What It Is To Be Human: Holobionts and the Microbiology of Myalgic Encephalomyelitis

Photos of Dr. Amy Proal
Dr. Amy Proal, of the PolyBio Research Foundation, explains how a human body is so much more than just a collection of human cells. Images courtesy of Dr. Amy Proal.

By Bronc

Dr. Amy Proal, of the PolyBio Research Foundation, is a microbiologist interested in the molecular mechanisms by which bacterial, fungal and viral pathogens dysregulate human gene expression, immunity and metabolism.

She is especially interested in how dysfunction of the human microbiome and/or the human virome can contribute to chronic inflammatory disease processes. We sat down with Dr. Amy Proal to learn more, and the following is an edited excerpt of our discussion.

divider artdeco

Phoenix Rising:

Thank you for talking with us. How did you get involved in the field of myalgic encephalomyelitis (ME) research?

Dr. Amy Proal:

When I was a pre-medical student at Georgetown University I got an Epstein-Barr virus infection and I got very sick afterwards. I developed a broad range of chronic symptoms and I actually received an ME/CFS diagnosis myself.

At that point I started to wonder: what’s going on? Like many patients, I also was not referred to doctors who would help me. Instead, I was referred to psychiatrists who incorrectly thought that the condition was psychosomatic or not biological. Immediately, that started to frustrate me greatly.

I have a fraternal twin sister, and when we were young I had gotten at least four very serious meningitis infections that landed me in the hospital between the ages of three and five. They had really been severe events where I almost died.

My sister hadn’t gotten any of these infections. So when I was trying to understand why I might have gotten so sick after the Epstein-Barr virus infection, I began to wonder if the childhood infections that I had sustained had played a part. So I became very interested in the topic of infection.

To make a long story short: I ended up doing some experimental treatments to greatly improve my symptoms over time, and then I started to reach out to scientists who were studying viruses, bacteria, and different infectious agents.

I also started to read a lot of literature where researchers had begun to look for pathogens in the human body — not just in the blood, but in tissue and in the brain.

I found the studies to be fascinating, and my former mentor at Georgetown University sent me to one of the first genetic sequencing courses that was using computer-based technologies to identify bacteria in the human body.

The course was at the J. Craig Venter Institute, which is a research foundation in San Diego, California. This was well over 10 years ago. When I got there, I saw this revolution in technology that allowed people to find microbes in the human body by identifying genetic material and then mapping it to genetic sequences that we can find online.

I just thought that that was going to be the future, so I decided to get involved. I got a PhD myself and just decided to keep researching the topic from there.

divider artdeco e1631309710870

Phoenix Rising:

Can you explain the role of the bacterial microbiome in the body?

Dr. Amy Proal:

Humans are not sterile. Many people realise that our guts contain many different bacterial species that are involved in our digestive processes, but over the years these computer-based tools that I mentioned have been turned onto areas of the human body from the gut to the mouth, the lungs, human blood, the pancreas, the bladder.

We started to realise that none of these body sites is completely sterile. They all can have interacting organisms in them. So we collectively refer to the bacterial components of those communities as the human microbiome.

In the last couple of years we started to focus on the fact that most of the bacteria in these ecosystems are, themselves, infected by viruses. These viruses are called bacteriophages. They’re tiny viruses that infect bacteria, and by doing so modulate the activity of the bacteria that they infect.

Overall, there are ten times more bacteriophages in any of these organism communities than there are bacteria. Current estimates are that there that there may be up to quadrillion bacteriophages in the human body at any given time. This opens up so many questions.

First of all, it starts to redefine what it means to be human. We have all our human cells, but we also have more bacterial cells in us than human cells. On top of that, we have ten times more of the bacteriophage viruses than bacteria, so this is part of what makes us what we are.

The organisms in these ecosystems are also intertwined with all of our signaling processes. They create proteins and metabolites as part of their life cycle, depending upon what they are doing. These different molecules can enter into our signaling pathways. For example, a bacterial protein can become involved in glucose metabolism.

A lot of people have started to refer to humans as “superorganisms” or “holobionts”. This means that we’re made up of not just our human genome, but also the genomes of the organisms that inhabit us as well. Under conditions of health, these ecosystems of organisms are basically persisting in a state of balance.

These communities can collectively shift towards a state in which they are no longer in a state of balance. That’s often referred to as dysbiosis. If you have these shifts in microbial ecosystems, you can have big shifts in human metabolic or neurological signaling.

