Prized Paper

(December 14th, 2015) What is your favourite scientific paper from last year? The PLOS Genetics editorial team recently picked their winner: E. coli adaptation to a novel environment by scientists from the Gulbenkian Institute in Portugal.

Since its foundation in 2005, PLOS Genetics has published an enormous amount of invaluable studies on gene discovery, comparative and functional genomics or chromosome biology. In light of its 10th anniversary this year, the editors decided, amongst other things, to offer a monetary prize to a group of scientists, who published their work in PLOS Genetics in 2014. Nominated articles were judged according to scientific excellence and community impact. After ticking all the boxes on the editors’ requirements sheet, the paper “The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps” came off as the big winner. Authors João Barroso-Batista, Ana Sousa, Marta Lourenço, Marie-Louise Bergman, Daniel Sobral, Jocelyne Demengeot, Karina B. Xavier and Isabel Gordo from the Instituto Gulbenkian de Ciência, Oeiras, Portugal were extremely delighted to receive the news.

The team from Portugal analysed the population dynamics of 450 generations of gut Escherichia coli (E. coli) in different mouse individuals, to find out how the bacteria adapt to a novel environment. “One of the most complex natural environments for E. coli is the mammalian intestine, where it evolves in the presence of many species comprising the gut microbiota,” the authors write in their paper. But how do the bacteria do it? Nice and slowly or intensely, fighting hard competition? “Adaptation to novel environments involves the accumulation of beneficial mutations. If these are rare the process will proceed slowly with each one sweeping to fixation on its own. On the contrary if they are common in clonal populations, individuals carrying different beneficial alleles will experience intense competition and only those clones carrying the stronger effect mutations will leave a future line of descent. This phenomenon is known as clonal interference,” Barroso-Batista et al. summarise.

After four years of hard work, the team was able to demonstrate that an initial phase of soft and slow adaptation, is followed by “a regime of intense clonal interference where haplotypes carrying more than one beneficial mutation compete for fixation”. The scientists revealed that bacterial clones claimed their own niche among the mouse gut microbiota in less than a week. To further prove their point, the researchers successfully reproduced these results on multiple occasions using different mice. The results show, for the first time, the evolutionary complexity of gut microbiota in a healthy organism.

The PLOS Genetics Research Prize winners are hopeful that their work will open new research possibilities into the study of the complex E. coli population dynamics in the human gut. “The recognition of our research gives us great enthusiasm to continue future experiments in this theme. The value of the prize (US$5,000) is a great benefit to us, since it provides financial support for a fellowship to continue this work”, says principal investigator Isabel Gordo.

Nadejda Capatina

Photo: Siedlecki

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