Interview with George Tetz: a look at how bacteriophages can act as novel mammalian pathogens

November 28th, 2018 by Amy Proal

George Tetz, MD, PhD is CEO of the Human Microbiology Institute in New York City. His research focuses on the study of bacteriophages: viruses that infect bacteria. Tetz studies how bacteriophages can contribute to microbiome dysbiosis in a range of human chronic inflammatory conditions. He also examines how bacteriophages can act as novel mammalian pathogens by interacting directly with human cells and the host immune response. His recent findings show an early role for bacteriophage activity in conditions such as Parkinson’s disease, Type 1 Diabetes and “leaky-gut” syndrome.

Please watch this video of our interview/conversation:

Here is a written transcript of the interview. I have edited the content for purposes of accuracy and clarity:

Amy: George hi. You’re the head of the Human Microbiology Institute in New York City. Tell me about the Organization’s primary goals.

George: Sure. We’ve been working in the microbiome area for over the past 15 years. We set up the Human Microbiology Institute several years ago to combine efforts from our scientific team. Currently we’re pioneers in Phagbiome Research: for instance, we’ve shown that bacterial viruses (named bacteriophages) are actually previously overlooked human pathogens. It’s something people should be concerned about and is definitely an area of study that needs a lot more scientific research.

Amy: Yes. I was very excited when I read your paper “Bacteriophages as potential new mammalian pathogens.” Can you tell me more? And to give people context: We’ve been studying the human microbiome but have mostly been looking at just bacteria. How do we add bacteriophages into the picture?

George: Indeed, the predominant part of microbiome research right now is dedicated solely to bacteria. That’s in part due to a lack of effective methods for studying the whole microbial population. Because genome sequencing using 16S RNA – which right now is the most cheap and broadly spread method used by scientific groups – allows for only identification of bacterial species. 16S RNA sequencing does not allow for the study of many other details associated with other components of the human microbiome. So [several years ago] when I analyzed a variety of data showing that the human microbiome is implicated in the development different pathologies, I noticed that all the analyses lacked one very important component: they lacked bacteriophages.

Right now there are a lot of debates. For example the role and modulation of antibiotic treatment on the early childhood microbiota and the development of different diseases. And that’s definitely an important topic. However the most influential, and most important regulators of microbiota stability are not antibiotics. They are bacterial viruses (bacterophages). And all these studies were lacking a deeper analysis of what was happening with the bacteriophage communities.

Just a little background. Bacterial viruses (bacteriophages) are regular viruses but their hosts are not human cells or eukaryotic cells…they are bacterial cells. That’s actually one of the reasons why they were previously overlooked. No one paid attention to them because they seemed to infect bacteria and “that’s it.” However, as I mentioned, once the concept of microbiome alterations in disease appeared, then bacteriophages as regulators of the microbiota became something the scientific community must care about. It is very complicated because there’s a lot of dark matter (things we have yet to understand) when it comes to bacteriophages. First of all they outnumber the total number of bacterial cells in the human body by 10-fold. There are also a lot of previously unknown or not-yet known bacteriophages at the moment. However if we’re talking about the bacteriophages that are currently well-known and can be studied, we have tried to evaluate their role and implications in different diseases. That is what we currently do here at the Human Microbiology Institute.

Amy: Yes. Bacteriophages obviously play a major role in regulating activity of the bacterial microbiome. Can you explain more specifically how bacteriophages modulate bacterial behavior?

George: Sure. Let me go even broader and talk about how bacteriophages can impact human health. Because their interplay with bacteria is just one way they can affect humans. Our research team has separated how bacteriophages can impact human health into two main pathways. One is direct interplay with the host. The other is indirect: bacteriophages impact the host by modulating the bacterial microbiota.

When it comes to the first mechanism (direct interaction) we see two main components. First, bacteriophages can interplay with human cells. Even in 2017 this interaction remained unclear. Then, our colleagues showed that bacteriophages can directly interplay with human cells and penetrate the human body. And of course, most of the ways bacteriophages do this are still unknown. But there is a lot of current research from Polish Institutes showing how bacteriophages can directly interact and interplay with leucocytes…leading to alterations in cytokine production, and modulation of Toll-like receptors and the human immune response.

