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A study in Nature Ecology & Evolution reveals a surprising evolutionary insight: sometimes, losing genes rather than gaining them can help bacterial pathogens survive and thrive.

The study was conducted by a group of scientists and coordinated by Jaime Martínez Urtaza, from the Department of Genetics and Microbiology of the Universitat Autònoma de Barcelona (UAB); Yang Chao and Falush Daniel, from the Shanghai Institute of Immunity and Infection, Chinese Academy of Science; and Wang Hui, from the Shanghai Jiao Tong University.

When we think of evolution, we often imagine organisms changing or gaining new genes to adapt, such as growing wings, developing resistance, or evolving new behaviors. Across the tree of life, both spontaneous mutations and gene acquisition are classic tools of adaptation. However, in this study, researchers went down a lesser known and scarcely explored evolutionary path, the one of gene loss.

The research focused on Vibrio parahaemolyticus, a bacterium behind many of the seafood-related infections worldwide, mainly those related to foodborne diseases, but also the cause of infections when seawater comes in contact with open wounds.

In particular, researchers studied a pandemic clone of the bacterium, made up of several subtypes or strains. This expanding clone is mainly present in Asia, where it was first detected in 1996 in Japan, and significant outbreaks have been subsequently reported on the west coast of the U.S. and in some Latin American countries such as Chile, Peru and Mexico.

In Spain, it was first detected in 2004, in Galicia, where it caused an outbreak of gastroenteritis that affected eighty people.

While studying the evolution of this pathogen, researchers noticed that different subtypes of the bacteria seemed to replace each other over time, like waves in the ocean.

Eventually, a dominant type, called Wave-4, took over and caused the majority of human infections. This dynamic was similar to how COVID-19 variants (alpha, delta, omicron) replaced each other during the pandemic.

Thanks to the analysis of Wave-4's genetic blueprint to understand what gave it its competitive edge, researchers discovered that it was not a new gene or a mutation that made this strain dominant, but rather the loss of certain genes.

How gene loss helps bacteria succeed

The group of genes Wave-4 had lost are involved in the use of putrescine, a small molecule found in the environment and in the human gut. Without these genes, the bacteria gained advantages in two key areas.

First, in environmental survival, since it could form more resistant biofilms, which protect the bacteria from stress and make it easier to adhere to surfaces, allowing it to survive during the long journeys from one point on the planet to another. And second, in human transmission, sticking to human cells more easily and colonizing the gut more effectively.

Gene loss also produces weaker bacterial infections. This supports the evolutionary idea known as the virulence trade-off hypothesis. Pathogens that are too deadly (high virulence) may kill their host too quickly and thus fail to spread.

In contrast, pathogens that strike a balance between harming and spreading, such as the seasonal flu, can become more successful over time. This trade-off might explain why Wave-4 became so dominant.

A common strategy across species

In the study, researchers also found similar gene loss in other bacterial species, such as Vibrio cholerae and Escherichia coli, which also resulted in stronger biofilms and greater cell adhesion. This points to a case of convergent evolution, which is produced when different organisms independently evolve similar traits because they face similar challenges.

According to the scientists, gene loss could be a common, powerful and underappreciated mechanism for adaptation in bacteria.

"For a long time, gene loss was seen as a kind of biological decay," says Yang Chao. "But our study shows it can be just the opposite—a smart evolutionary move. In our model species, it wasn't mutation or gene gain that made the pathogen more successful—it was losing the right genes at the right time."

An enigma solved after 30 years and yet another to be discovered

The findings of the study shed light on an enigma that had not been solved in the past 30 years related to the global expansion of V. parahaemolyticus. And this was possible thanks to the volume of data currently available: the scientists worked with a set of large-scale genomic data from around the world, with 8,600 genomes representing six continents and 34 countries.

The research provides "the most complete genomic view of the origin and evolution of the pandemic clone V. parahaemolyticus and allows inferring the history of its geographic transmission. A future study will give us new important hints about how these types of pathogens manage to travel from continent to continent through oceans," says UAB Professor of Genetics Martínez Urtaza.