Building on basic metagenomics with complementary technologies

Abstract

Metagenomics, the application of random shotgun sequencing to environmental samples, is a powerful approach for characterizing microbial communities. However, this method only represents the cornerstone of what can be achieved using a range of complementary technologies such as transcriptomics, proteomics, cell sorting and microfluidics. Together, these approaches hold great promise for the study of microbial ecology and evolution.

Figure 1

Enhancing the basic metagenomic approach through complementary technologies. The metagenomic analysis of microbial communities by random shotgun sequencing (arrow 1) is being enriched in one dimension by parallel detection and analysis of transcripts ('metatranscriptomics', arrow 2) and of expressed proteins ('metaproteomics', arrow 3). In addition, because of the complexity of most natural microbial communities a separation of the community into populations enriched in a particular group of microorganisms and even into individual cells would be advantageous. Whole-genome amplification (WGA) is beginning to be validated as an approach to metagenomic and metatranscriptomic analysis in such samples, but there are still some methodological constraints to be overcome (see text). The horizontal arrows indicate examples of techniques that can be used to move to the next level of analysis, for example, (a) flow sorting and filtration and (b) microfluidics and flow sorting. SIP, stable isotope probing.