Therefore, we begin to look at how these organisms are impacting any of the metabolic changes we see in disease, or any of the immune-related changes we see in disease.

divider artdeco e1631309710870

If you start to look at studies on organisms in the human body and then dig into the idea that ME/CFS would be caused by psychosomatic or failed thinking, it becomes so ridiculous — especially when there are so many obvious possibilities for how these organisms or pathogens can be contributing to so many of the symptoms, in just straightforward ways.

—Dr. Amy Proal

Phoenix Rising:

How can microbiome research be helpful to the study of chronic illnesses such as ME?

Dr. Amy Proal:

The activity of the microbiome or virome doesn’t have to be the whole disease process, but it’s almost inevitable that their activity is getting caught up in at least part of the disease process, and there are so many ways in which this could happen.

For example, the organisms in those communities can begin to produce products that actually catalyse inflammation, or be drivers of what the immune system reacts to. One of the things we can study is whether, in conditions like ME/CFS, there is altered immune signaling in blood or aberrant immune activity.

We can also ask “are any organisms leaking?” In the gut and in the mouth, as people become more ill, the barriers of those ecosystems wear down and more organisms can leak into the blood, where there shouldn’t be too many organisms in a healthy person.

As that happens, there are many ways for how the organisms themselves or the products they create can contribute to a broad range of inflammatory processes.

Another way in which organisms and their activity can impact the ME/CFS disease process would be by signaling of the nervous system. There is a very important nerve called the vagus nerve that basically enervates every major organ of the body, especially the gut where it can receive signals from the organisms in the gut.

If those organisms are imbalanced or creating products that are detrimental to health, the vagus nerve might sense inflammation that is generated in response to that, and it can convey that information to an area in the back of the brain called the brainstem.

The brainstem has overlapping nerve bodies that control the feeling of being sick, malaise, flu-like symptoms, autonomic symptoms, nausea, and pain signaling.

The takeaway from that is that activity of organisms in the gut, via the vagus nerve, might actually contribute to some of the symptoms we see in patients with ME/CFS — like the autonomic dysfunction, or the flu-like symptoms, or pain, or nausea.

So these organisms can contribute to cognitive symptoms or brain-associated symptoms as well. There are lots of avenues by which we can begin to correlate their activity with the symptoms we see in patients with ME/CFS.

divider artdeco e1631309710870

Phoenix Rising:

Many people with ME develop the illness, as you well know, after a bacterial or viral infection and these people with ME develop a variety of symptoms which fluctuate over time.

Several studies suggest that neurological illnesses such as ME are associated with a neuro-inflammatory response to a persistent infection.

So how does study of the human microbiome help us understand this possibility in ME? Could it help in the treatment of the disease? 

Dr. Amy Proal:

I already mentioned some ways that the human microbiome may be altered and may contribute to symptoms in patients with ME/CFS.

One more way that I’ll throw in: In ME/CFS, there are some documented metabolic abnormalities in patients. It’s very important to understand that the bacteria in the human body are constantly producing metabolic products that become part of our human metabolism. So, there can be microbial contributions to the metabolic imbalances.

I wrote a paper with my colleague Mike VanElzakker, who is a neuroscientist, last year on how many major pathogens — bacterial, viral, or fungal — actually hijack the metabolism of the cells that they infect as part of the way that they drive disease.

When such pathogens infect a human cell, they need substrates to be able to replicate. They need compounds from the host cell for their nutrition purposes and so they take over the mitochondria of the cells they infect. Mitochondria are the powerhouses in the cell that are producing energy for humans in the form of ATP, and the pathogens hack that.

The pathogens start to redirect metabolites and proteins out of the energy cycle that should be going to the human cell, and instead take them for themselves. That inevitably alters the metabolic output of the infected cell.

So, one of the most interesting topics that we can explore right now is whether the activity of the pathogens connected to ME/CFS — the herpesviruses, the enteroviruses, certain bacterial pathogens — is connected to some of the metabolic changes that we see in the disease. In there may lie some of the central mechanisms that contribute to the disease process.

In terms of treatment, it’s actually exciting to me because there are potential treatment strategies that could stem from this.

I’ve mentioned that the gut or oral microbiome can sometimes become leaky when the barriers get worn down. Then an organism can leak into the blood where it can be problematic and possibly drive inflammation. There is a growing number of compounds, for example, that people are using to try to repair the lining of the gut so it won’t be as leaky.

There are also companies that are working on microbiome-based therapeutics.

I’m in Boston and there are a couple of companies here who are beginning to work on products for patients with Crohns disease or ulcerative colitis. These are very clear gut diseases involving organisms, and what these therapeutics attempt to do is to bring beneficial organisms into the gut to begin to replace the more imbalanced or pathogenic organisms.

