevant receptors and pathogens, and 3) the identification of probiotic species that produce receptor-active ligands with the ability to modulate human physiology.

National Institute of Health (NIH)
National Center for Complementary & Alternative Medicine (NCCAM)
Research Project (R01)
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Kim, Hye-Sook
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Rockefeller University
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New York
United States
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Milshteyn, Aleksandr; Colosimo, Dominic A; Brady, Sean F (2018) Accessing Bioactive Natural Products from the Human Microbiome. Cell Host Microbe 23:725-736