by Gregory Brunette
figures by Daniel Utter

Every year, new biology students dig for tiny, bacteria-infecting viruses called phages. Short for bacteriophages, these ubiquitous viruses thrive unseen in the world around us, replicating endlessly through their host bacteria. Phages outnumber all other living organisms on Earth; and their overwhelming diversity presents a challenge to the researchers who study them. In a program administered by Dr. Graham Hatfull at the University of Pittsburgh, “phage hunters” learn the science of collecting, isolating, and characterizing these phages from the soil.

Hatfull’s program takes a crowd-sourcing approach to discovery, with beginner scientists working in parallel to uncover different phages around the globe. A database of 17,652 phages represents the collective efforts of these students, who now number in the thousands. This database provides a resource to phage researchers who strive to understand the diversity of processes used by phages to persist and multiply. Beyond this, there is growing interest in the therapeutic potential of phages, which infect a broad range of bacteria, including the ones that infect us.

Bacteria’s natural enemy 

“Superbug” bacterial infections like C. difficile and MRSA emerge when antibiotic treatment favors the survival of resistant bacteria. Over time, these infections become unresponsive to the antibiotics originally used to treat them. In response, scientists continue developing new antibiotics at great effort and cost, all with the understanding that once enough bacteria are exposed to the drug, new resistant cases will almost certainly emerge. But while bacteria’s ability to evade killer antibiotics continues to vex clinicians, phages have maintained their ability to infect bacteria over millions of years, outsmarting their hosts’ evolution by adapting in tandem.

When phages infect bacteria, they can hijack the host cell, using its machinery to copy themselves over and over. Then, the bacterial cell explodes, releasing newly made phages (Figure 1). This cycle progressively kills the surrounding bacteria. Doctors could take advantage of this process, using phages that are tailored to a patient’s bacterial infection. But how do the phages isolated from the soil by phage-hunters make it from the dirt to the clinic?

Digging for discovery

“Phage hunting” begins with students collecting soil and water samples from the outdoors (Figure 2). Phages are so abundant and diverse that each sample has a high chance of containing a novel phage. Once phages have been isolated from the sample, they can be grown in host bacteria that are cultured in the lab. In the lab, phages do exactly what they do in the wild: infect bacteria and multiply. But in the lab’s controlled environment, this allows students to isolate single phages and generate enough material for further study (Figure 2).

Phages can be characterized physically by their size and shape. Adaptations in both have conferred phages with the ability to infect a wide range of bacteria, evading the bacteria’s defense tactics. Phages can also be defined by their genetic material. A phage’s genetic sequence may reveal important clues about its life cycle, including its lethality to host bacteria. 

In addition to a phage’s innate characteristics, phage hunters study the dynamic interactions between phages and the bacteria they infect. Individual phages cannot necessarily infect all species of bacteria. But by systematically exposing individual strains of bacteria to an individual phage, students can determine which types of bacteria a phage will infect, also known as a phage’s host specificity. If a particular bacterium is a good host for the phage, many bacterial cells in the culture will die from the phage infection. By counting the population of bacteria before and after phage exposure, students can determine whether the virus is an efficient killer.

Life-saving science

Information in Hatfull’s phage database became vitally important in June 2018, when antibiotics could no longer treat rampant M. abscessus in a teenage patient recovering from a double lung transplant. While doctors could no longer treat the infection, unhindered M. abscessus continued to spread in the patient, endangering her life. But if the bacteria in this infection could be matched to a phage, the patient could be saved.

One phage, named Muddy, was scraped from the bottom of a rotting eggplant and turned out to be a natural killer of M. abscessus bacteria. However, treatment with a single phage will likely lead to resistance, whereas multiple phages are more likely to wipe out the whole infection. Two additional phages, BPs and ZoeJ, could infect M. abscessus, but were ultimately less lethal to the bacteria than Muddy. Luckily, clues from their genetic sequencing revealed small alteration that Hatfull and his team could make that would give them the same lethality to M. abscessus as Muddy. 

With these modifications, carefully prepared infusions of the three phages were given to the patient, who experienced noticeable improvements within one month of phage treatment (Figure 3). The patient’s infection was effectively cured by the cocktail of phages, and incredibly, she did not experience side effects like the ones that forced her to discontinue antibiotics in the first place.

Locked with bacteria in their ancient battle for survival, phages have developed bacteria-killing capabilities that measure up to modern antibiotics. Because phages naturally prey on bacteria, learning more about phages may aid our own efforts to eradicate drug-resistant bacteria from hospitals. While phages have been used to treat infections in the past, this practice quickly diminished with the rise of powerful antibiotics in the twentieth century. However, as superbugs continue to evade antibiotic treatment, recent reports—along with Hatfull’s study—suggest a comeback for these humble viruses. While the past century has left phages more or less in the dirt, this promising case may bring them out from the soil and into the spotlight.   

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Gregory Brunette is a PhD student in Bioinformatics and Integrative Genomics.

Daniel Utter is a 5th year Ph.D. student in Organismic and Evolutionary Biology at Harvard.

Cover image: “Soil Survey09.tif” by NRCS Montana is licensed under CC PDM 1.0 

For More Information: 

• To learn more about Hatfull’s phage discovery program, check out their homepage.
• The phage database containing Muddy, BPs, ZoeJ, and more can be found here.
• To hear Dr. Hatfull discuss phage discovery and phage therapy, listen to this episode of microTalk, a podcast hosted by the American Society for Microbiology.