Our recent work has also identified a number of of prion-like domains on the surface of bacteriophages. These mis-folded prion proteins lead to the consequent appearance of other mis-folded proteins. And whether it’s amyloid beta in Alzheimer’s or alpha-synuclein in Parkinson’s, this leads to the deposition of highly neurotoxic composites in the human brain…which then leads to the development of neurodegenerative diseases that are unfortunately killing many people.

So the prion-like proteins we’ve identified on the surface of bacteriophages: they’re important because they can act as a “seeding component” or initial trigger for the prion mis-folding. We have some very interesting data on this that should be ready to share in 2019.

With respect to the indirect pathways by which bacteriophages impact human health…first of all, they can drive a decrease or increase in the number of certain bacterial populations in the human gut. For example, in a study we published on Parkinson’s disease, we identified that Lactococus bacteriophages led to a decrease in Lactococcus bacteria…which in turn led to the disappearance of these populations prior to the onset of first symptoms in the Parkinson’s patients.

To go into more detail, the same concept has been noticed by other scientists in Crohn’s disease and in obesity – where the microbiota is already well-known to be associated with the triggering of those diseases. So we are expanding this research to other neurodegenerative diseases and certain “autoimmune” pathologies, including our latest research on Type 1 Diabetes.

And a final indirect pathway is that, once bacteriophages kill bacteria, or lead to the disruption of microbial biofilms…that can lead to the release of pathogen-associated molecular patterns such as LPS or bacterial cell-free DNA…which in turn are pretty well-known triggers of cascades of immunological reactions that can affect (and be suggested as triggering factors) in different muti-faceted human diseases.

Amy: Got it. Wow you’re looking at a lot of relevant topics. In the case of the Lactococcus phages, you found that they modulated the activity of bacteria that produce dopamine, correct?

George: Yes in the Parkinson’s study we compared two patient populations. One with very early-stage Parkinson’s (they were even treatment naive). The other was an age-matched control group. We identified that the Parkinson’s patients had a decreased number of Lactococcus bacteria, and this decrease was due to the highly lytic infection of these microorganisms with Lactococcus bacteriophages. And Lactococcus bacteria play a very particular role in the human gut. First, they are important regulators of intestinal permeability. And increased intestinal permeability is an important mechanism implicated in Parkinson’s that leads to the chronic inflammation. Also, Lactococcus bacteria are important producers of different neurochemicals, which are important components of the enteric nervous system. In particular, Lactococcus bacteria produce intestinal dopamine. And it’s fairly well-known that an initial step of Parkinson’s disease starts not in the brain, but in the enteric nervous system. And then, via the vagus nerve goes up to the brain, leading to alterations that are pretty well-known as Parkinson’s disease.

So to highlight. In these patients we identified that bacteriophages killed microorganisms that are important regulators of the enteric nervous system…microorganisms that are known to be associated with maintenance and balance of intestinal dopamine.

Amy: That’s what interested me most about the findings. It’s such a clear mechanism. There’s an actual connection between the dysbosis and neurotransmitter production.

George: Yes. We’re very happy because here at HMI we have not only bioinformatics staff, but also MDs who understand how certain microorganisms are involved in human biology (and what happens when something goes wrong with that).

Amy: That is great. Because you can get the bioinformatics data, but you have the biological knowledge with which to best interpret the data. So in the Type 1 Diabetes study what did you find with bacteriophages there?

George: We have not published yet. But we did a longitudinal microbiome study of children from birth to three years old. All children had certain HLA mutations that made them highly susceptible to Type 1 Diabetes. However, at three years of age, only a number of these subjects converted to islet autoimmunity and Type 1 Diabetes. Other subjects, despite having the altered genes, never developed signs of autoimmunity. What we identified is that the children that sera-converted to diabetes had, initially, very high levels of E. coli in their guts. But when we followed these E. coli populations over time, we found that the diabetic children, BEFORE the appearance of autoantibodies, had a complete disappearance of E. coli in their gut. This was due to the fact that those subjects had an active prophage infection, meaning that bacteriophages were responsible for the elimination of the gut E. coli populations. E. coli are members of the Enterobacter family. And it’s pretty well-known that one of the pathogenic-associated molecular patterns (PAMPs) that can be released from their biofilms is highly immunogenic. That means they can trigger other pathologies and diseases including, for example Systemic Lupus Erythematosus. So to summarize, we found that bacteriophages – through this indirect mechanism – led to the appearance of highly immunogenic proteins that in turn could trigger the “autoimmunity”, and in turn, Type 1 Diabetes.

