What's the 'meta' with metagenomics?

Genomics, a field of study concerned with the sequencing and analysis of whole genomes, has traditionally advanced through the accumulation of data from individual sequencing projects, each being devoted to completing the genome of a single strain or an individual. Metagenomics is the application of the methods of genomics to microbial assemblages. For this purpose, microorganisms are harvested from the environment by simple physical means, and their DNA is extracted and processed to create a single community ‘shotgun’ library. The great appeal of metagenomics is that it circumvents cultivation and provides proportional representation of all of the genomic information in a sample that can then be mined for new insights. The simplicity of the metagenomic approach also results, unfortunately, in the degradation and loss of information that is difficult, if not impossible, to recover. First, the extraction of DNA en masse from a diverse microbial assemblage destroys all the phenotypic information content. Then the remaining genomic information is effectively scrambled in the process of generating smaller, clonable DNA fragments. Although it is clearly inefficient to first scramble information that must be later reassembled, this has been the state of the art because of the limitations of existing cloning and sequencing technology. Inefficient though it may be, the random shotgun approach has worked well for reconstructing the genomes of the dominant microorganisms harvested from unusual environments having limited microbial diversity (Tyson et al., 2004; Legault et al., 2006). When applied to other natural environments, however, such as soil, sediment and sea water, the yield of assembled genomes has been poor. Nearly eight billion bases of sequence have been generated so far by metagenomic analyses of prokaryote communities, yet only a handful of genomes have been partially reconstructed (Tyson et al., 2004; Venter et al., 2004; Rusch et al., 2007), some of which may be contaminants (DeLong, 2005). Another 0.2 billion bases have been sequenced from metagenomic libraries of marine DNA viruses, but only one small phage genome has been reconstructed (Edwards and Rohwer, 2005; Angly et al., 2006). Random sampling of metagenomic libraries has resulted in the discovery of many new genes (Venter et al., 2004) and proteins (Yooseph et al., 2007) and has provided glimpses of how the prevalence of different functional categories of genes may vary among habitats (Tringe et al., 2005; Angly et al., 2006; DeLong et al., 2006; Rusch et al., 2007), but these unassembled sequence data are sorely lacking in genomic and organismal context. A metagenome is, ultimately, just a phantom genome whose appearance varies depending upon how, when, and on what spatial scale it is sampled. For a field focused on genomic analysis of natural microbial communities, one of the major goals ought to be the reconstruction of actual genomes. The current trend in metagenomics is to sequence at increasingly high throughput (Rusch et al., 2007), sometimes at the expense of read length (Angly et al., 2006; Edwards et al., 2006), and to rely on more sophisticated bioinformatics and more powerful computing resources to make sense of the mess (Chen and Pachter, 2005; Seshadri et al., 2007). Investments in improving these downstream processes are needed and are welcomed, but no matter what the sequencing capacity or computing power available, metagenomics will always be an inefficient use of the available resources, because it is built upon a foundation that sacrifices information content for upstream technical convenience. A more economical way to solve the assembly problems of metagenomics would be to focus on improving upstream processing steps to generate more meaningful and tractable starting material. In particular, isolating individual populations, or even limited consortia of intact microbes, before genomic analysis would allow more efficient reassembly of genomes, especially for rare populations and would facilitate the interpretation of those genomes by allowing parallel analyses of a microorganism’s genotype and phenotype. Enrichment or isolation of microbial populations may be achieved through cultivation, but it is also possible to use physical means to separate complex communities into constituent populations or less diverse consortia. Having a microorganism in pure culture offers unique advantages that make this an attractive option whenever it is achievable. The ability to relate physiological responses to gene expression under controlled conditions, for example, provides information still not obtainable in any other way. Cultivation methodologies have advanced in leaps and bounds in recent years and efforts to isolate additional representative microbes from diverse environments for whole genome sequencing, as well Commentaries