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Metagenomics Hints at Natural Product Potential of Microbes in New York City Parks

Central Park, NYC

NEW YORK (GenomeWeb) – A Rockefeller University-led team has taken a phylogenetic approach to identifying natural products produced by soil bacteria in New York City parks, uncovering sequences coding for bacterial products that may be medically relevant.

The researchers collected soil samples from hundreds of topsoil samples from parks across New York City's five boroughs, using targeted metagenomic sequencing to characterize genes from biosynthetic pathways producing non-ribosomal peptides, polyketides, and other natural products. From phylogenetic assessments and other analyses, they saw signs that the urban park soils may contain bacteria that pump out natural products resembling those described in other parts of the world. The results appeared online today in the Proceedings of the National Academy of Sciences.

"A comparison of sequences derived from New York City parks to genes involved in the biosynthesis of biomedically important [natural products] 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," senior author Sean Brady, a researcher affiliated with the Rockefeller University, and his co-authors wrote.

The search for natural products that can be used in the clinic or inspire new treatment strategies has often focused on far-flung locales around the world, the researchers noted. But they reasoned that it may not always take a trip to forests or fields far away to find medically useful microbes.

"Although previous efforts to identify metabolites have focused on the global-scale culturing of bacteria from natural environments, [natural products] capable of improving human health may lie hidden much closer to home, in the urban park soil microbiomes of our large cities," they wrote.

The team collected 275 top soil samples from New York parks. It used Illumina instruments to sequence amplicons produced with primers corresponding to a wide range of biosynthesis-related enzymes — from non-ribosomal peptide kinase to polyketide synthase enzyme-coding genes suspected of contributing to natural product repertoires in the mixed microbial samples.

The researchers also targeted adenylation-related genes in almost 100 more samples from non-urban sites in other parts of the US, generating sequences to assess the diversity and clustering of microbes in urban and non-urban sites. Though there appeared to be slightly lower diversity in the urban samples, for example, they found that the New York park samples contained distinct microbiomes with robust biosynethetic potential.

In New York, meanwhile, the team saw some clustering in individual parks, along with a cluster of distinct microbial communities found mainly in Staten Island parks. A comparison done with other microbial products — conducted through the environmental surveyor of natural product diversity, or eSNaPD, informatics and data aggregation platform — indicated that New York's parks contain microbes with gene clusters coding for natural products with potential bioactivity, including a cluster associated with the anticancer compound epothilone.

"Our analyses of urban microbiomes show the existence of tremendous biosynthetic diversity throughout urban park soils," the authors wrote, "suggesting an equal effort should be applied to studying and cataloging urban microbiomes, as they appear to encode diverse, potentially biomedically relevant [natural products]."