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
Many of the most useful medicinal drugs—including antibiotics and cancer
drugs—are derived from bacteria living in the soil that produce these
chemicals as part of their natural life cycle. Many of these chemicals have been
found by culturing bacteria in the laboratory, but this approach is limited because
it only provides access to the chemicals produced by the small fraction of bacteria
species that we can culture in this way. Also, many bacteria do not produce as many
different chemicals when they are grown under these artificial conditions, instead of
their natural environment. This suggests that bacteria living in the environment are
likely to provide an additional source of new chemicals that could have medicinal
benefits.
Here, Charlop-Powers et al. tackle this issue by employing a high-throughput genetic
method for assessing the potential of soil-dwelling bacteria to make compounds with
biological activity. They extracted DNA directly from soil samples collected from
five continents, in part through the efforts of a citizen-science project called
‘Drugs from Dirt’ (drugsfromdirt.org). These samples came from many different
environments, including rainforests, deserts, and coastal sediments.
After extracting the DNA from the soil samples, Charlop-Powers et al. focused on
sequencing the genes that encode enzymes called NRPS and PKS. These enzymes are
involved in the production of a range of diverse compounds, including many clinically
useful antibiotics. By comparing the sequences of the genes found in the different
soils, it was possible to estimate how common the genes were in each sample, and also
to compare the collections of genes found in different soil types. This comparison
revealed that the DNA sequences of the genes encoding NRPS and PKS vary widely among
the soil samples, except for samples that came from similar environments in close
proximity to each other.
These findings show that populations of soil-dwelling bacteria living in different
locations are likely to produce related, but different and largely unexplored,
natural compounds that could have the potential to be used in drug therapies or in
other industries.
DOI:http://dx.doi.org/10.7554/eLife.05048.002
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