Metagenomics and its connection to microbial community organization

Abstract

Microbes dominate most global biogeochemical cycles, and microbial metagenomics (studying the collective microbial genomes) provides invaluable new insights into microbial systems, independent of cultivation. Metagenomic approaches targeting specific genes, e.g. small subunit (ssu) ribosomal RNA (rRNA), can be used to investigate microbial community organization by efficiently showing which taxa of organisms are present, while shotgun approaches show all genes and can indicate what functions the organisms are capable of. But collecting and organizing comprehensive shotgun data is extremely challenging and costly, and, in theory, predicting functionalities from microbial identities alone would save immense effort. However, we don't yet know to what extent such predictions are applicable.

Figure 1.. Schematic of shotgun and targeted metagenomic analysis

The metagenome is the collective genomic DNA of organisms (usually microorganisms) in a given sample. After sampling, and sometimes attempts to separate microorganisms from larger organisms, DNA is extracted from the total biomass. For overall genomic analysis, older studies cloned various size fragments and sequenced them. Next generation sequencing shotgun sequencing studies now generally fragment the DNA and sequence the fragments directly, assembling some of them into overlapping ‘contigs’, larger ‘scaffolds’, or even whole genomes. In contrast, tag sequencing uses polymerase chain reaction to amplify specific genes of interest, most often 16S rRNA, and the amplified fragments are sequenced directly.