Metagenomics and novel gene discovery

Metagenomics is a term that describes both a field of scientific research and a set of techniques that enables the culture-independent analysis of a microbial community in any environmental sample. The field has grown exponentially in the last 10 to 15 years; allowing researchers unparalleled access to the “uncultured majority” of our microbial counterparts in our environments and closer to home, on and in our own bodies. This review aims to provide a concise overview of the principal methods of metagenomic analysis and how metagenomics can be used for the discovery of novel genetic loci. We will also discuss the potential uses of such genes for the creation of bioengineered probiotics, as well as the potential for the discovery of novel biotherapeutics for human medicine. A wealth of information has been gained in the relatively short history of metagenomics and thus, it is timely to discuss the future directions of this ever expanding field of research. It has been estimated that there are more than 10 microbial cells on Earth; 9 orders of magnitude greater than the number of known stars in the universe. It is estimated that over 99% of microbes in many environments are, as yet, uncultured, while cultured prokaryotic representatives are overwhelmingly from just four phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Metagenomics provides a means to access, characterize, and quantify this untapped diversity of microbes and discover novel genes, metabolic pathways, and important products with biotechnological, pharmaceutical, and medical relevance. Metagenomic analysis can take a sequence-based or a functional approach (or a combination of both) to study a complex microbial community, but always begins with the isolation of DNA from the environment of interest.