Fast and Furious: E. coli edition

Andrew Kirsop

After studying thousands of generations of E. coli, UT scientists have discovered something unexpected: Some strains of the bacteria evolve much faster than previously thought.

Jeffrey Barrick, an assistant professor of molecular biosciences at UT and co-author of the study published in scientific journal Nature, worked with an international team to research over 50,000 generations of E.coli. Barrick and his team analyzed hundreds of complete genomes from 12 different populations of the bacteria using software they developed. 

Through their work, they reconstructed evolutionary histories of E. coli populations and determined the impact of specific mutations.

“This is one of the first studies where people have started merging microbiology and evolutionary biology, which is a large part of what makes this study so unique,” Barrick said. “People who studied those fields had trouble getting well-controlled experiments.” 

The samples used for the study came from a collection of E. coli curated by Richard Lenski, a professor of microbiology and molecular genetics at Michigan State University. Lenski’s E. coli, some of which had been stored in freezers from as early as 1988 as part of his Long-term Evolution Experiment, were revived and further examined for mutations in DNA. The data and bacteria from the experiment have proved phenomenally helpful for the study, Barrick said. 

Scientists studying microbes have generally thought that mutations are passed down at a predictable rate, and those mutations are almost always neutral in terms of helping the organism adapt to its environment, according to Barrick. 

The study found some strains of bacteria can mutate at higher rates than others and most mutations passed on were beneficial. 

“This could have implications for personalized medicine, as it suggests that E. coli in my gut will evolve idiosyncratic differences from those in your gut over time,” Barrick told UT News. 

Half of the populations evolved to mutate at a faster rate, dubbed “hypermutating” strains. Additionally the mutations were able to slow down when there were fewer ways to improve and the E.coli had reached its fitness peak. Barrick said the populations were as adaptable in the lab as they would be in nature, meaning evolution experiments could be completed in a short time frame.

This study helped provide valuable data in a setting with fewer variables and many more generations to analyze than most conducted in the field, according to Barrick. 

“I think the coolest thing about this study is that they show that most mutations that actually reached high frequencies were those that were beneficial, and thus favored by natural selection” said Claire Hemingway, an evolution teaching assistant at UT. 

When bacteria with higher mutation rates breed more, they are more likely to adapt and thrive, especially the hypermutating strains, Hemingway said.

“With bacteria you can make these evolutionarily relevant statements with 50,000 generations which is unmatched in any other systems,” she said.

The assumption that mutations occur steadily over time is an integral piece of dating models for how long ago related organisms diverged, Barrick told UT News. The possibility that bacteria may have variable mutation rates is therefore a big deal in the evolution community. 

“I think that instead of saying that this challenges most of our models it would be more accurate to say that data like this helps to inform our models empirically,” Hemingway said.

Environmental science junior Blake Bringhurst said he found the results of the study surprising. Bringhurst, who is currently taking an evolution course, said this study could potentially change scientists’ understanding of evolution. 

“[The research] seems tedious and boring, with lots of replication, but I can definitely see the benefits for evolutionary theory,” Bringhurst said.