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.

Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters

“…Metagenomics, unlike qPCR and conventional sequencing approaches, does not rely on prior knowledge of the organisms of interest and, thus, organism-specific primers are not required (Wooley et al, 2010). However, metagenomics does still suffers from biases introduced during DNA extraction, enzymatic cutting during library preparation and PCR amplification.…”

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

“…This removed all sequences identified as chimeric by DECIPHER (as well as other rare sequences) but retained the 'false positives' referred to above. Sequences were binned into OTUs by using USearch 6.0 (drive5) (Edgar 2010), set at 95% sequence identity between reads (Supplementary Table 2) (Wooley et al, 2010). Bacterial 16S rRNA gene reads were aligned against SILVA (v.115; Max Planck Institute for Marine Microbiology, Bremen, Germany) and fungal ITS reads were aligned against the full Genbank database.…”

Characteristic changes in microbial community composition and expression of innate immune genes in acute appendicitis

“…Typically, an OTU is assigned using rDNA sequences, where a percent similarity threshold is set for classifying microbes within the same, or different, OTUs. 24 Following this, a sample/OTU table stating the number of sequences belonging to a certain OTU for each sample was created. This sample/OTU table was further utilized for comparative analysis of microbial diversity in the samples.…”