I feel that if we do the research in ME/CFS and show that such scenarios may be impacting the ME/CFS disease process, then we can tap into such therapeutic developments in related disorders. By doing so, we would begin to have some more tangible tools to restore microbiome balance and begin to get in the way of the ability of the microbiome to drive problems with immune response.

divider artdeco e1631309710870

Phoenix Rising:

That does take us a very long way from the idea of it just being psychosomatic, doesn’t it?

Dr. Amy Proal:

It’s ridiculous, yes. It’s unfathomable.

If you start to look at studies on organisms in the human body and then dig into the idea that ME/CFS would be caused by psychosomatic or failed thinking, it becomes so ridiculous — especially when there are so many obvious possibilities for how these organisms or pathogens can be contributing to so many of the symptoms, in just straightforward ways. Yes, it is absurd.

divider artdeco e1631309710870

Phoenix Rising:

Post-exertional malaise (PEM) is the central defining characteristic of ME.

Unfortunately, it is poorly understood by many health professionals, public health bodies, mainstream media outlets and the wider public. Here in the UK, the Department for Work and Pensions, which administers disability benefits, completely fails to understand the impact of post-exertional malaise on people with ME.

So what does the latest research into post-exertional malaise tell us?

Dr. Amy Proal:

It’s devastating to hear the situation related to ME/CFS and the understanding of post-exertional malaise. To clarify what we mean by post-exertional malaise: Many patients with ME/CFS can do small amounts of activity, either physical or cognitive, but then 24 hours to 48 hours later they crash. They feel dramatically worse.

In other words, exercise or exertion is actually causing them to get worse and leads to an increase in their symptoms. Which, as you know, is very hard for some to understand because one of the ingrained themes in our health care system is that, if someone’s sick, they should exercise more.

A lot of ME/CFS patients come in and say “I’m very, very ill.” They don’t look sick because ME/CFS patients don’t have some dramatic growth or something occurring with them.

What’s happening is likely in the central nervous system, in the gut, in the interior of the body itself. They look OK, they can do some things in the moment, and so doctors say “oh you’re OK, you should exercise.” When they recommend that, the patient gets way worse and crashes.

I agree with you that understanding the reasons for post-exertional malaise is one of the million-dollar questions of ME/CFS. There are a number of different topics that we are trying to explore when it comes to post-exertional malaise.

One ties back to the microbiome that I mentioned. There was a team — I think it was at Ohio State University — who had patients with ME/CFS do what’s called a ‘symptom provocation challenge’ involving an exercise bike. It’s very hard on the patient but it’s one of the ways to document that post-exertional malaise is occurring.

What happens is that patients are asked to bike, and then 24 or 48 hours later some testing can be done to show that they could not recover well from the biking exercise. There are some teams, including ours, trying to collect samples from patients before they do the exercise challenge and then afterwards when they crash, in order to try to understand what might be going on.

One team did find that afterwards there was more leakage of bacteria into the blood. So after exercise, patients had a higher bacterial load in their blood that might be capable of stimulating inflammation. That to me suggests that the stress of trying to exert actually pushes more microbes through those barriers into the blood, in a manner similar to the leakage I’ve described before.

That being said, the post-exertional malaise is so severe that it likely involves signaling between the body and the central nervous system which affects the body’s ability to bounce back from activities. You may also have problems with blood vessel response, and then also the muscles themselves are of interest to me.

One of the topics in ME/CFS research that people have historically studied is that viruses can actually directly infect tissue muscle. The enteroviruses are single-stranded RNA viruses that have been linked to ME/CFS.

In a number of outbreaks of ME/CFS — where patients in a certain geographical location got sick at the same time and developed ME/CFS — they were able to trace the initiating virus back to an enterovirus.

There were a couple of teams that got muscle tissue samples from these patients and found enterovirus genetic material and protein right in those muscle samples. So you may have a scenario where a person’s muscles are themselves infected. Certainly that would be a straightforward way in which exercise could be very difficult.

Of course, post-exertional malaise involves cognitive symptoms as well. Since I mentioned that the vagus nerve can sense inflammation in other body sites and convey that to the brain, it may all actually be related. It’s possible that problems in muscle or problems with the blood vessels will lead to signaling that impacts cognitive ability and may lead to inflammation in the brain itself.

I don’t want to go on too much, but one of the topics that my colleague Mike VanElzakker is doing is neuroimaging on patients with ME/CFS. There are immune cells called microglia in the brain that can become activated in patients who have chronic disease. When they remain activated, it’s called a neuro-inflammatory state.

