Gregory Stephanopoulos, a chemical engineer at MIT and a leader in the metabolic-engineering field, is more skeptical about the impact of the San Diego approach. Sequencing genomes and analyzing them to find relevant mutations is not the problem, he says. In Palsson and Herring's growth experiment, it was obvious that E. coli that grew well were worth resequencing to find the relevant mutations, he says. But when working on a complex problem like improving a microbe's ethanol-production efficiency, he says, "in some cases you can identify superior strains, but in general it's not straightforward."

Still, Stephanopoulos and the others say that comparative genome sequencing can now help researchers attribute changes in microbes' traits (such as the ability to thrive on glycerol) to changes in genotype. In doing so, the technology could help microbiologists and pharmaceutical companies study how strains of antibiotic-resistant bacteria, a major health problem, emerge, and what mutations are responsible.