Genetically Encoded Small Molecules Mining Metagenomes for Drugs
Screen soils for molecules

Genetically Encoded Small Molecules
Mining Metagenomes for Drugs

Human microbiome
Digging soil sample

Culture independent studies (eDNA, metagenomics)

It is now widely recognized that the vast majority of bacteria are not readily cultured in the laboratory. The inability to culture these bacteria renders them incompatible with the most heavily relied upon techniques for characterizing bioactive natural products. Although it is still not possible to easily culture most bacteria from the environment, it is possible to extract microbial DNA directly from environmental samples and clone this DNA into model cultured bacteria where, for the first time, it can be functionally characterized. Our group has pioneered the use of culture independent methods to guide the discovery of novel bioactive secondary metabolites from natural microbial communities.

Homology approaches: We are developing homology-based approaches for studying gene clusters predicted to encode novel metabolites from within soil metagenomes.  With homology screening strategies, clones containing genes known to be involved in the biosynthesis of natural product substructures commonly seen in bioactive compounds are recovered from environmental DNA (eDNA) libraries, and then each new gene cluster is assessed for its ability to encode novel bioactive small molecules in model cultured hosts.  These studies are designed to provide access to both previously inaccessible derivatives of pharmacologically important classes of natural products, as well as completely novel natural products that are only linked to known metabolites by a single, highly conserved biosynthetic step.  Gene clusters and the molecules identified in these studies form the basis for subsequent biosynthetic and mode action studies in the lab.

Functional approaches: The second strategy we are using to identify small molecule producing biosynthetic systems in large eDNA libraries is phenotype (expression-dependent) screeningWith this approach, large insert eDNA libraries are examined directly in simple high throughput assays designed to identify clones exhibiting phenotypes traditionally associated with the production of bioactive small molecules (e.g. antibiosis, antifungal activity, cytotoxicity, etc.).  In essentially all reported cases, these studies have been carried out in Escherichia coli.  We are working on expanding the phylogenetic diversity of the model bacterial systems available for hosting and screening large eDNA libraries.

Molecular diversity studies: The true diversity of biosynthetic genes present in the environment remains a mystery. We are using next generation sequencing to assess the diversity of natural product biosynthetic genes present in diverse environments in an effort to provide a more complete picture of the natural product biosynthesis genes found in these libraries.

Syn-BNP. Extracts of bacterial culture broths have been the starting point for the development of numerous therapeutics. However, only a very small fraction of bacterial biosynthetic diversity is accessible through this strategy. We have developed a discovery approach that bypasses the culturing step entirely. This approach starts with bioinformatically predicting small molecule structures from the primary sequences of biosynthetic gene clusters. These structures are then chemically synthesized to give synthetic-bioinformatic natural products (syn-BNPs). Syn-BNPs are not meant to be exact replica of natural products; instead they are close structural mimics to facilitate the discvoery of bioactive molecular scaffolds. This approach has led to a growing collection of novel bioactive small molecules from the human biota and soil bacteria. As DNA sequencing technology and prediction algorithms continue to improve, the syn-BNP approach is poised to uncover even more bioactive molecules in years to come.

The development of robust DNA-based methods to functionally access previously inaccessible natural product biosynthetic pathways found in the genomes of both cultured and as yet uncultured bacterial should significantly increase the number and diversity of natural products that are available to test as probes of biological processes. This in turn, should shed light on how best to use this collection of previously inaccessible small molecules "for the benefit of humanity".

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Digging soil sample

Human microbiome

Functionally characterizing the chemistry of the human microbiome: A natural extension of our exploration of environmental bacteria is the exploration of the human microbiota. Although the human microbiome is believed to play an important role in human health and disease, the mechanisms by which human associated bacteria affect host physiology remain poorly understood. In other ecosystems, bacteria are known to rely heavily on small molecules to interact with their environment, and it is likely that the human microbiota also relies heavily on small molecules to interact with its human host. Even though tremendous resources have been allocated to the sequencing and bioinformatic organization of the microbial metagenome, very few genes have been demonstrated to encode for either proteins or, indirectly, for small molecules that affect the human host through specific cell receptors. Addressing this gap in our mechanistic-level characterization of host-microbial interactions is critical to understanding the role the microbiota plays in human health and disease and, therefore, essential for opening the door to new microbiome derived therapeutics. A variety of approaches have been proposed for systematically identifying the small molecules of the human microbiome. We believe “function first” small molecule discovery methods will be the most useful for identifying the diverse ligands that are likely to be involved in host-microbial interactions. With this in mind, we are adapting and applying diverse functional discovery approaches to the study of the human microbiome.

Functional metagenomics. Functional metagenomics is a culture-independent approach to simultaneously access bacterial genes and small-molecules based on a phenotype of interest. Large DNA fragments are cloned into model bacteria, and screened for physiologically relevant bioactivity. In the context of the human microbiome, this method allows for the identification of bioactive bacterial effectors directly affecting mammalian cellular processes. Unveiling the largely unknown mechanisms by which human-associated bacteria interact with their host is likely to be important to understanding how the microbiome shapes human physiology and to identifying specific host-microbial interactions that can be therapeutically developed to promote health or to prevent disease.

