Top Reasons E. coli Is Used for Gene Cloning

The microorganism Escherichia coli has a long history of use in the biotechnology industry and is still the microorganism of choice for most gene cloning experiments. Although E. coli is known to the general population for the infectious nature of one particular strain (0157:H7) few people are aware of how versatile and useful E. coli is to genetic research. There are several reasons E. coli became so widely used and is still a common host for recombinant DNA.

Genetic Simplicity

SEM Micrograph of E coli on keyboard
Rolf Ritter/Cultura Science/Oxford Scientific/Getty Images

Bacteria make useful tools for genetic research because of their relatively small genome size compared to eukaryotes. E. coli cells only have about 4,400 genes whereas the human genome project has determined that humans contain approximately 30,000 genes. Also, bacteria, including E. coli, live their entire lifetime in a haploid state, with no second allele to mask the effects of mutations during protein engineering experiments.


Weaver, R. and Hedrick, P. 1989. Genetics. Wm. C. Brown Publishers, Dubuque, IA, USA.

Madigan, M., Martinko, J. and Parker, J. 2000. Brock Biology of Microorganisms, 9th ed. Prentice Hall, Upper Saddle River, NJ, USA.

Growth Rate

Bacteria typically grow much faster than more complex organisms. E. coli grows rapidly at a rate of one generation per twenty minutes under typical growth conditions. This allows for preparation of log-phase (mid-way to maximum density) cultures overnight and genetic experimental results in mere hours instead of several days, months or years. Faster growth also means better production rates when cultures are used in scaled up fermentation processes.


E. coli is naturally found in the intestinal tracts of humans and animals where it helps provide nutrients (vitamins K and B12) to its host. There are many different strains of E. coli that may produce toxins or cause varying levels of infection if ingested or allowed to invade other parts of the body. Despite the bad reputation of one particularly toxic strain (O157:H7), E. coli are generally relatively innocuous if handled with reasonable hygiene.

Conjugation and the Genome Sequence

The E. coli genome was the first to be completely sequenced. Genetic mapping in E. coli was made possible by the discovery of conjugation. E. coli is the most highly studied microorganism and an advanced knowledge of its protein expression mechanisms makes it simpler to use for experiments where expression of foreign proteins and selection of recombinants is essential.


Weaver, R. and Hedrick, P. 1989. Genetics. Wm. C. Brown Publishers, Dubuque, IA, USA.

Ability to Host Foreign DNA

Most gene cloning techniques were developed using this bacterium and are still more successful or effective in E. coli than in other microorganisms. E. coli is readily transformed with plasmids and other vectors, easily undergoes transduction, and preparation of competent cells (cells that will take up foreign DNA) is not complicated. Transformations with other microorganisms are often less successful.