Author Archives: Amy Proal

Interview with Robert Moir: Infection in Alzheimer’s/brain microbiome

December 18th, 2017 by Amy Proal

Robert Moir is an assistant professor of neurology at Harvard Medical School and Massachusetts General Hospital (Boston). He studies Alzheimer’s disease and other inflammatory conditions characterized by neurodegeneration. His research team has shown that the amyloid beta protein associated with Alzheimer’s “plaque” is a potent antimicrobial peptide. Please read this blog post for more context on this important discovery. 

Background information:

Antimicrobial peptides: “Natural antibiotics” created by the human immune system. They are able to kill a range of bacteria, viruses, fungi, and other pathogens.

Innate immune system: The branch of the immune system that creates antimicrobial peptides. These peptides and other innate immune system cells form the body’s “first line of defense” against infectious agents.


Robert hey! Thanks for taking the time to speak with me. First question: your discovery that amyloid beta is an antimicrobial peptide is HUGE. What made you decide to investigate its possible antimicrobial properties in the first place?

The idea came from a somewhat chance discovery. On Fridays I go through my walkabout time on PubMed (a website that catalogs scientific journal articles). I rove wherever impulse takes me. I read a paper about LL37, a well-described human antimicrobial peptide. It was obvious from this paper that LL37 and amyloid beta share clear similarities: both structural similarities and the ability to form amyloid (protein-like deposits that can accumulate in tissues in certain disease states known as amyloidopathies).

At the same time, my mentor Rudolph Tanzi (he’s in the office next door) had just gotten back results from a screen of Alzheimer’s linked genes. He got the results back literally the same day I read the LL37 study. Well, most of the Alzheimer’s linked genes he characterized were also innate immune system genes. We both looked at one another and thought: “Antimicrobial peptides and the innate immune system are the way to go.” Then we did a bunch of experiments that went nowhere. It turns out that several classical methods used to study antimicrobial peptides don’t work for amyloid beta.

In some cases amyloid beta’s ability to target certain microbes is more than 100-fold stronger than penicillin.

Then I went on vacation with my six year-old son to the White Mountains. James Kirby of Beth Israel Deaconess Medical Center had invited us, and the trip gave me the opportunity to get his feedback. He helped us develop assays to correctly test amyloid-beta’s antimicrobial activity. Key to this correct assay preparation was the fact that amyloid beta had to be in its more oligomeric forms (the biologically active form of the peptide). Once we got these assays right, we immediately found that amyloid-beta had very potent antimicrobial activity. In some cases its ability to target certain microbes is more than 100-fold stronger than penicillin.

Me: Wow very interesting. Can you explain a bit more about what it means for amyloid beta to have “oligomeric forms”?

Amyloid-beta is the chief name for a peptide that self-associates to build multiple differently shaped molecules, each with its own molecular structure and activities. Small proteins that can self-assemble and generate diverse structures like this are sometimes called “lego peptides.” Amyloid-beta assemblies are called “oligomers.” Each particular oligomer structure has unique antimicrobial activity. In this way, amyloid-beta spontaneously generates a population of diverse oligomers able to target a broad spectrum of pathogens, and even microbial toxins released during infection. This turns out to be key for amyloid-beta’s effectiveness as an antimicrobial peptide in the brain. Oligomers can target many different microbes while non-oligomeric amyloid-beta is only effective against a limited range of pathogens. This strategy is so effective that we have not been able to find a pathogen that oligomeric amyloid-beta can’t inhibit to some degree.

Me: So these oligomers are a little like antibodies? In the sense that the immune system creates a range of antibodies in response to an infectious threat, each with the ability to target different species/strains of microbe(s)? 

Yes, they are like a cheap man’s antibodies. But antibodies need whole cells in order to be produced and are metabolically complex and expensive to make. Amyloid beta’s ability to form into a wide range of different oligomers is a simpler, metabolically cheaper, and far more ancient immune strategy. Even very ancient animals like jellyfish (which are 500 million year old primitive multicellular organisms) have this ability to create antimicrobial peptides that recombine to increase molecular diversity.

Moir (right) with colleague Rudy Tanzi (left) (Image: Jon Chase/Harvard Staff Photographer).

What’s hard to believe is that many researchers still regard amyloid-beta’s generation and activities as an ‘accident’ and continue to develop therapeutic strategies around this idea. This assumption was reasonable back when amyloid-beta was discovered in 1984. The peptide was thought unique to the human brain and believed to be only generated under the disease conditions found in Alzheimer’s. In addition, amyloid-beta is made by cutting the peptide out of a larger precursor protein that is embedded in cell membranes. No other peptide was known to be generated this way, so it was considered something that must only occur under disease conditions.

However, it’s been known for over two decades that amyloid-beta is continually made in the normal brain throughout our lives – and not just the human brain. All vertebrates make amyloid-beta in their brain, most of them the exact same peptide as we make. Furthermore, the mechanism that generates amyloid-beta is now known to be a common cellular pathway that is involved in making many different important normal peptides. But, the assumption that amyloid-beta is junk persists, even though the key assumptions underpinning this idea have been disproved. I still frequently hear the ‘amyloid-beta is junk’ idea justified by an old argument that is demonstrably wrong. It goes something like this: “Since Alzheimer’s occurs in individuals past reproductive age (that is post-menopause) there is no evolutionary pressure to remove it from the genome.”

