The Microbiome’s Most Abundant Resident

Bacteriophages infecting our bacteria can impact their bacterial hosts in various ways. Some phages operate as straightforward predators of bacteria, others form surprisingly intricate – and at times even mutually beneficial – relationships with their hosts. In the gut, phages can shape the composition, diversity, and function of bacterial populations.

One obvious influence is through bacterial lysis — the killing of specific bacteria — which can directly affect human health depending on whether the target is harmful or beneficial. For example, eliminating a pathogen like Salmonella enterica, a major cause of foodborne illness, can reduce infection risk. In contrast, destroying a beneficial bacterium such as Bacteroides fragilis, which helps produce vitamin K for blood clotting and supports immune regulation, can disrupt essential physiological processes.

But phages’ influence extends far beyond simply killing bacteria. Many can integrate their genetic material into the bacterial genome, altering bacterial metabolism, toxin production, or resistance to environmental stress. In doing so, they can modify how bacteria interact with one another, sometimes fostering cooperation, other times intensifying competition. They can also change the way bacteria engage with the human immune system, potentially dampening inflammation or, conversely, triggering immune overactivation.

P-crAssphage is among the most prevalent and abundant phages in the human microbiome, found in individuals in every corner of the world. It was first ‘discovered’ in DNA sequencing data from human stool samples in 2014. Since that time, no one has been able to reliably grow it outside the human body, and researchers haven’t been able to isolate it in a test tube. Hints from prior efforts to isolate and study p-crAssphage suggested that it has an unusual life cycle and that it doesn’t readily kill its host, suggesting that it may have a more cooperative interaction with its host bacterium. In spite of its abundance in the gut, we had been unable to study it effectively in the lab until now.

Phages typically kill their host cells to release new viral particles, leaving visible “plaques” on a Petri dish in standard lab tests. Traditional isolation methods rely on spotting these plaques, but that approach misses phages like p-crAssphage, which don’t kill many of their hosts. Instead, p-crAssphage produces very few viral particles and keeps most of its DNA inside bacterial cells.

Because plaque-based methods overlook such phages, they’ve been largely unstudied. Developing new ways to detect and grow them is important, as research shows most phages in the human gut aren’t actively killing bacteria. Studying these phages will help us understand how they influence their bacterial hosts — and in turn, how they may affect or even benefit human health.

Both phages and plasmids are “mobile genetic elements” — pieces of DNA that have to hitchhike inside a bacterial host to survive and reproduce. (Fun fact: plasmids were first discovered in 1952 by former Stanford faculty member and chair of the Genetics Department, Nobel Laureate Joshua Lederberg!)

We think p-crAssphage has been evolving alongside its bacterial host for a very long time, and over that time it’s learned how to infect that host in a way that causes minimal harm. If a phage constantly kills its host, it may wipe out said host, or force the host to evolve resistance, outcomes which would limit the phage’s ability to persist. By contrast, a phage that can quietly remain in many cells at once, without killing them, gains a big survival advantage.

P-crAssphage can thus switch between two strategies: sometimes producing viruses and releasing them from the host, and sometimes living harmlessly inside as a plasmid. This flexibility of being able to toggle between aggressive and low-impact modes is likely a key reason why crAssphage is so common around the world.

Our research determined p-crAssphage is the first major human microbiome-related phage that has this ‘duality’ of lifestyles. We think that this phage can replicate harmlessly inside of its bacterial host (or even benefit its host) and change the gene functions that are available to these hosts. Therefore, this phage might change the amounts or types of bacteria that are present in the microbiome through methods other than cell death. Understanding how it interacts with bacteria or other phages in the gut allows us to better understand how to manipulate the microbiome to promote health and prevent infection.

We plan to continue studying p-crAssphage to better understand how it affects its bacterial hosts. Over time, we hope to expand this research to explore its interactions with human hosts as well — and whether it might influence disease, either by offering protection or, in some contexts, promoting illness.

By defining what a “healthy” microbiome and its accompanying viral community look like, we can more easily recognize when they become “unhealthy” and develop strategies to restore balance and promote health.