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Metagenomics

Main article: Metagenomics

The advances in modern sequencing technologies in the late 1990s allowed scientists to investigate DNA of communities of organisms in their natural environments, so-called “eDNA”, without culturing individual species in the lab. This metagenomic approach enabled scientists to study a wide selection of organisms that were previously not characterized due, in part, to an incompetent growth condition. These sources of eDNA include, but are not limited to, soils, ocean, subsurface, hot springs, hydrothermal vents, polar ice caps, hypersaline habitats, and extreme pH environments. Of the many applications of metagenomics, chemical biologists such as Jo Handelsman, Jon Clardy, and Robert M. Goodman who are pioneers of metagenomics, explored metagenomic approaches toward the discovery of biologically active molecules such as antibiotics.

Overview of metagenomic methods

Functional or homology screening strategies have been used to identify genes that produce small bioactive molecules. Functional metagenomic studies are designed to search for specific phenotypes that are associated with molecules with specific characteristics. Homology metagenomic studies, on the other hand, are designed to examine genes to identify conserved sequences that are previously associated with the expression of biologically active molecules. Functional metagenomic studies enable scientists to discover novel genes that encode biologically active molecules. These assays include top agar overlay assays where antibiotics generate zones of growth inhibition against test microbes and pH assays that display the molecule synthesis phenomenon using pH indicator on an agar plate. Substrate-induced gene expression screening (SIGEX), a method to screen for the expression of catabolic genes that are induced by chemical compounds, has also been used to search genes with specific functions. These led to the discovery and isolation of several novel proteins and small molecules. For example, Schipper group identified three eDNA derived AHL lactonases that inhibit biofilm formation of Pseudomonas aeruginosa via functional metagenomic assays. However, these functional screening methods require a good design of probes that detect molecules being synthesized and depend on the ability to express metagenomes in a host organism system. In contrast, homology metagenomic studies led to a faster discovery of genes that have homologous sequences as the previously known genes that are responsible for the biosynthesis of biologically active molecules. As soon as the genes are sequenced, it can investigate thousands of bacterial genomes simultaneously. The advantage over functional metagenomic assays is that homology metagenomic studies do not require a host organism system to express the metagenomes, thus it can potentially save the time spent on analyzing nonfunctional genomes. These also led to the discovery of several novel proteins and small molecules. For example, Banik et al. screened for clones containing genes associated with the synthesis of teicoplanin and vancomycin-like glycopeptide antibiotics and found two new biosynthetic gene clusters. An in silico examination from the Global Ocean Metagenomic Survey found 20 new lantibiotic cyclases. There are challenges to metagenomic approaches to discover new biologically active molecules. Only 40 % of enzymatic activities present in a sample can be expressed in E. coli.. In addition, the purification and isolation of eDNA is essential but difficult when the sources of obtained samples are poorly understood. However, collaborative efforts from individuals from diverse fields including bacterial genetics, molecular biology, genomics, bioinformatics, robots, synthetic biology, and chemistry can solve this problem together and potentially lead to the discovery of many important biologically active molecules.