Abstract
Bacterial polyketides are highly biologically active molecules that are frequently used as drugs, particularly as antibiotics and anticancer agents, thus the discovery of new polyketides is of major interest. Since the 1980s discovery of polyketides has slowed dramatically due in large part to the repeated rediscovery of known compounds. While recent scientific and technical advances have improved our ability to discover new polyketides, one key area has been under addressed, namely the distribution of polyketide-producing bacteria in the environment. Identifying environments where producing bacteria are abundant and diverse should improve our ability to discover (bioprospect) new polyketides. This review summarizes for the bioprospector the state-of-the-field in terrestrial microbial ecology. It provides insight into the scientific and technical challenges limiting the application of microbial ecology discoveries for bioprospecting and summarizes key developments in the field that will enable more effective bioprospecting. The major recent efforts by researchers to sample new environments for polyketide discovery is also reviewed and key emerging environments such as insect associated bacteria, desert soils, disease suppressive soils, and caves are highlighted. Finally strategies for taking and characterizing terrestrial samples to help maximize discovery efforts are proposed and the inclusion of non-actinomycetal bacteria in any terrestrial discovery strategy is recommended.
Highlights
Polyketide natural products are exquisite molecules, often with extraordinary and diverse structures ranging from macrolides to polyethers and polyphenols
We review where to sample for bacterial polyketides in terrestrial environments
Matches to the open reading frames (ORFs) were all non-actinomycetal, while the KS and AT domains of the PKSI module clustered away from their actinobacterial counterparts when treed with the SEARCHPKS database [103]
Summary
Polyketide natural products are exquisite molecules, often with extraordinary and diverse structures ranging from macrolides to polyethers and polyphenols. Studies often at a single environment lookprimers at changes in the microbial caused extract DNA from thelook environment, amplify itand with and analyze thecommunity fingerprints or sequences by treatments, such as the effect of different tillage on soil bacteria [42], the changes in the microbial of the amplicons They often use a unique combination of extraction method, primers, and community during composting [43], or the bacteria found in different kinds of office dust. Delmont et al [44] compared a range of DNA extraction methods on two grassland soils extractionexample, methods and two primer sets to measure the bacterial community of a beach sand sample, and found that they gave very different pictures of the microbial community. Even when the same methods are carried out in different be significant differences in be results [47].differences in results [47]
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