Sounds plausible, until you start looking beyond the narrow precepts of the Alzheimer’s field and consider amyloid-beta in a broader biological context. Only three species of animals undergo menopause: us, dolphins, and pilot whales. Most other animals reproduce to within 1-2% of when they drop dead – and many social animals live well into old age. And yet, all vertebrates make amyloid-beta, with over 60% making the exact same form of the peptide we do. Moreover, they have been doing this for over hundreds of million of years! (The human amyloid-beta gene is expressed in coelacanths, a family of ‘living fossil’ fish that date back over 400 million years). In fact this data would suggest the exact opposite of the ‘amyloid-beta is junk’ argument – it supports the idea that amyloid-beta contributes to survival fitness throughout life in all vertebrates.

Also, anyone with grandparents knows that they typically play an important part in helping successfully raise children. In biology it’s known as the “grandmother hypothesis.”  Simply put, the grandmother hypothesis says that menopause allows aging mothers with an increasingly high risk of death from childbirth to stop direct reproduction and pass on their genetic material to future generations by helping raise their grandchildren. Grandparents are not reproductively irrelevant!! Any gene that intrinsically causes dementia and negatively impacts grandparent survival and their valuable store of accumulated experience, is going to be selected against. The gene is going to change or be eliminated. But amyloid-beta is 100% conserved from 400 million years ago.

The human amyloid-beta gene is expressed in coelacanths (Image: American Museum of Natural History).

What all this is telling us is that amyloid beta must actually be very important. It must be at the heart of important biological processes.  Indeed, human amyloid-beta is one of the top most conserved proteins in all of biology (as far as I have been able to ascertain, second only to the protein ubiquitin).

Me: Yes it seems clear that amyloid beta must have an important role in human health and disease. How has your research moved forward based on that possibility?

We set out to test whether amyloid beta has antimicrobial activity. We found that if you add amyloid beta to a microbial broth it will inhibit or straight out kill a range of microbes. We published a paper with those and related results in 2010. It was greeted with mixed reception. Some researchers (mostly young researchers) were enthusiastic about it. Older researchers not so much. From these detractors we got feedback like, “That’s fine, but battery acid can kill organisms in a test tube too.” In other words, they were critical that the experiments were done in a test tube and not in a living organism. For most antimicrobial peptides, demonstrating potent microbial killing activity in a test tube is enough to establish identity (it’s a very difficult activity for a protein to pull off), but it’s not an unreasonable critique. Showing protective activity in a living animal is the gold standard for confirming a protein is an antimicrobial peptide.

So we set out to show that amyloid-beta could have antimicrobial activity in living organisms. We tested its activity in genetically modified mice, fruit flies, nematode worms, and cultured cells. The work took us four years to complete. Our keystone finding was that the ‘plaque’ amyloid-beta generates is as important as the peptide itself. These amyloid-beta “plaques” directly entrap and neutralize microbes. Then, by chemically generating a burst of oxygen radicals – bleach in lay terms – they destroy the trapped pathogen. Just to be on the safe side, the plaque remains intact in the brain, entombing forever any microbe that may have managed to survive. This “entrapment” mechanism is not unique to amyloid beta. For example, alpha-defensin 5 and other human antimicrobial peptides create amyloid structures that function similarly.

So to summarize, expression of amyloid-beta protects cultured cells and nematode worms from lethal infections. In unpublished work we have also confirmed that amyloid-beta also protects against infection in fruit flies. In mice, the most important animal infection model, over-expression of amyloid-beta is protective against bacterial and viral encephalitis (brain inflammation driven by infection). Finally, if you “knock out” mouse (murine) amyloid-beta the mice develop increased susceptibility to encephalitis. So what we now have is convincing data from animal models that that amyloid-beta functions in humans as an antimicrobial peptide.

Me: Has it been hard to advance these findings?

One side of the story has gotten the most attention. If amyloid-beta is an antimicrobial peptide, one plausible inference is that Alzheimer’s is caused by an infection or infectious processes. I’m kind of agnostic about that implication, in that Alzheimer’s could also be a disease where immune pathways have gone wrong. There are a number of examples of ‘sterile inflammatory’ disease in which an immune pathway has become dysregulated and pathological. No pathogen involved.

Alois Alzheimer

But having said that, there’s mounting circumstantial evidence suggesting that infection plays a role in the disease’s etiology. The first guy to support that was Alois Alzheimer himself. In the 1970s-80s many Alzheimer’s researchers thought infection played a central role. But the discovery of amyloid-beta in 1984 (ironically) shifted the focus away from infection. Amyloid-beta was assumed to be all bad, bad, bad, and its accumulation blamed for the disease. It’s a simple explanation to a complex problem, which made it attractive. But it’s increasingly at odds with emerging data. The drug company Merck’s last Alzheimer’s drug lowers amyloid beta levels but did not slow the disease.

Amyloid-beta alone does not give you Alzheimer’s disease. You also need inflammation and tauopathy, another pathology in brain. It may still be effective to control amyloid-beta if you get it early enough in the disease process. Controlling amyloid-beta may help slow the cascade of events that promotes the neuroinflammation that ultimately kills neurons in Alzheimer’s. But, the question remains: what is driving the deposition of amyloid plaques in the first place? Old models hold that amyloid-beta does it because it’s catabolic junk with an unfortunate propensity to form functionless plaques that induce inflammation. But…could plaques and neuroinflammation in Alzheimer’s actually be an immune response to a genuine immune challenge from microbes in the brain? Perhaps. If it is, then targeting microbes in the brain may be a better way to go. What is clear is that more data on the role of microbes in Alzheimer’s etiology is needed. At the moment the “amyloid is bad” idea continues to dominate and most academic efforts are still focused on this model.

