Oysters filter seawater for food. In the process, they concentrate a wide variety of microorganisms from their environment—including bacteria and viruses—into a tiny space.
At the Institut Courtois d’innovation biomédicale, a team led by Frédérique Le Roux, a professor in UdeM’s Department of Microbiology, Infectiology and Immunology, used oysters as living mini-laboratories to track the evolution of microbial communities in a marine environment over a four-year period.
“The oyster isn’t just a farmed species for human consumption,” explained Le Roux, holder of the Canada Excellence Research Chair in Eco-Evo-Patho of Microbes in Nature. “It can also be an extraordinary research tool for exploring the abundance and diversity of microbial communities, and their interactions.”
In their four-year study recently published in Nature Communications, Le Roux and her team revealed an unexpected paradox: Some populations of bacteriophages—viruses that infect only bacteria—remained stable despite intense genetic activity in the bacteria they infected.
“In an open marine environment with tides and constant water movement, where there are strong evolutionary pressures on microbial communities, this stability is surprising,” Le Roux said. She had expected rapid changes in viral populations.
This discovery could help predict how microbial communities will evolve in response to environmental change, she said.
Working with colleagues in France at the Institut Pasteur, the Roscoff Biological Station (affiliated with Sorbonne Université and the Centre national de recherche scientifique) and the Institut français de recherche pour l’exploitation de la mer, Le Roux’s team found that oysters facilitate horizontal gene transfer, a process by which bacteria directly exchange DNA fragments.
Unlike complex organisms, which pass genes primarily to their offspring, bacteria can rapidly acquire new functions from other bacteria.
“This is a much faster driver of evolution than genetic mutations,” Le Roux said. “The transfer of genetic material supports the circulation of genes that promote adaptation, resistance and survival.”
Highly controlled experiments
Currently, most of what scientists know about the dynamics of microbial ecosystems comes from highly controlled laboratory experiments.
To understand how microbial communities evolve in the natural environment, Jeffrey Liang, a postdoctoral fellow in Le Roux’s lab and co-first author of the study, compared samples from an oyster farm in northwestern France’s Bay of Brest taken four years apart.
The Montreal team analyzed more than 1,000 bacteriophages and 600 genomes of Vibrio crassostreae, a marine bacterium in the Vibrio genus, to compile one of the most comprehensive datasets ever assembled for this type of marine ecosystem.
Sentinels of ecosystem health
In addition to serving as a natural laboratory for microbial evolution, oysters could also become sentinels of marine ecosystem health, Le Roux believes.
She and her team are preparing a project to track the evolution of certain Vibrio species in Quebec, in Chaleur Bay off the Gaspé Peninsula, to better understand the effects of climate change on these environments.
Publication details
Jeffrey Liang et al, Complex temporal dynamics of phage-bacteria populations in an animal-associated marine system, Nature Communications (2026). DOI: 10.1038/s41467-026-71398-9
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