So there can be issues with blood vessels or issues with infection of tissue, and the vagus nerve can sense it and can convey it to the brain. Those signals can lead microglia in the brain to activate in ways that might drive inflammatory processes — which may make it even harder for people to recover from exercise.

So, while these ideas don’t explain all of post-exertional malaise, they are some of the trends we have on our radar that we can start to explore further in order to understand what’s going on.

divider artdeco e1631309710870

Phoenix Rising:

Can you tell us about research projects you are currently involved in and the outcomes you hope to achieve?

Dr. Amy Proal:

Sure. I mentioned that we are working to try and analyse tissue from patients with ME/CFS and related diagnoses like Long Covid or post-treatment chronic Lyme disease. This is because, while we can do a lot of interesting studies on the blood, the pathogens that initiate and exacerbate many cases of ME/CFS are often neurotropic.

In other words, they preferentially infect nerves. The herpesviruses, which include Epstein-Barr virus, have life-cycles that actually require movement through nerves.

If we’re going to look for these viruses, the most straightforward possibility is that the virus or pathogen that starts or exacerbates ME/CFS may not fully clear from the patient. The patient may still have the pathogen in their bodies. If that’s occurring, then the pathogen and its genetic material are very unlikely to be in the blood of the patient.

The reason for that is that over time, it is not smart for a pathogen to just wander around in the blood. It’s very exposed because that’s where many parts of the immune system live, and so it’s more likely to be recognised and targeted by the immune system.

What many pathogens and viruses tend to do is hide in tissue. They get into tissue where they can remain at a low level, so a little bit of virus remains in the intestinal tissue or muscle tissue or a different bodily site. There, the virus can drive many symptoms.

If we want to know if that’s happening, we have to go beyond just studies of the blood in ME/CFS. We have to collect tissue samples from patients with the diagnosis to be able to see if they still have virus in them.

We’re working with several teams who are doing this. One really great team is from the J. Craig Venter Institute in San Diego. We’ve created a tissue pipeline, where we can take a sample and identify all of the organisms that may be in that sample — bacterial, viral, or fungal.

Not just identify them — we can actually understand their activity. We can figure out what genes they are turning on and off, and we can also correlate their presence with the immune response.

We can say, “oh look, there’s a pathogen here and the immune cells around it are acting differently.” We can even correlate the absence or presence of pathogen in tissue with changes in the human genome that may be occurring in that tissue sample.

Building that pipeline and the technology to be able to do these analyses has been one of our primary research projects. Some of the other projects we’re doing are neuroimaging studies of patients with ME/CFS — studies that go beyond just imaging one or two components and begin to actually integrate some of the trends I’ve mentioned.

For example, I mentioned that vagus nerve signaling may become dysregulated or pro-inflammatory in patients with ME/CFS. My colleague Mike VanElzakker is running a study at the Martinos Center for Biomedical Imaging where patients with ME/CFS are subjected to vagus nerve stimulation while in the scanner.

In this way, you can begin to measure what’s happening in the patient in this scanner tied to the activity of the nerve.

Mike VanElzakker is also doing another study on brain fog in patients with Long Covid and ME/CFS, where they do a cognitive challenge in the scanner. Then they can see whether the correct regions of the brain are responding to that cognitive challenge. Or, are patients struggling with specific regions of the brain?

Neuroimaging studies like that don’t necessarily tell us the root cause, they don’t necessarily tell us why a certain brain region may be dysregulated in cognitive dysfunction. But they help us to understand which pathways are dysregulated, what areas of the brain are not signaling correctly.

Then we can take the data we have on infection, on pathogens, on the microbiome, and we can begin to ask “what if the pathogens infect or affect that region of the brain?”

In this way we can begin to take the trends and connect them together. Part of our research is making sure that we don’t study topics in isolation — that we don’t have one study that only looks at neuroinflammation, one study that only looks at the microbiome, but that we’re actually connecting those topics together by doing many of the analyses in the same patient.

divider artdeco e1631309710870

Phoenix Rising:

Thank you so much for your time today, it is most appreciated. We look forward to following your research as it progresses over the next period.

Dr. Amy Proal:

Thank you for your interest in our work!

divider artdeco

Note: The above interview is an edited excerpt of a discussion conducted on March 24, 2022. You can watch the entire interview here:

Click here to comment on this article.

Bronc is a former historian who is active in his local ME support group. He enjoys interviewing scientists involved in ME research to help himself and others better understand their illness.

Acknowledgment: The author would like to thank his family and editors for help with conducting, transcribing, and preparing this interview.

Share this!