There are more microbes in, on and around the planet than there are stars in the sky. However, the vast majority of these microorganisms have not yet been studied, in part because many of them do not thrive when moved out of their natural environment.
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A spoonful of soil contains a complex and diverse microbial community. Informatics capabilities are proving to be bottlenecks in metagenomicstudies.  by Chiot’s Run |
Sequencing microbial communities or metagenomes allows researchers to get around this obstacle and assess individual species within a community. Advances in sequencing technologies have led to more in-depth analyses of complex and diverse communities. However, the bioinformatics tools have not scaled in conjunction.
In an article published in the February 2012 issue of Current Opinion in Biotechnology, DOE JGI’s Patrick Chain at Los Alamos National Laboratory and colleagues discuss the bottlenecks in current metagenomic studies. One example of an informatics obstacle is that the short-read sequencing algorithms currently used to assemble individual genomes from a community take up too much computer memory. Another problem is that the current annotation tools used for metagenomic studies are based on bacterial annotation tools and as such, don’t consider the viral or eukaryotic components of the sample.
“The computational resources required for assembly, annotation and analysis have already become the main bottlenecks for metagenomics projects,” the researchers wrote in their conclusion. “It is highly probable that sequencing centers will begin to serve principally as bioinformatics resources that lend computational resources and expertise to the community. However, without novel algorithms for assembly and analysis, it is clear that the sheer volume of sequencing data will overwhelm available resources.”