Interestingly, we may be seeing the beginnings of a shift in the way “Big Pharma” is looking at Alzheimer’s. Their costly drug failures seem to be making them open to exploring alternative models, including the “antimicrobial protection hypothesis of Alzheimer’s” – which is what we are calling this new emerging model of the disease. For example, “Big Pharma” is exploring if neuroinflammation in Alzheimer’s can be dampened down independent of amyloid-beta production or plaque deposition. My colleague Rudy Tanzi has discovered that the gene CD33 is a big on/off switch for immune cells in the brain. Maybe switching the gene off could help patients manage early Alzheimer’s symptoms. Most current first-line anti-inflammatories wouldn’t have the same effect since they tend to target the adaptive immune system. Antimicrobial peptides and amyloid-beta are part of our much more ancient and primitive innate immune system (the “front-line troops” of the immune response). Companies are now pursing CD33 as a possible drug target.

Dr Doo Kim’s lab in research Unit at Massachusetts General Hospital has created a special three-dimentional human neuronal cell culture system that’s dubbed “Alzheimer’s in a dish” by the media. The system helps us scan innate immune system drug candidates. The technology accelerates drug screening and reduces cost more than 10-fold compared to conventional approaches. It should allow new potentially useful drugs to be identified much faster.

Me: Interesting. But I’m confused. Do you think amyloid beta should be removed in patients with Alzheimer’s (despite its antimicrobial activity)?

Maybe not removed, but it’s certainly a good idea to control it. Amyloid beta may be a little like cholesterol – heart attacks are exacerbated if cholesterol is in the wrong place at the wrong time. But if you remove cholesterol completely, other serious health problems arise. So as was done with cholesterol targeting therapies, I think the first goal should be to better understand what amyloid-beta is actually doing in the brain and develop strategies accordingly. That would mean reducing bad effects while preserving amyloid-beta’s role in immunity.

What may be happening is that initially, amyloid-beta rises to do battle in cases of brain microbiome dysbiosis (imbalance). Part of this response is amyloid-beta induced inflammation. But, prolonged activation of innate immune inflammation by amyloid-beta leads to tissue damage and neurodegeneration.

One thing is that any treatment aimed at managing amyloid beta would work best if administered in a preventative fashion. Again it’s a little like cholesterol and statins. After a third heart attack it rarely helps to give a patient statins. You would want to begin treating 10-20 years ahead of time to prevent this. But with amyloid-beta in Alzheimer’s we currently have no effective assays to predict who will get the disease and when to intervene. You can’t give a drug to everyone over 65.

Me: Wouldn’t it make the most sense to just target whatever infection(s) are causing amyloid beta to be produced in the first place?

Well yes, a longterm solution may be vaccination against the microbe giving you trouble. But here’s the thing about that: there are research groups that have been pushing the role of infection in Alzheimer’s for a long time, but different pathogens are identified in their studies. Herpes simplex virus 1 is a common candidate, but also chlamydia pneumonia. This suggests there is no single pathogen driving the illness. Instead, many different bugs may be involved in Alzheimer’s. For example, our studies have found that amyloid-beta has strong antimicrobial activity against the herpes viruses and these viruses are linked to increased plaque deposition, However, herpes virus are only detected in about 60% of Alzheimer’s cases. What about the other 40%?

So it’s clear that we’re not dealing with a “classical” infection.” The findings don’t support Koch’s postulates: the idea that only ONE microbe can cause ONE disease. But we’re moving away from this “classical” infection model. We’ve been taking a close look at what microbes are found in the brain and started what we are calling the ‘Brain Microbiome Project’.

Me: Your lab is also studying the brain microbiome!?

Yes. We’ve been scanning brains as part of collaborative work with Mt. Sinai. And we have found that even “non-sick” humans harbor over 200 organisms in the brain. Those numbers don’t even include the virome (viruses). And we know that a bunch of herpes viruses can also survive in the brain. There’s even vertical transmission of certain viruses in the human genome.

So infection in Alzheimer’s may be similar to what we’re seeing in conditions like Crohn’s disease. In Crohn’s the bowel is disrupted but the entire gut microbiome is involved. It’s not a single pathogen but disruption of a whole microbial community. Within that framework certain key pathogens may “push” the community out of balance and contribute to disease more than others. In Crohn’s it’s where the microbiome meets the innate immune system that things go wrong and host pathologies arise. That’s where the problem in Alzheimer’s may also lie: at the interface between microbes and a foot soldier of innate immunity – amyloid-beta.

Going back to the brain microbiome: the microbes don’t just sit there. They cooperate, they’re competitive, they interact with the host and each other: it’s a true microbiome. What this means for Alzheimer’s is there could be general dysbiosis (imbalance) of the brain microbiome. There’s a normal brain microbiome, but in Alzheimer’s something may go “out of whack” and some of the bugs go bad (they become bad players). It could be compared to ulcers. Ulcer formation is linked to the bacterium H. pylori. But H. pylori is actually also a member of the normal gut microbiome. That means H. pylori contributes to ulcers under certain negative conditions. This is tentative, but in Alzheimer’s maybe the herpes viruses also go out of control. That is the model we are exploring at the moment. 

The brain microbiome and gut microbiome communicate via the Vagus Nerve

Linked in with that model is the gut microbiome because the gut microbiome and the brain microbiome communicate a lot via the vagus nerve. There’s lots of traffic, with bacteria in the brain/gut talking to one another via this highway all the time. Some products of gut fermentation like Short Chain Fatty Acids (SCFAs) literally travel the Vagus Nerve (physical translocation). Immune cells in the brain need these gut microbial SCFAs to mature correctly. Conversely, certain bacteria in the gut live exclusively off chemicals generated in the brain that are transported to the gut. Vagus Nerve traffic may include bacterial signaling molecules called quorum sensing molecules. In this sense microbes in the gut and microbes in the brain may be “talking,” and possibly reaching decisions about what to do next.

