Screening for novel small molecule‐encoding sequences using environmental DNA cosmid libraries created from Pingry School soil metagenomes

The genomes of culturable bacteria have been a rich source of pharmaceutically useful genetically encoded small molecules. However, only a very small portion of bacteria are culturable using traditional laboratory methods (less than 1%) and recent shotgun‐sequencing projects has shown that the remaining species are a rich source of biosynthetic pathways that produce novel small molecules. To avoid culture‐dependent screening methods, environmental DNA cosmid libraries were constructed from soil metagenomes. Genes involved in a pathway producing a small molecule are often located adjacent to each other in the genome and cosmids can be used to isolate all of these genes into individual clones. The cosmid libraries were expressed in E. coli and screened in a high throughput fashion for clones producing genetically encoded small molecules. Since the small molecules often cause the bacteria to change in appearance, the clones can simply be screened for changes in appearance. In addition, overlay screens were utilized to identify clones producing small molecules capable of lysing other bacteria. This represents a rapid method to screen soil metagenomes for novel genetically encoded small molecules. This work was made possible by the Rockefeller University Summer Outreach Program and the Camille and Henry Dreyfus Foundation in the Chemical Sciences.