Global biogeographic sampling of bacterial secondary metabolism

Abstract

Recent bacterial (meta)genome sequencing efforts suggest the existence of an enormous untapped reservoir of natural-product-encoding biosynthetic gene clusters in the environment. Here we use the pyro-sequencing of PCR amplicons derived from both nonribosomal peptide adenylation domains and polyketide ketosynthase domains to compare biosynthetic diversity in soil microbiomes from around the globe. We see large differences in domain populations from all except the most proximal and biome-similar samples, suggesting that most microbiomes will encode largely distinct collections of bacterial secondary metabolites. Our data indicate a correlation between two factors, geographic distance and biome-type, and the biosynthetic diversity found in soil environments. By assigning reads to known gene clusters we identify hotspots of biomedically relevant biosynthetic diversity. These observations not only provide new insights into the natural world, they also provide a road map for guiding future natural products discovery efforts.DOI: http://dx.doi.org/10.7554/eLife.05048.001

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

“…2E). Similar geographic distance-dependent differences in species beta diversity as well as NP biosynthetic diversity have been observed in other environmental surveys of bacterial species (14, 15) (16,17). It is still unclear whether these differences arise from selection in the environment or if they indicate limits to the natural dispersion of microorganisms over long distances.…”

Minimum Information about a Biosynthetic Gene cluster

“…This will generate opportunities for a range of analyses, such as the biogeographical mapping of secondary metabolite biosynthesis 22 , thereby identifying locations and ecosystems harboring rich biosynthetic diversity. But even if the contextual data associated with the genome sequences cannot always be made MIxS compliant (perhaps because the origin of a strain can no longer be traced), the MIBiG standard itself provides a comprehensive reference dataset for annotating large-scale MIxS-compliant metagenomic data from projects such as the Earth Microbiome Project 23 , Tara Oceans 24 and Ocean Sampling Day 25 .…”

Leveraging ecological theory to guide natural product discovery

“…The readily-analyzed phylogenetic markers may not provide fine-enough resolution to predict the full complement of BGCs, which varies much faster than housekeeping genes [84]. NP diversity is known to vary over geographic spatial scales, habitat physicochemical characteristics, and biotic community composition [16,17,23,48,67]. While these correlations are poorly understood, they lead to readily testable hypotheses that can lead to more systematic characterization of NP potential in the future.…”