So, what’s going on in the brain can have dramatic effects on the gut. But, the gut microbiome can also affect neurological functioning. For example, the disruption of the gut microbiome is now linked to depression – it’s a two-way axis.

And remember, because amyloid-beta can form a vast number of oligomers, it’s able to react against an large range of pathogens. So right now amyloid beta’s activity leaves open a big question mark as to the exact nature of the infection it may be targeting in Alzheimer’s or related conditions. Which means that vaccination against one pathogen in Alzheimer’s (that I mentioned as a possibility before) might prove too simple an approach. Instead, we may want to ask “Can we modulate disease progression by manipulating the microbiome and/or the gut/brain axis.”

Me: You’ve been studying amyloid beta’s antimicrobial activity against HHV6. Where is that study?

Yes, we’ve tested amyloid beta’s activity against herpes simplex virus 6 (HHV6). There are no good animal models of chronic HHV6 infection, so we are using the “Alzheimer’s in a dish” system to look at this at the moment. Each chip is like a little human brain, that is basically thinking and shooting signals back and forth. This makes the experimental model more human-like and allows for better testing. We found that HHV6 induced a large amyloid burden in the “Alzheimer’s in a dish” system within a day. Key to our findings is that these herpes viruses are “low and slow” microbes whose pathogenic activity ramps up with opportunity. This makes HHV6 extremely effective at seeding amyloid beta deposition over time, even over the course of decades. We hope to get funding from the Cure Alzheimer’s Fund to develop a Alzheimer’s disease mouse that can be infected with human HHV6 (the mice need to be ‘humanized’ for a receptor critical for HHV6 infectivity).

But you can’t formally read about the results of that study at the moment. We submitted a paper with the findings to the journal “Cell.” The journal insisted on publishing an online pre-print before the paper was formally accepted. That pre-print was critiqued by researchers who reject a role for infection in Alzheimer’s etiology – not that our study actually claimed that. It showed strong data that amyloid-beta protects against herpes in the lab. Then, Cell rejected it after 6-weeks. The situation has hurt that study tremendously. While I understand that scientific journals are motivated by a genuine belief that expediting dissemination of new and exciting data is a good thing, I would caution other research teams not to allow a pre-print to go up before the study is accepted for publication. It can go disastrously wrong and it’s not worth it. Not worth it at all. We are submitting the findings to another journal.

Having vented a little on this… I have to say that healthy skepticism is key for advancing science. My problem is not criticism – throughout my career legitimate concerns and criticisms have been invaluable for refining our ideas and showing the way forward. My problem is when strong data with no obvious flaws are rejected out of hand because they do not fit current dogma and are dismissed for perfunctory reasons.

Phew! It’s sure hard to get new findings published. With that in mind, how do you get funding for your research?

This past October, Moir and Tanzi spoke about infection/Alzheimer’s at this “Cure Alzheimer’s Fund” Symposium.

NIH funding is hard for us to get – they are somewhat risk adverse and typically fund studies that explore prevailing ideas: “Evolution not revolution.” Fortunately, we are supported by some foundations that are willing to take risks. One is the Cure Alzheimers Fund in Boston, whose founders include successful Venture Capitalists. They are used to high risk ventures. For them, if only 50% of their funded projects have a successful outcome that’s a good result – it’s much better than the success rate among new businesses! I also get funds from Good Ventures, which is part of the Open Philanthropic Project out of California.

Me: Have you read some of the recent studies that have detected a range of fungi in Alzheimer’s brains?

Yes. And amyloid-beta is strongly anti-fungal. But of course there are fungal communities in healthy brains too. The organisms we’re finding in the human brain are incredible. For example there are amoeboid worms! Up to 20% of humans harbor toxoplasmosis (the Toxoplasma gondii parasite) in the brain. We’ve even detected another worm in some of our brain samples that was previously only thought to infect dogs. Remember that the nasal bulb is a primary source of entry for these and other microbes. Interestingly, efferent nerves from the nasal bulb trace straight back to brain areas where amyloid-beta formation starts.

Have you seen the Lund University study showing that PrP (prion) protein is also a potent antimicrobial peptide?

Yes. And we’ve tested PrP’s activity in our own lab. It’s a strong antimicrobial peptide. But it goes beyond that – amyloid creation happens in a range of human inflammatory conditions. Diabetes is an amyloid disease (in both type 1 and type 2 diabetes amylin is created in the pancreas). At high levels, this amylin is toxic to pancreas islet cells and highly pro-inflammatory. But it’s also one of the most potent antimicrobials we have ever tested – it’s able to target most pancreatic pathogens, including E, faecalis, a common cause of pancreatitis. There’s also an amyloid generated in the heart that is linked to heart disease. So the potential importance of recognizing amyloid can play a normal and protective role in immunity has legs well beyond just Alzheimer’s.

Me: Do you talk to other research teams studying these other forms of amyloid?

Yes. We have multiple collaborations going on around the world. In fact I collaborate so often with other labs that I spend half my time on the phone. There’s both a collaborative and competitive atmosphere that helps drive things along. I am delighted we are no longer alone in pursuing this line of investigation.

That being said, most research teams aren’t thinking this way. And for many of these teams, accepting amyloid-beta’s role as an antimicrobial peptide is like trying to turn around an 800 pound gorilla on a dime. It’s a paradigm shift, so it will likely take years for the focus to shift.

