Our paper was one of the first in a relatively new field, known as metagenomics or environmental genomics, in which DNA is isolated directly from environmental samples and shotgun sequenced without screening or amplification. A number of subsequent papers have used the gene-centric approach described in this study, as opposed to the organism-centric approach previously taken, to analyze extremely complex metagenomic data.

“We demonstrated that DNA sequence can be a valuable tool in understanding the biochemistry of microbial communities inhabiting various environmental niches, providing insights into the environment.”

Yes, it presents an analytical approach that allows one to compare the genomic potential of environmental microbes in the absence of genome assembly. Previously, lack of genome assembly had been seen as the major hurdle to productive application of shotgun sequencing to complex microbial communities. Our method compares samples based on the functional annotation of short sequence segments, which we refer to as Environmental Gene Tags (EGTs).

We demonstrated that DNA sequence can be a valuable tool in understanding the biochemistry of microbial communities inhabiting various environmental niches, providing insights into the environment.

Our institution, the Department of Energy’s Joint Genome Institute, is one of the largest sequencing centers in the US and has a large microbial genome program. Metagenomics seemed like a natural expansion to this program. The major obstacle we encountered was the low sequence coverage obtained from the organisms in the sample, which we overcame by using the gene-centric EGT approach.

We are currently using the EGT approach to advance bioenergy technology and thus reduce our dependence on oil. For example, we are analyzing DNA sequence from the cellulolytic consortium of organisms found in the termite digestive system to identify new enzymes involved in the breakdown of lignocellulosic material. Harnessing these enzymes could eventually allow us to exploit new sources of energy, such as corn stover, poplar trees, or switchgrass.