The article below is based on a podcast interview with Michael Shamash.
In the intricate world of the human microbiome, where trillions of microorganisms live within our bodies, we often hear mostly about the bacteria. And this is mostly due to the fact that most studies have focused on identifying them and understanding their vital role in maintaining our health. But there’s a group of microbes in the microbiome that scientists are beginning to learn more about: the viruses, collectively known as the virome.
Interestingly, most gut viruses are bacteriophages, which target bacteria rather than us. They interact with the bacteria in our gut microbiome, potentially promoting a healthier gut balance. Understanding their positive role in our microbiome helps shift the narrative about viruses from being solely harmful to a nuanced and balanced view of their role in our bodies.
In this article, you will learn about the remarkable gut virome and how its viruses contribute to our health, the unique viral communities within us, and how harnessing the interaction between viruses and bacteria can potentially benefit our microbiome. This knowledge will help you appreciate the often underestimated world of gut viruses and their essential role in maintaining our well-being.
The Gut Virome
The gut virome is part of a larger ecosystem known as the gut microbiome. This microbiome encompasses various microorganisms, including bacteria, fungi, and viruses, residing in our gastrointestinal tract, primarily in the colon and small intestine. These microorganisms serve vital functions to maintain our health, such as aiding in digestion and supporting a robust immune system.
When we narrow our focus to the gut virome, we’re specifically looking at the viral component of this microbial community in the gut. What’s fascinating is that each individual has a unique virome, even if they live in the same household or have close contact. Recent studies have revealed this distinct “fingerprint” of viral communities in our guts.
The Players: Bacteriophages and Eukaryotic Viruses
Most of these viruses are bacteriophages, which means they target and interact with bacterial hosts rather than harming us directly. However, there is also a smaller fraction of eukaryotic or human viruses present, depending on factors like viral infections.
The Role of Gut Viruses
Now, let’s delve into the role of these viruses in the gut. Bacteriophages, being bacterial predators, can influence the metabolic activities of the bacteria they interact with. This influence might involve killing certain bacteria or altering their metabolic and physiological functions. Importantly, this isn’t necessarily a negative impact; it’s simply a dynamic interaction happening constantly in the gut.
In fact, we can potentially harness this interaction for our benefit. For instance, we could use specific phages that target harmful or pathogenic bacteria in the gut. This approach holds promise as a way to promote a healthier microbial balance in our digestive system.
Should we be worried about viruses in us?
The idea of viruses living within us might be surprising and even a little worrying. But fear not, because most of the viruses in our bodies are not harmful to us. As mentioned earlier, they are mostly bacteriophages, which target bacteria, not us. And just like we’ve become accustomed to the idea of beneficial bacteria in our gut, we’re gradually learning that there are also beneficial viruses that coexist with us. Despite the recent challenges posed by viruses like the one that caused the COVID-19 pandemic, it’s essential to recognize that there are viruses that don’t directly harm us and may even play a positive role in our microbiome. This perspective can help shift the narrative about viruses from being solely harmful to having a more nuanced and balanced view of their role in our bodies. So, rest easy knowing that these viruses are simply a part of our gut microbiome interacting with the bacterial inhabitants within our gut ecosystem and potentially serving us in positive ways.
Phage Therapy vs. Probiotics
In light of our increasing understanding of the importance of the microbiome, there has been much interest in ways to harness the power of these microbes through probiotics. Probiotics are live microorganisms, often bacteria or yeast, that may provide various health benefits when consumed. These benefits include aiding digestion, supporting the immune system, and maintaining a healthy balance of gut microbiota.
However, does the idea of probiotics apply to our gut virome? Can we create a “phage version” of a probiotic?
The closest treatment we have to a viral probiotic is phage therapy. Phage therapy, however, differs greatly in its use because it is primarily for targeting and infecting specific pathogenic bacteria to reduce or eliminate them. Whereas probiotics are bacteria or yeast that are taken for the purpose of adding beneficial organisms and not necessarily eliminating other harmful ones.
