Accessing the Genomes of Uncultivated Microbes for Novel Natural Products

Recent findings suggest that only 1% or less of the total number of soil microbial species can be easily cultivated. The fact that uncultured species represent spectacular microbial diversity has sparked great interest in these microorganisms as a potentially prolific source of untapped genetic diversity encoding novel natural products. Multiple approaches are being developed to access this diversity, such as methods to improve the ability to cultivate some of these organisms, most of which are not easily grown under standard laboratory conditions. Here we discuss an alternative approach, aimed at developing technologies for gaining access to the genomes of uncultivated microbes by creating environmental DNA libraries. This method involves isolating large DNA fragments (100–300 kb) from soil microorganisms (or from microorganisms derived from other environments), and inserting these fragments into a bacterial vector, thus generating recombinant DNA libraries. Such libraries are then used to identify novel natural products by various means, including expression of the DNA in a heterologous host strain and screening for activities, or by directly analyzing the DNA for genes of interest. The recombinant approach thus obviates the need for culturing diverse microorganisms and provides a relatively unbiased sampling of the vast untapped genetic diversity present in various microenvironments. As an additional advantage, the genes encoding a product of interest are already isolated and can be analyzed using the tools of bioinformatics, thus providing a potential boost to the efforts of analytical chemists to identify the product. Furthermore, the possibility of regulating the expression of isolated environmental gene clusters or combining them with genes for other pathways to obtain new compounds could furnish a further advantage over traditional naturalproduct discovery methodologies.