For example, when we tried to publish our 2010 paper on amyloid beta’s antimicrobial activity, the peer review process was extremely frustrating. We submitted the paper to the journal “Nature.” From the start the editors seemed hesitant about publishing the findings. Then they consulted with an Alzheimer’s “expert”, who it seems from comments didn’t even bother to read the paper, but rejected it anyway. The most recent paper in 2016 was rejected six times without review. The reviews we did get from one top-tier journal were some of the most appalling I’ve ever read in my life. One reviewer kept asking why we did not see amyloid in our control worms – the ones that DO NOT express amyloid-beta.

After decades of rejection, Barry Marshall and Robin Warren won the Nobel Prize (Picture:

Me: That is extremely frustrating. I find it interesting that the scientific community frequently references the story of Barry Marshall and Robin Warren. The two researchers discovered that h.pylori bacteria plays a key role in driving ulcer formation (during a time when ulcers were believed to be caused only by stress and spicy foods). When they first presented these results, they were ignored and in some cases even mocked by other research teams. It took decades for their new finding to be taken seriously. Then, in 2005 they were awarded the Nobel Prize. The story is often referenced as though the scientific community has learned from this experience and is now more open minded. But when I look at how your work has been received thus far I’m not sure I see much progress.  

Yes. Also, Barry Marshall was my old microbiology instructor when I studied at the University of Western Australia. He did struggle with recognition for a long time. There are all sorts of urban legends about how he kept the research going in the face of the wall they kept butting up against.

Me: True. And final question: What studies are you planning to do next?

In a next study, we hope to look at the actual microbiome in the brain. Then remove amyloid plaque from this tissue and see if we can identify the exact microbes the plaques have trapped. We’ll do this by seeing if we can recover the genetic material of the seed microbe.

Me: That’s amazing. I can’t wait to see what you find. I’m going to let you go because I want you to get back to work immediately:)


Cholesterol, fat, and human metabolism: a microbiome-based paradigm shift

December 15th, 2017 by Amy Proal

At the age of 64, after a morning playing golf, president Dwight D Eisenhower had his first heart attack. As Pulitzer Prize winning author Gary Taubes describes in his book “Good Calories, Bad Calories” Eisenhower’s heart attack “constituted a learning experience on coronary artery disease (CAD).” After the event, his doctors, considered the top experts in the field, gave the public a “lucid and authoritative description of the disease itself”, followed by twice-daily press conferences held on the president’s condition. Soon, most of America, particularly middle-aged men, became intently aware of dogma promoted by these “experts”: the notion that CAD is caused by eating foods high in fat and cholesterol.

Like much of the rest of the nation, Eisenhower began to avidly lower his fat and cholesterol intake. Yet this plan of attack was counterintuitive for Eisenhower who, before his heart attack, had none of these supposed risk factors connected with CAD. His blood pressure was only seldom elevated, his weight throughout his life remained around 172 pounds (considered optimal for his height). His total cholesterol was below normal – his last measurement before the attack was 165 mg/dl, a level that heart disease specialists today consider safe. He had even quit smoking six years earlier in 1949.

President Eisenhower after his first heart attack.

After gaining four pounds, the ex-president reduced the amount of food he ate for breakfast, then eventually sacrificed lunch completely. His doctor was mystified at “how a man could eat so little, exercise regularly, and not lose weight.” Eisenhower then renounced butter, lard, and cream. But despite these additional dietary changes his cholesterol levels began to rise. “He’s fussing like the devil about cholesterol,” wrote his doctor. “He has eaten in the last week only one egg, one piece of cheese.” It got to the point where Eisenhower’s doctor started to lie about his cholesterol levels in order to keep the president calm. At one reading, Eisenhower was told his level was 217 when it was actually 223. On his final day in office, he was made to believe his cholesterol was 209 when in reality it had soared to 259. Finally, in 1969 at the age of 78, Eisenhower died of heart disease. By that time he’d had six other heart attacks.

We now know that the medical experts advising Eisenhower and the American public were wrong. In CAD, lipids, or fatty molecules, do accumulate in the arteries of patients with the disease. Indeed, CAD results from atherosclerosis: a gradual hardening and clogging of the arteries due to lipid accumulation. However, a growing body of research demonstrates that these lipids are not sourced from dietary fat and cholesterol. As Taubes describes it, the long held dogma about heart disease, in which cholesterol clogging the arteries and excess body fat are viewed as culprits, “as though the fat of a greasy hamburger were transported directly from the stomach to the artery lining” is no longer support by scientific evidence.

“Consensus thinking” led to incorrect CAD guidelines

It’s worth reading Taubes’ full book to better understand the scientific climate that, over the past decades, incorrectly linked to heart disease to dietary fat and cholesterol. For one thing, regulatory bodies were attracted to the simplicity of the “dietary fat/cholesterol clogs arteries” disease model. It was easy to communicate and implied that basic nutritional guidelines could prevent the illness. The model was also promoted at numerous “consensus” conferences: large meetings at which evidence to the contrary was often blatantly excluded.

For example, the largest diet-heart trial ever carried out in the United States was not included in medical or political debates about the best diet for the America public. Because the results opposed what was becoming the consensus view on diet and CAD, they went unpublished, (they were later published in a small cardiology journal that very few people read). The trial, which included 9,000 residents of various mental hospitals found that men on a low-fat diet had a slightly lower risk of heart attacks, although women did not. Overall, patients who had eaten a low-cholesterol diet were associated with a greater risk of heart disease.

Ancel Keys on the 1961 cover of Time Magazine. There, he advanced the idea that dietary fat “clogs the arteries”

A scientist named Ancel Keys played a central role in perpetuating the belief that dietary fat/cholesterol clog the arteries. He famously linked dietary fat to heart disease after studying seven distinct populations around the world who ate diets relatively low in fat and also seemed to have a lower incidence of CAD. However, researchers at the University of California, Berkeley later found that Keys had chosen only six countries for his comparison though data was available from 22 countries. When all twenty-two were included in the analysis, the link between fat and heart disease vanished.

