Jonathan A Eisen

“ Binning increases in difficulty exponentially as the number of species increases: the populations and species start to merge together, and the populations get more and more polymorphic and variable in relative abundance (such as in the paper about the Global Ocean Sampling expedition in this issue [25] ) . Further complicating binning is the phenomenon of lateral gene transfer, where genes are exchanged between distantly related lineages at rates that are high enough that random sampling of a genome will frequently include genes with multiple histories. ”

“ Abstract Environmental shotgun sequencing promises to reveal novel and fundamental insights into the hidden world of microbes, but the complexity of analysis required to realize this potential poses unique interdisciplinary challenges.Since their discovery in the 1670s by Anton van Leeuwenhoek, an incredible amount has been learned about microorganisms and their importance to human health, agriculture, industry, ecosystem functioning, global biogeochemical cycles, and the origin and evolution of life. ”

“ A community is, of course, more than a list of types of organisms. One approach to understanding the properties and functioning of a microbial community is to start with studies of the different types of organisms and build up from these individuals to the community. ”

“ Some universal protein coding genes are better than rRNA both for distinguishing closely related strains (because of third position variation in codons) and for estimating numbers of individuals (because they vary less in copy number between species than do rRNA genes) [8] . Perhaps most significantly, ESS is providing groundbreaking insights into the diversity of viruses [18] , [19] , which lack rRNA genes and thus were left out of the previous revolution. ”

“ This is largely because physical appearance does not provide a valid taxonomic picture in microbes. Appearance evolves so rapidly that two closely related taxa may look wildly different and two distantly related taxa may look the same. This vexing problem was partially overcome in the 1980s through the use of rRNA-PCR (Table 1) . This method allows microorganisms in a sample to be phylogenetically typed and counted based on the sequence of their rRNA genes, genes that are present in all cell-based organisms. ”

“ Such searches need to be done with caution because any time you analyze such a large amount of data patterns can be found. In addition, as with the Internet, there is certainly some hype associated with ESS that gives relatively trivial findings more attention than they deserve. ”