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Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):14811-14816. doi: 10.1073/pnas.1615581113. Epub 2016 Nov 28.

Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity.

Author information

1
Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065.
2
Natural Areas Conservancy, New York, NY 10029.
3
Department of Biology, Barnard College, Columbia University, New York, NY 10027.
4
Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027.
5
Science Outreach Program, The Rockefeller University, New York, NY 10065.
6
Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065; sbrady@rockefeller.edu.

Abstract

Numerous therapeutically relevant small molecules have been identified from the screening of natural products (NPs) produced by environmental bacteria. These discovery efforts have principally focused on culturing bacteria from natural environments rich in biodiversity. We sought to assess the biosynthetic capacity of urban soil environments using a phylogenetic analysis of conserved NP biosynthetic genes amplified directly from DNA isolated from New York City park soils. By sequencing genes involved in the biosynthesis of nonribosomal peptides and polyketides, we found that urban park soil microbiomes are both rich in biosynthetic diversity and distinct from nonurban samples in their biosynthetic gene composition. A comparison of sequences derived from New York City parks to genes involved in the biosynthesis of biomedically important NPs produced by bacteria originally collected from natural environments around the world suggests that bacteria producing these same families of clinically important antibiotics, antifungals, and anticancer agents are actually present in the soils of New York City. The identification of new bacterial NPs often centers on the systematic exploration of bacteria present in natural environments. Here, we find that the soil microbiomes found in large cities likely hold similar promise as rich unexplored sources of clinically relevant NPs.

KEYWORDS:

biosynthesis; metagenomics; natural products

Comment in

PMID:
27911822
PMCID:
PMC5187742
DOI:
10.1073/pnas.1615581113
[Indexed for MEDLINE]
Free PMC Article

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