A primer on metagenomics

Abstract

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics.

Figure 1. Environmental Shotgun Sequencing (ESS).

(A) Sampling from habitat; (B) filtering particles, typically by size; (C) DNA extraction and lysis; (D) cloning and library; (E) sequence the clones; (F) sequence assembly.

Figure 2. Pyrosequencing.

Single stranded DNA template is first hybridized with the sequencing primer and mixed with the enzymes along with the two substrates adenosine 5′-phosphosulfate (APS) and luciferin. In each cycle, (1) one of the four nucleotides (dTTPi, in this case) is then added to the reaction. (2) If the nucleotide is complementary to the base in the template strand then the DNA polymerase incorporates it into the growing strand. (3) Pyrophosphate (PPi)—in an amount equal in molarity to that of the incorporated nucleotide—is released and converted to ATP by sulfurylase in the presence of APS. (4) ATP then serves as a substrate to luciferase, causing a light reaction. Photon emission is in equimolar quanta to the amount of nucleotide incorporated in a given cycle. (5) The excess nucleotides are degraded by apyrase.

Figure 3. Fragment assembly.

(A–C) Hamiltonian. (A) A sequence with overlapping reads; (B) Each read is represented as a vertex, with edges connecting the overlapping vertices; (C) the assembly solution is a Hamiltonian path (all vertices are visited, no vertex is visited more than once) through the resulting graph; (D) For short reads assembly, each vertex is a k-mer (or a hashed collection of k-mers), and the reads are threaded between vertices as edges. The solution is a Eulerian path, where each edge is visited once. Repeats are merged into a single edge. For detailed algorithms see , , –.

Figure 4. Rarefaction curves.

Green, most or all species have been sampled; blue, this habitat has not been exhaustively sampled; red, species rich habitat, only a small fraction has been sampled.