期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2016
卷号：113
期号：51
页码：14811-14816
DOI：10.1073/pnas.1615581113
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceBacterial natural products (NPs) have served as inspiration for many therapeutics. The hunt for new bioactive NPs has led to a global search for natural ecosystems from which bacteria can be cultured. Here, we used NP-focused metagenome sequencing to explore biosynthetic diversity in urban park soil of New York City. Our analyses reveal rich biosynthetic diversity in these microbiomes and predict that gene clusters encoding many clinically approved NPs families discovered using bacteria cultured from around the world are actually present in the soil microbiomes of a single city. Contrary to traditional NP discovery efforts that involve shallow explorations of diverse environments, our data suggest that a deeper exploration of local microbiomes may prove equally, if not, more productive. 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.
