E. coli K-12 Evolution Potentially Undermines its Model Status

A new study published in Microbial Genomics has revealed that the bacterial strain Escherichia coli K-12, which has been used as a model organism in laboratories for the past 100 years, has evolved so extensively that it may no longer be fit for its intended purpose. The research team from Aston University, the University of Birmingham, and the University of Nottingham, made this discovery after re-examining early preserved samples and comparing them to current DNA sequences.

The research found numerous differences in the DNA sequences of the original bacteria and those currently used in labs, highlighting the dangers of using one strain as a sole model. It also confirms that bacterial sequences evolve rapidly over short time scales, providing valuable insights into the evolution of molecular microbiology.

Lead author Doug Browning of the School of Biosciences at Aston University says, “The past 10 years have seen a massive amount of bacterial genome sequencing and the picture that is emerging is that bacterial genomes change very fast. This was unimaginable 100 years ago, and, of course, this is why folk back then were quick to adopt the K-12 strain as the model for everything.”

Escherichia coli K-12 was first isolated in 1922 from the feces of a patient at Stanford University and has since become a cornerstone of molecular biology research. However, due to its repeated culture, passaging, and mutagenization over the past century, the bacterium has developed many genetic changes that may raise questions about its continued use as a model organism.

The research team sequenced the genomes of two ancestral E. coli K-12 strains, WG1 and EMG2, to understand more about the bacterium’s evolution. Their analysis confirmed that the strains still carry genetic elements such as bacteriophage lambda and the F plasmid, but also indicated that they have undergone extensive laboratory-based evolution.

While the number of genetic variations may represent new research opportunities for some, it also highlights the importance of considering the evolution of model organisms and whether they are still fit for purpose. The findings of this study may prompt researchers to consider using alternative bacterial strains or a combination of strains for future experiments.