In fact, Keys theory implicating diet as the cause of heart disease appeared on the cover of Time Magazine in 1961 despite the fact that at the time, only two studies had directly tested the connection. One of these studies actually proved Keys wrong. It was a British trial, in which the fat content of the meals of a group of men who had previously suffered from heart attacks was reduced to 1/3 of its previous level. A control group continued to eat a normal diet. After three years the average cholesterol levels dropped from 260 to 235, but the recurrence of heart disease in the control and experimental groups was essentially identical. “A low-fat diet has no place in the treatment of myocardial infarction,” the authors concluded in 1965 in the Lancet medical journal.

Recent studies continue to disprove the “dietary fat/cholesterol” model  

Lipids are “fatty molecules”

Despite studies like that described above, the “dietary fat/cholesterol clog arteries” model for CAD became so popular that debate on the topic continues in 2017. Many physicians and policy makers still issue “heart-healthy guidelines” urging Americans to lower dietary cholesterol/fat despite ever-increasing evidence to the contrary.

For example, a 2016 study by researchers in Finland found that a relatively high intake of dietary cholesterol was not associated with an elevated risk of coronary heart disease. Another meta-analysis found no association between consumption of saturated fats and either coronary heart disease, ischemic stroke, type 2 diabetes, death from heart disease or early death in healthy adults. A different study even demonstrated an inverse association between saturated fat and stroke (i.e. those who ate more saturated fat had a lower risk of stroke).

The authors of the first meta-analysis conclude their paper by stating: “Coronary artery disease pathogenesis and treatment urgently requires a paradigm shift. Despite popular belief among doctors and the public, the conceptual model of dietary saturated fat clogging a pipe is just plain wrong.”

In 2014 Time Magazine reversed its position on dietary fat and CAD

In 2014, even Time Magazine published a cover story reversing its position on Ancel Key’s earlier claims. The article was titled: “Eat butter. Scientists labelled fat the enemy. Why they were wrong.”

So where do the lipids (fatty molecules) driving CAD come from?

This begs the million dollar question: if lipid accumulation in CAD is not sourced from dietary fat and cholesterol, then where do the lipids in arterial plaque come from!? The results of a seminal study by researchers at the University of Connecticut provide a novel “answer” to at least part of this question. Indeed, the team’s findings are so important that they are positioned to change the future of heart disease research.

The team, led by Frank Nichols, found that two important forms of lipid detected in diseased artery walls are created by bacterial members of the human microbiome. More specifically, both lipids (Lipid 430 and Lipid 654) are made by bacteria from the phylum Bacteriodetes: a family of bacteria so common to the human body that they represent 1/3 of bacteria currently able to be cultured from the human intestine.

The team arrived at their results by analyzing lipids in atheroma collected from patients at Hartford Hospital in Connecticut. They identified bacterial Lipids 430 and 654 in the samples, and distinguished them from human lipids by analyzing their chemical structure. Both Lipid 430 and Lipid 654 contain fatty acids with branched chains and odd numbers of carbons (a structure not typically associated with human/mammalian lipids).

In a press release about the study, Nichols stated the following about Bacteriodes bacteria: ”I always call them greasy bugs because they make so much lipid. They are constantly shedding tiny blebs of lipids. Looks like bunches of grapes.”

Recovery of Lipid 430 and Lipid 654 in common Bacteroidetes bacteria.

Interestingly, both Lipids 430/654 were shown to activate TLR2 – a protein at the heart of the immune system’s response towards foreign/infectious threats. This suggests that the human immune system recognizes Lipids 430/654 as foreign, and mounts a sustained inflammatory response to their presence. These results “jive” with the fact that atherosclerosis is now understood to be a serious chronic inflammatory disease.

Nichols and team contend that Lipids 430/654 are created by Bacterioides bacteria in the gut/mouth. Under such conditions, lipids produced by these microbes would travel to the arteries via the bloodstream. However, additional research is needed to confirm that bacteria capable of living directly in the arteries don’t additionally contribute to lipid creation. For example, one study found that periodontal bacteria in the mouth can directly invade human arterial skin cells in culture.

In addition, Stanford researcher Stephen Quake recently reported the presence of thousands of previously undetected microbes in human tissue/blood. Many of these “new” microbes may also produce lipids capable of collecting in the arteries. It’s also worth noting that dead white blood cells (macrophages) are often found near lipids in arterial plaque. Since many intracellular pathogens directly infect macrophages, these dead cells may represent those parasitized by infectious agents.

Bacterial lipids may disrupt human metabolic feedback pathways

The accumulation of bacterial lipids in human arteries helps account for the “plaque” and chronic inflammation characteristic of atherosclerosis. However, bacterial lipids may also promote various forms of disease by interfering with human metabolism.

An extremely important paper by Tony Lam and team at the University of Toronto details feedback pathways that control hormonal signaling between the human gut and the human brain. These pathways help the body regulate appetite control, energy expenditure, and other important mediators of human metabolism. Lam’s paper shows that, in conditions like diabetes, glucose levels are regulated by a complex network of these pathways – many of which sense hormone/nutrient production in the gut and relay this information to the brain via the nervous system.

