Scientists have studied tens of thousands of generations of E. coli bacteria, which they brought out from a nearly 30-year rest in the freezer for the research.
In a paper published in the current issue of Nature, the team sequenced the entire genomes, or genetic code, of the bacteria to pinpoint the genes with beneficial mutations that gave the bacteria a competitive edge over their ancestors.
Being able to go back into the freezer to study samples from years ago is one of the reasons Richard Lenski, professor of microbiology and molecular genetic at Michigan State University, calls the long-term evolution experiment, or LTEE, “the experiment that keeps on giving.” The experiment has now surpassed 65,000 generations.
“One of the nice things about such a long-term experiment is that new technologies come along that didn’t exist when I started the LTEE in 1988,” says Lenski.
“The first bacterial genome was not sequenced until 1995, and now, in this single paper, we’ve sequenced 264 complete genomes from this one experiment.”
The team sequenced hundreds of E. coli genomes to examine how the bacteria had changed in their DNA over 50,000 generations. The researchers found more than 14,000 changes across the LTEE’s 12 populations. Each population changed in different ways, but there were some important commonalities as well.
Most significant, and most simply, the mutations were concentrated in a subset of the genes—those where mutations gave the bacteria a competitive edge. One of the striking differences that arose between populations is that half of them evolved to mutate at much higher rates than the other populations, even though they all started from the same ancestral strain that had a low mutation rate.
“Even in the simplest microcosm we can imagine to study evolution—a single bacterium kept in the laboratory under monotonous conditions for years—we are learning new things about the rates and processes of evolution,” says Jeffrey Barrick, an assistant professor of molecular biosciences at the University of Texas at Austin. “This quantitative information is important for human health, as it improves our ability to predict how bacteria evolve, particularly in chronic infections and in our microbiome.”
Researchers from several institutions, including Michigan State, Université Paris Diderot, the University of Massachusetts, and ETH Zurich, took part in the project. The National Science Foundation contributed funding to Lenski’s work.
Source: Michigan State University