Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules

Abstract

Bacteria grown in pure culture have been the starting point for the discovery of many of the antibacterials now in use. Metagenomics, which utilizes culture-independent methods to access the collective genomes of natural bacterial populations, provides a means of exploring the antimicrobials produced by the large collections of bacteria that are known to be present in the environment but remain recalcitrant to culturing. Both novel small molecule antibiotics and new antibacterially active proteins have been identified using metagenomic approaches. The recent application of metagenomics to the discovery of bioactive small molecules, small molecule biosynthetic gene clusters and antibacterially active enzymes is discussed here.

Figure 1

Overview of metagenomic methods: Environmental DNA isolated directly from an environmental sample (1) is cloned into an easily cultured model bacterial host (2). Libraries (or eDNA) can then either be enriched for genes of interest (2a), transferred into another heterologous host (2b), or screened directly. The search for bioactive small molecules using a metagenomic approach has generally been conducted using either homology based methods (3a) or functional screening (3b). Novel sequences found in homology-based screens (4a) can be examined for the ability to encode the biosynthesis of novel small molecules in heterologous expression experiments (5). The characterization of hits from functional screens can lead directly to the identification of bioactive small molecules (4b) and their biosynthetic gene clusters (5).

Figure 2

Representative natural products heterologously produced in model cultured bacteria from metagenomic derived genes and gene clusters. N-acyltyrosine (1), isocyanide functionalized indole (2), indigo (3), turbomycin A (4), cyanobactin patellamide D (5), nocardamine (6) and cyanobactin patellamide A (9).

Figure 3

Natural product families that have been explored using metagenomic methods. Pederin (7), methylated mycalamide A (8), glycopeptides (10), patellamides (11) and microviridins (12). The cyanobactin and microviridin precursor peptide diversity found in metagenomic studies is displayed on patellamide A and microviridin B, respectively.