Syn-BNP. Extracts of bacterial culture broths have been the starting point for the development of numerous therapeutics. However, only a very small fraction of bacterial biosynthetic diversity is accessible through this strategy. We have developed a discovery approach that bypasses the culturing step entirely. This approach starts with bioinformatically predicting small molecule structures from the primary sequences of biosynthetic gene clusters. These structures are then chemically synthesized to give synthetic-bioinformatic natural products (syn-BNPs). Syn-BNPs are not meant to be exact replica of natural products; instead they are close structural mimics to facilitate the discvoery of bioactive molecular scaffolds. This approach has led to a growing collection of novel bioactive small molecules from the human biota and soil bacteria. As DNA sequencing technology and prediction algorithms continue to improve, the syn-BNP approach is poised to uncover even more bioactive molecules in years to come.

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Publications

  • Accessing Bioactive Natural Products from the Human Microbiome. 06-2018. Milshteyn A, Colosimo DA, Brady SF. Cell Host & Microbe.
  • Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens. 02-2018. Hover BM, Kim SH, Katz M, Charlop-Powers Z, Owen JG, Ternei MA, Maniko J, Estrela AB, Molina H, Park S, Perlin DS & Brady SF. Nature Microbiology.
  • Human Microbiome Inspired Antibiotics with Improved beta-Lactam Synergy against MDR Staphylococcus aureus. 01-2018. Chu J, Vila-Farres X, Inoyama D, Gallardo-Macias R, Jankowski M, Satish S, Freundlich JS, Brady SF. ACS Infectious Diseases.
  • Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library . 01-2018. Cohen LJ, Han S, Huang YH, Brady SF. ACS Infectious Diseases.
  • An Optimized Synthetic-Bioinformatic Natural Product Antibiotic Sterilizes Multidrug-Resistant &ITAcinetobacter baumannii&IT-Infected Wounds . 01-2018. Vila-Farres X, Chu J, Ternei MA, Lemetre C, Park S, Perlin DS, Brady SF. Msphere.
  • Commensal bacteria make GPCR ligands that mimic human signalling molecules. 09-2017. Cohen LJ, Esterhazy D, Kim SH, Lemetre C, Aguilar RR, Gordon EA, Pickard AJ, Cross JR, Emiliano AB, Han SM, Chu J, Vila-Farres X, Kaplitt J, Rogoz A, Calle PY, Hunter C, Bitok JK, Brady SF. Nature.
  • Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale . 08-2017. Lemetre C, Maniko J, Charlop-Powers Z, Sparrow B, Lowe AJ, Brady SF. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES.
  • Antimicrobials Inspired by Nonribosomal Peptide Synthetase Gene Clusters. 02-2017. Vila-Farres X, Chu J, Inoyama D, Ternei MA, Lemetre C, Cohen LJ, Cho W, Reddy BVB, Zebroski HA, Freundlich JS, Perlin DS, Brady SF. Journal of the American Chemical Society.
  • Biotechnological potential of Actinobacteria from Canadian and Azorean volcanic caves. 01-2017. Riquelme C, Dapkevicius M, Miller AZ, Charlop-Powers Z, Brady SF, Mason C, Cheeptham N. Applied Microbiology and Biotechnology.
  • Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity. 12-2016. Charlop-Powers Z, Pregitzer CC, Lemetre C, Ternei MA, Maniko J, Hover BM, Calle PY, McGuire KL, Garbarino J, Forgione HM, Charlop-Powers S, Brady SF PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES.

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News

  • Feb 14, 2018Malacidins: a new class of antibiotics isolated from dirt

    Bradley Hover of the Brady lab, recently reported in a Nature Microbiology article the discovery of a new class of calcium-dependent antibiotics isolated from soil samples. This new class, malacidins is reported to display activity against multidrug-resistant pathogens. The breakthrough discovery has been highlighted in Nature and was also feat... continue reading

  • Jan 16, 2018Wired magazine article

    The Brady lab as well as drugsfromdirt are being featured in this January 2018 Wired magazine edition. You can read all about it here. Have a look! The DFD Team continue reading

  • Dec 6, 2017Enrolling interested teachers

    The DFD program is interested to work with a school teacher or a college professor to develop a curriculum around this Citizen Science project. If you are a school teacher and interested in this, please reach out to us at drugsfromdirt@gmail.com. We are looking forward to be working with you on this. A summer internship is available. The DFD team continue reading

  • Nov 29, 2017We're back!

    We are delighted to announce that the new version of the Drugs From Dirt website and program are now up and running. A new team has taken over the project. As the program resumes, and the analysis is conducted we will release the data as it comes. Stay tuned! The DFD Team continue reading

  • Sep 15, 2017Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale

    The Rockefeller University laboratory of genetically encoded small molecules led by Dr. Sean Brady succesfully published another study in the prestigious scientific journal PNAS. The results of this study were also featured in an article by Andrea Du Toit in Nature Microbiology Reviews as a research highlight, as well as in the November 2017 TE... continue reading

  • Oct 20, 2016Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity

    A new research article by Dr. Sean Brady and his team at the Rockefeller University laboratory of genetically encoded small molecules has been published in the prestigious scientific journal PNAS focusing on the biosynthetic diversity of bacterial natural products across different urban parks in the New York City area. The study suggests that de... continue reading

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