Below is a comparison of probiotics and phage therapy.
| Probiotics | Phage Therapy | |
|---|---|---|
| Nature and Function | ISAPP definition – “Live microorganisms that, when administered in adequate amounts, confer a health benefit on the host” | Viruses known as bacteriophages (phages) that are used to specifically target and infect harmful bacteria to reduce or eliminate them. |
| Mode of Action | Primarily exert their effects by interacting with other microbes, producing beneficial compounds, and modulating the immune system. Overall, there is still a lot of research to be done in this area. | Involves using viruses to infect and kill specific bacteria. Phages are highly specific and only target particular bacterial strains, making them a precision tool against infections. |
| Applications | Commonly used to promote overall health, alleviate digestive issues like diarrhea and irritable bowel syndrome, and may help with immune function. Available in certain supplements and food products (when containing the right dose and strain). | Primarily considered for treating bacterial infections, especially those that are antibiotic-resistant. It’s used as a targeted approach to combat specific pathogens. |
| Products and Availability | Probiotic supplements, yogurt, fermented foods, and drinks are readily available in most markets. They are often used preventively and as part of a daily health regimen. *Note: Not all foods are technically probiotic foods. They must contain the effective strains at the right doses supported by scientific studies. | Phage therapy is more specialized and requires medical administration. Phage-based products, such as creams and gastrointestinal preparations, are emerging but not as widely available. |
| Research and Efficacy | Extensive research, with many strains demonstrating health benefits. However, not all product claims are supported by robust scientific evidence. | An evolving field with promising results, especially in cases of antibiotic-resistant infections. Research is ongoing to establish its effectiveness for various conditions besides infections. |
The Dynamic Nature of the Gut Microbiome in Early Life
An emerging area of gut microbiome research is in understanding the microorganisms involved in the first few years of life. Initially, infants start with formula, milk, or breast milk, and eventually transition to solid foods around two or three years of age. During this period, both the bacterial and viral communities, including bacteriophages (phages), within the gut are in a state of flux.
Phage Activity in Microbiome Establishment
Now, regarding how phages influence the early stages of microbiome establishment, it’s important to note that direct evidence of this influence is still somewhat elusive in scientific studies. However, what research has indicated is that in the early stages of life, phages appear to be more active and often exhibit a lytic or virulent behavior. This means they are actively preying on and killing their bacterial hosts within the gut.
Interestingly, as a child reaches the age of two or three and their microbiome starts to stabilize and resemble that of an adult, the phage community undergoes a shift. It becomes more stable and is dominated by temperate or prophages, which are less likely to cause bacterial turnover.
A lot happens in a baby’s microbiome during those first few years. We often focus on changes in the bacterial composition, but the role of viruses, such as phages, in shaping these changes is equally important. The fact that phages are more active and predatory early on suggests they could have a significant impact on which bacteria ultimately become part of the adult gut microbiome.
Potential Use of Phages in Early Childhood
Currently, research is exploring the possibility of using phages during early childhood in this highly dynamic phase of microbiome development to potentially reshape (when necessary) the bacterial community before it stabilizes at two or three years of age.
Phage therapy, in the traditional sense, on the other hand, could be applied in various contexts in early childhood, similar to its use in adults and teenagers. This includes treating conditions such as skin infections and lung infections.
Ongoing research is helping us unravel the complex interactions between phages, bacteria, and the early development of the gut microbiome. It’s an exciting area of study that holds the potential to enhance our understanding of how these communities form and influence our health later in life.
Summary
- The human microbiome consists of various microorganisms living in our bodies, and while bacteria often take the spotlight, scientists are increasingly studying the virome, which comprises the viruses in our gut.
- Most gut viruses are bacteriophages, which target bacteria, not humans. They interact with the bacteria in our gut microbiome and can play important roles in maintaining a healthy gut balance.
- Recent studies reveal that each individual has a distinct “fingerprint” of viral communities in their gut, emphasizing the uniqueness of one’s virome.
- Bacteriophages can influence the metabolism and physiology of gut bacteria, potentially promoting a healthier microbial balance. This interaction opens the door to harnessing phages to target harmful bacteria and improve gut health.
- While the idea of viruses in our bodies may sound concerning, most gut viruses are bacteriophages, which do not harm us. They contribute to the complex ecosystem of our gut microbiome, much like beneficial bacteria.
- Phage therapy, which uses viruses to target specific pathogenic bacteria, differs from probiotics, which introduce beneficial strains of bacteria or yeast at specific doses for a variety of purposes. Phage therapy is specialized and is used in treating antibiotic-resistant bacterial infections.
- Research is exploring the role of viruses, particularly phages, in the early development of the gut microbiome in infants and young children. Phages may influence the composition of the microbiome during this dynamic phase, and their use in early childhood is being investigated.
The Gut Virome: Michael Shamash