Gut peptide hormones and regulatory signals are released along the length of the gastrointestinal tract. (Lam et al)

Most of the pathways described in Lam’s paper are too complex to detail here, but the CCK pathway provides a good example of their general function. CCK is a gut hormone released following a meal. It acts on local gut receptors to help the body regulate glucose levels. CCK is secreted in the small intestine in response to fatty acids or lipids. It conveys information about these lipids (amount, composition, structure) to the brain. The brain integrates this information with signals arriving from related pathways and signals back to the gut to adjust glucose levels accordingly.

Under conditions of health, the CCK pathway is tightly controlled by the human body. It is governed by a series of “checks and balances” that help keep glucose and other hormones/nutrients in a normal range. This begs yet another important question: what might happen to the CCK pathway (and related pathways) if foreign, bacterial lipids accumulate in the body?

While there are differences between human and bacterial lipids, the fatty molecules created by both species also share many common chemical structures (molecular mimicry). For example, the Nichols study found that Lipids 430/654 are similar enough in structure to human lipids that they can be “broken down” by the same human enzyme (PLA2).

This means that human signaling molecules may be able to “sense” the presence of bacterial lipids. In the case of the CCK pathway (in which CCK is created in response to lipid concentration) this could significantly change the information the hormone conveys to the brain: in simple terms, the brain would begin to adjust glucose levels based off a sum total of human lipids AND bacterial lipids.

Many of the Bacteriodes bacteria that create lipids are major human pathogens – eg. members of the genera Prevotella, Tannerella, Capnocytophaga and Porphyromonas (a driver of to tooth decay). If the human brain integrates lipids created by these pathogens into the input it uses to adjust glucose levels and other aspects of human metabolism, serious illness may result.

In summary, there are three main ways bacterial lipids can drive human heart/metabolic disease:

  1. Bacterial lipids are created (or travel) to human arteries where they may contribute to formation of arterial “plaque.”
  2. The human immune system reacts to these foreign bacterial lipids, which results in sustained, chronic inflammation.
  3. Human feedback pathways may incorrectly “sense” foreign bacterial lipids, and factor them into signals controlling human glucose levels and other aspects of human metabolism. This would “throw off” or “mess with” these human pathways in a manner that promotes disease.

Imagine the satisfaction of going back in time to tell President Eisenhower about the Nichols and team findings. While preliminary, they suggest that he could probably relax, eat a second egg, and feel a little less crazy. The same goes for millions of patients around the globe, who must “re-learn” basic heart disease guidelines – but in the context of research that may better address the “root cause” of their symptoms.

Interview with neuroscientist Michael VanElzakker: Vagus Nerve, ME/CFS, latent infection and more

December 7th, 2017 by Amy Proal

Michael VanElzakker Phd, is a neuroscientist affiliated at Massachusetts General Hospital, Harvard Medical School, and Tufts University. He has two primary research interests: PostTraumatic Stress Disorder, or PTSD, and Myalgic encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). He recently published a paper describing a novel hypothesis for ME/CFS that centers on infection of the Vagus Nerve.

Note: This interview was transcribed from written notes and not an audio recording.

Background information:

Hypothesis: a proposed explanation made on the basis of limited evidence as a starting point for further investigation.

The UK PACE Trial on ME/CFS: A highly criticized trial on ME/CFS. The Trial’s results don’t fit with what most ME/CFS patients experience in real life. Please read journalist David Tuller’s detailed critique of the trial.

Unrest: A 2017 Documentary about ME/CFS. Summary: “Jennifer Brea is about to marry the love of her life when she’s struck down by a fever that leaves her bedridden. When doctors tell her “it’s all in her head,” she turns her camera on herself and her community as she looks for answers and fights for a cure.”


Me: Hi Mike, thanks for taking the time to talk! How are you?

Mike: No problem. I’m good, actually working on setting up a second screening of “Unrest” here at the Martinos Center. We’ll show the documentary on a big screen in one of the conference rooms. Have you seen it?

Me: Yes, it’s very good. My story has a lot of parallels with Jen’s. It accurately portrays a lot of what I’ve dealt with for over 12 years. It’s very painful for me to watch. How do you feel about it?

Mike: It’s great. I’m glad they showed the story of Karina Hanson being taken away from her parents – that’s something only the ME/CFS community knew about for many years. It was sort of surreal to see the story presented on a big screen. It really adds to the film.

Me: Definitely. Also Mike, before I forget, can you clarify your different jobs? You work at both Harvard and Tufts?

Mike: The office I’m sitting in now is at the Martinos Center for Biomedical Imaging, which is part of Massachusetts General Hospital. Mass General is the teaching hospital for Harvard Medical School, so I get a semi-automatic Harvard Med affiliation with my position. But I’m almost never on the main Harvard campus.

Me: Cool, and you teach at Tufts?

Mike: Yes, I’m an adjunct instructor. This semester, I’m teaching a class on research methods that’s required for undergrad clinical psychology majors – the idea is that it will help them to better think critically about the scientific literature by being able to understand methods. I also teach “abnormal psychology” to clinical psychology majors. And next semester I’ll teach a seminar that focuses on the intersection of stress and memory.

Me: Interesting. I’m glad you’re teaching research methods so that your students might learn how to not set up a trial like the UK PACE Trial on ME/CFS.

Mike: I know. In these classes, I work in ME/CFS as a subject as often as I can. And I have used the PACE trial as an example in the research methods class. First to show the importance of choosing reliable/realistic study outcomes. Also though, I’ve pointed out how the PACE trial team went on a press tour with claims that went well beyond their data. I feel that the impact of PACE on patients would not have been so negative if the team had stuck to talking about what they actually found (in terms of results). But they decided to tell the popular press that they discovered how to make people with ME/CFS recover. Again, a claim that’s just way beyond their actual data, even setting aside critiques of how they arrived at those data. Also, in the abnormal psych class I talk about how in some cases psychosocial models for disease aren’t as strong as many people assume and that many conditions that were once thought to be psychosomatic are now understood to not be.

