Metagenomics
is infinitely scalable, and so it is difficult to know if it is cheaper than traditional methods. To process the first 10,000 samples from the Earth Microbiome Project (see below) using 16S rRNA amplicon metagenomics has cost approximately $576,000. This is significantly cheaper than existing methods for typing samples, although there are cheaper methods out there, they often lack taxonomic or sample resolution. It is currently possible using the EMP’s pipeline to process (amplify, sequence, click here analyze and publish data online) ∼500 environmental samples in under 5 days. So this technique is considerably faster than anything used before. The method achieves higher longitudinal, cross-sectional and taxonomic/functional resolution than ever achieved previously. Potential advantages of Phylogenetic Diversity (PD)-based biodiversity analyzes discussed earlier for DNA barcodes also extend to metagenomics contexts. A recent review of microbial ecology applications, by McDonald et al. (2013) notes the advantages of the phylogenetic diversity framework: “Phylogenetic diversity calculations allow us to determine the relative similarity of microbial communities, using similarity of the fragment of the marker gene as a proxy for the relatedness of the organisms represented by those marker genes⋯in
practice the difference in gene content between two organisms closely tracks the differences in marker genes such as the 16S rRNA gene.” They noted in contrast the weaknesses of operational taxonomic units or OTUs: Dichloromethane dehalogenase “⋯this definition is known to be problematic for several reasons. One is that the rate of Epigenetic signaling inhibitors evolution of the 16S rRNA gene differs among taxonomic lineages. The PD-based measures of similarity among samples or communities open the door to a range of strategies for assessment and monitoring. Indeed, many methods conventionally employed at the species level (e.g. analyzes based on ordinations) extend directly to PD analyzes (Faith et al., 2009). These offer fresh prospects for the toolbox for marine monitoring, including assessments of marine health. While shotgun metagenomics
has considerable advantages over amplicon metagenetics (e.g. it does not involve PCR amplification or primer biases), it also has some notable limitations. Firstly, some studies have reported that the abundance of taxa and their functional genes in a metagenomic library do vary depending on the DNA extraction protocol used to acquire the nucleic acid from the environmental sample. Secondly, metagenomic datasets are often only sequenced to a low depth compared with the quantity of DNA in a sample, which results in only the extremely dominant populations being observed. Thirdly, it is difficult to annotate the function or taxonomy of a short sequence fragment, resulting in a large portion of data lacking an appropriate annotation. The Earth Microbiome Project (EMP; http://www.earthmicrobiome.org) (Gilbert et al.