Amy: Very interesting. So it doesn’t seem that what’s really going on in Type 1 diabetes is “autoimmunity” in the classical sense (a reaction to “self”). It seems that instead we need to better study how the immune system reacts to persistent pathogens…

George: Yes a lot of research is dedicated to that topic. The most important questions is: “Even in people with altered genetics – why do some people develop these diseases and some not?” What happens in the patients who do develop them? And sometimes a simple microbiome analysis cannot complete that process, so it’s necessary to go into more detail in both humans and animals (research we are doing).

Amy: Right. Because now we treat “autoimmune” disease patients with strong doses of immunosuppressive drugs. How do you think those drugs impacts the survival of bacteriophages that may be driving a large part of the dysbiosis?

George: It’s dark matter (a basically unexplored topic). Because there’s not much data on how current therapies impact bacteriophages. Not in chemotherapy or antibiotics. Meaning that certain alterations that can follow from such therapies, and their impact on bacteriophages, is completely unknown.

Amy: Yes, there are very few studies that even look at the effects of immunosuppressive drugs on the bacterial microbiome. I find that frustrating. Because it’s concerning that our “standard of care” treatments focus solely on shutting down the immune response in “autoimmune” patients…when the microbiome and virome seem to be playing a large role in driving the conditions.

George: On the other hand, patients right now don’t have many other options.

Amy: Oh I know. I’m talking about future treatment development.

George: One of the most important things in future treatment development is what we do here at HMI. If you can figure out the real cause of the disease, it is possible to develop programs for primary disease prevention. To completely eradicate the condition. But to do that you need to know what is the true, causal mechanism – what actually leads to the development of these pathologies.

Amy: Yes. So if we can better understand “root cause” mechanisms by studying bacteriophages and the entire microbiome…we can probably develop some better “root cause” therapies for “autoimmune” disease. That’s the goal right?

George: Absolutely. I agree with you.

Amy: Ok. I’ve read studies on bacteriophages that stem back over the past century. Why did bacteriophages almost “fall out of favor” in the mainstream research community until recently?

George: Yes. Historically there have been (and there continues to be) phage research centers in the former USSR (in Georgia). There are also a lot of USA and European companies that employ bacteriophages for the treatment of multi-resistant bacteria. There is a lot of sense for doing that. Because bacteriophages are highly selective, meaning certain phages kill only their specific bacterial hosts. Which is why people are trying to use bacteriophages as therapy to overcome antibiotic resistance. Some of these efforts have been very successful. For example, there are a number of bacteria like MRSA or multi-resistant Pseudomonas aeruginosa that infect children with cystic fibrosis. These strains are completely insensitive to the total panel of antibiotics, so the children have no other treatment options. The same is true of diabetic ulcers that are also caused by polymicrobial infections. There are attempts to use bacteriophages topically to eradicate such infections, which is great.

So to be clear, what we are discovering here at HMI doesn’t go against such uses for bacteriophages (phage therapy). We’re talking about a different question: can bacteriophages (not those used for Pseudomonas, MRSA etc) be overlooked human pathogens?

Amy: Yes. In my opinion the situation is similar to how we use some bacterial species as probiotics. In those cases, we know certain bacterial strains have that capability. But we don’t use known pathogens as probiotics. The same would go for phages. If we better work to understand specific phage targets, we can better know which phages to use for effective phage therapy.

George: Yes extra knowledge of how bacteriophages contribute to human health can add an extra level of safety to the selection of phages for phage therapy.

Amy: Yes. Can you explain your research on bacteriophages and “leaky gut?”

George: Sure. The topic was our first publication in the area, with one paper done in collaboration with New York University. We identified that bacteriophages, acting as regulators of microbiota stability, can increase intestinal permeability. This leads to chronic inflammation. This chronic inflammation can, in turn, increase “leaky gut.” “Leaky gut” is associated with a variety of human diseases including neurogenerative diseases and autoimmune pathologies.

