New insights into the vast diversity of nature’s most abundant viruses

Phages, viruses that infect bacteria, are the most abundant and diverse biological entities on earth, where they can be found anywhere from soil to oceans to the human gut — and typically outnumber bacteria and other cellular organisms 10-fold. They are so abundant in the natural environment, in fact, that scientists have long speculated that each species of phage relies on different strains of their host bacteria, a kind of winner-take-all champion in its own particular microbiome. 

A new study reveals a different story, suggesting that multiple phage species can coexist even when competing for a single, genetically identical population of bacterial cells. 

The reason, researchers say, is that each species of phage has its own “niche,” with each virus specializing on a subpopulation of bacterial cells that have different growth phenotypes.

The findings, published in the journal Science, offer new insights into the emerging study of virus “social lives” (virus-virus interactions), contradicting the notion that species will struggle to compete over shared resources, the researchers say.

“Much like the diversity we find in the macroscopic world, these microscopic entities can compete and coexist,” said Nora Pyenson, who conducted the research as a member of the lab of Yale’s Paul Turner and is now a postdoctoral fellow at New York University. “This discovery helps explain and uncover a new mechanism supporting the incredible diversity of phages found in nature.”

For the study, Pyenson collaborated with Turner, the Rachel Carson Professor of Ecology & Evolutionary Biology in Yale’s Faculty of Arts and Sciences and director of the Center for Phage Biology and Therapy at Yale, and of Yale’s QBio Institute.

In his Yale lab, Turner and his team are developing phages to treat bacterial infections, a line of research that has emerged as a new frontier in the treatment of drug-resistant bacterial infections. (“Phage” is short for bacteriophages, or “bacteria eaters.”)

For the study, the researchers isolated different mixtures of phage species collected during field work in and around New Haven. They examined whether these viruses could grow on the same bacterial population, by allowing the phages to infect bacterial cells that were replenished every 24 hours, Pyenson said. After 12 days, they determined which phage species were present and then sent their genomes for deep sequencing. 

Their finding that single bacterial populations tend to become portioned into cells at different growth stages, Turner said, helps explain why such a diverse range of phage species can coexist in the same system, a phenomenon that might otherwise violate the principle of competitive exclusion, which predicts that only the best competitor in a system should thrive on a single, limiting resource.

“One of Yale’s most influential biologists, the ecologist G. Evelyn Hutchinson, famously grappled with the ‘paradox of the plankton’, where he sought to understand why so many plankton species can inhabit aquatic systems given the often-limited nutrients and other resources available,” said Turner. “Our study similarly suggests that we’ve underestimated niche availability for phages, and how differing growth stages of host cells alone can help explain the abundance and diversity of phage species seen in nature.”

The results also offer key insights in the development of phage treatments. Specifically, the findings suggest that phages administered to patients may not successfully kill the diverse physiologies of the infecting bacterial population. For instance, phage therapy shows promise in treating lung infections caused by Pseudomonas aeruginosa in cystic fibrosis patients, Pyenson said. But these bacteria will have many different physiological states, even within a single person’s lung. 

Phage therapy may be more successful, the new study suggests, if researchers can find phage species to target all the bacterial physiological “niches” that are present within an infection. 

“Currently, when phage therapy fails to kill all the bacteria, we find that the bacterial populations evolve resistance to the phages,” Pyenson said. “This is similar to how bacteria can evolve antibiotic resistance if they survive antibiotic treatment. If we can design phage therapies that consider the physiological diversity of the host cells, then we will be better able to treat infections and avoid this arms race.”

One finding in the new study is that most phage species negatively interact with one another, inhibiting the growth of other species even while they were able to coexist, Pyenson said. However, the researchers also found that some phage species did not interfere with the replication of their community partner. 

“We could improve phage therapy if we studied phage-phage interactions as a factor in determining which phage species to use in a mixture, or cocktail,” she said. “Ideally we would want phage species that can synergize with one another and do not negatively impact the fitness of another phage species.”

Other authors of the new study include Asher Leeks and Odera Nweke, former members of Turner’s Yale lab, and researchers from New York University, California Institute of Technology, the University of Oxford, and the University of Salamanca.