Metagenomics and beyond: new toolboxes for microbial systematics

Abstract

An extraordinary DNA sequencing revolution has taken place over the past decade, which has seen exciting, yet challenging times for microbial genomics and systematics. Numerous metagenomics and metatranscriptomics projects have provided us with an unprecedented glimpse at the vast biological diversity that exists in minute amounts of samples obtained from environments such as ocean water, soil or human distal gut. One of the key challenges is how we catalogue and classify this vast diversity of microbial life (much of which represents unculturable mixtures) discovered in the last few years alone. Of even greater challenge is the fact that biological mechanisms that rule bacterial plasticity and ecological fitness are far more complex than previously thought, resulting in new concepts of ‘pan’ or ‘supra-genomes’ that appear to be much larger than any individual bacterial genome.