We took rats and gave them a cocktail of different bacteriophages commonly found in waste water plants. So phages against Pseudomonas, Staph aureus, E.coli…and not (I want to highlight) against Lactococcus species or Fusobacterium species. The results were interesting. After the animals were given the strong bacteriophage cocktail with water (the phages were swallowed, not injected) the phages caused significant alterations in the rat intestinal microbiota (as revealed by whole genome sequencing). Moreover, we measured signs of increased intestinal permeability in the same animals. We found that all rats exposed to the bacteriophages had an increase in intestinal permeability and a decrease of Lactococcus bacteria (bacteria known to be important regulators of gut permeability). And again, we did not give the rats phages that would directly eliminate Lactococcus. It follows that bacteriophages can lead to a cascade of microbiota alterations, finally leading to a decrease in certain bacterial species.

Amy: Yes and chronic inflammatory conditions are closely tied to the environment. So what you also showed is that phages in our environment – let’s say in contaminated water – could be a contributing factor in chronic inflammatory disease.

George: I don’t want to scare anyone, but waste water contains 10^8 bacteriophages on average.

Amy: I don’t think that should scare anyone. We must face the reality of that knowledge to move forward.

George: Yes a lot of research must be done in this area.

Amy: Yes because we can easily pick up phages from our environment right? In fact, isn’t there a study which shows that ~30 billion bacteriophages traffic from the gut throughout the body every day?

George: Yes. It was published in 2017 in MBio. And the article also highlighted that bacteriophages can interact with human cells.

Amy: Yes. So there are billions of bacteriophages in the human body. And they are found outside the gut frequently correct? In the cerebrospinal fluid, the placenta, the brain right?

George: Yes.

Amy: So bacteriophages persist in most human tissue and blood.

George: Yes. And they can persist in two ways. One state is as free-presenting elements like lytic phages. Or bacteriophages can integrate into bacterial genomes (prophages). In those cases they can regulate how they exit the bacterial cell and lead to productive infection. So there can be bacteria in the cerebrospinal fluid (for example) that have phages within their genomes.

Amy: You are originally from the USSR? Is that how you got into bacteriophage research?

George: Yes. I’m originally from St. Petersburg, Russia and my sisters are from Estonia. I started doing microbiome research and then noticed the discrepancy in studies that did not account for bacteriophages.

Amy: And bacteria can also modulate phage activity right?

George: Of course. Particularly when the phage is incorporated into the bacterial genome. There are a number of ways in which bacteria then interplay with the phages. For example, there are different ways bacteria manage the initial steps of phage infection (in an effort to prevent the phages from penetrating).

Amy: What about inherited phages? Do you think inherited phages influence how diseases are passed in families?

George: We are working on that. Particularly, taking into consideration the fact that a very important part of the microbiome is translated vertically from the mother. That means a number of bacteriophages, both lytic and prophage, are inherited from our parents as well.

Another important consideration is how bacteriophages influence the long-term safety of fecal microbiome transplantation (FMT). Particularly because a very big number of prophages (both lytic and lysogenic) enter the gut of FMT patients and colonize them. So in terms of the long-term safety of that…I have no answer yet. More research must be done to find algorithms that should be targeted to the individual patient.

Amy: What about passing phages from person to person. That happens right?

George: Yes just like viruses, bacteriophages are transmitted from person to person. The main difference is that bacteriophages can be passed as lytic phages or together with their bacterial hosts.

Amy: Yes. Because there have been clusters or outbreaks of certain chronic conditions like sarcoidosis and ME/CFS. I’ve always wondered if there could be a sharing of organisms in such cases.

George: Yes that poses another question – an important, although speculative question. If there are so-called bacteriophage diseases, can they be transmitted? And can they be contagious or not? From my perspective it can happen. But it may be that you need the “right” recipient for disease development…the person might not just have a certain genetic susceptibility…but also a certain microbiome. That adds an extra level of complexity that is hard to compute and analyze with current bioinformatics methods. But it’s something we work on and keep an eye on.

Amy: OK what’s next for you?

George: It will be a surprise to everyone:) But something related to neurodegenerative diseases and autoimmune pathologies.

Amy: Great we need more research on that! Thanks for speaking with me today.