Me: Yeah, the metrics they set for “recovery” in the trial are pretty ridiculous.

Mike: Yes, not to mention that they sent out a biasing flyer in the middle of the trial to all participants, a trial based in subjective measures. Quotes from selected patients saying things like “I feel good” or “This is helping me.”

Me: That’s crazy, I didn’t know that. What an incredible form of bias (once subjects read what other subjects say it can influence how they might rate their own experience).

Mike: Yes it sometimes looks like the PACE team so strongly believe their hypothesis that they can’t see perfectly plausible alternate interpretations of their data. And the ME/CFS UK atmosphere seems to be particularly politically charged, more so than here.

Me: The whole thing is very frustrating. I get particularly annoyed because I’ve now found doctors, friends etc. who take my ME/CFS really seriously. So in my own case, I’m not forced to deal with the “psychosomatic” mindset anymore. Which has freed me up to spend more time learning/reading about actual biological dysfunction in ME/CFS. I wish it could be that way for everyone.

Mike: Yes, it’s frustrating for me in that sense too. When joining the ME/CFS research community I had to make a decision: to put my head down and just do science, or to also really make an effort to interact with and advocate for patients. I decided to advocate for patients, and in order to do that I’ve had to spend hours reading about PACE and digging into related critiques (because that’s what patients are dealing with day-to-day). But that’s time I could spend researching the biology. Also the 5 million that went to PACE: I could do a lot of really relevant/important ME/CFS research with that money.

In terms of doctors, ME/CFS patients have to do a lot of work to find a doctor. Few doctors are familiar with the condition. Sometimes I’m asked “Who’s a good ME/CFS doctor in Boston”, and I don’t know someone to recommend. I know well-intentioned physicians, but they haven’t necessarily kept up with the ME/CFS literature. Also, I think doctors find it harder to accept ME/CFS patients because it takes more time per patient to figure out what might be going on. As we know, its certainly not a situation where they can just prescribe an ME/CFS pill. So right now there isn’t much of a place for the condition to “sit” in the medical world – should it be in infections disease? or neurology? – and we’ll likely see ME/CFS shift and change between specialists for a while.

For example, right now I’m collaborating with a pulmonologist to run exercise tests on ME/CFS patients. It’s a collaborative study where we’ll do patient brain scans before and then after exercise testing (with a focus on tracking changes in the autonomic nervous system). But even this great pulmonologist doesn’t exactly specialize in treating ME/CFS patients, specifically.

Also medical textbooks need to be updated to describe ME/CFS more accurately. In my abnormal psychology class I’ve made a point of showing my students how our own textbook poorly describes the illness. The textbook description isn’t terrible, but it could be way better. There’s mention of ME/CFS in the section of the book that gets into somatoform disorder (a mental disorder that manifests as physical symptoms). Somatoform disorders are a real phenomenon, but is probably vastly over-diagnosed. So I’ll tell students, “Somatoform disorders are real but they ought not to be the first place doctors look!…and should not form the default thinking on any disease. Also it’s not OK to resort to assuming someone has a somatoform disorder because the blood tests you’re running don’t show clear results.”  The influential psychiatrist Allen Frances, the primary author of the previous DSM (the manual of psychiatric diagnoses), recently stated that somatoform disorder should not be the default diagnosis for unexplained physical symptoms, and I agree.

Returning to the textbook we use in class, I actually met the textbook author at a conference. We got a drink. In a very collegial way I pointed out how the book’s description of ME/CFS could be updated. For example the XMRV controversy that the book mentions is behind us in my opinion. I’m not sure how seriously the textbook author took my feedback but he sounded sincere and said thank you.

You know what has also been frustrating lately? It seems like each new press release about ME/CFS research states, “Our findings put to rest the idea that ME/CFS is a psychosomatic illness” But IMO, research has existed for decades showing ME/CFS is a biological disease. So by mentioning the psychosomatic theory for ME/CFS we are actually giving it credit. I think we should act like it’s not even worth referencing.  

Yes. I’ve realized I need to change my own approach. In the past I’ve been using the standard ME/CFS intro sentence when writing about it: Something like “Chronic Fatigue Syndrome is a poorly understood, crazy complicated disorder/mystery that has everyone completely baffled.” But over the last months I’ve realized that description is just untrue. Of course not everyone agrees on what triggers the illness, but in some cases we kinda do. Many patients (if you ask them!) can tell you how their symptoms started (I got Mono, I got sick when traveling in Colombia and never got better, etc.). It’s hardly like we’re dealing with a complete black box of information. Also, there’s “mystery” surrounding almost every human chronic disease. For example in cancer, we don’t understand why cancer cells can’t stop replicating. But we don’t describe cancer as a hopeless mystery. So I’m going to stop using that kind of language. I feel like it intimidates clinicians/researchers and adds to an aura of debate (“is this psychosomatic or not?”) that’s not justified. It also gives clinicians an excuse to throw up their hands up and say, “It’s just too hard to treat patients with ME/CFS.”

Me: That’s great. I hope other research teams follow your lead. Also, considering this climate, what made you willing to research ME/CFS?

Mike: I have a friend with serious ME/CFS. I was a late user of the internet but when I got on Facebook I reconnected with people I hadn’t talked to for years. I messaged a high school friend of mine, “What have you been up to?” It turned out she had been forced to drop out of law school because of ME/CFS. She was sick as hell. And before having to drop out she was so talented that she was set to graduate early. She’s an engaging person and I could feel her frustration about being sick. Also anger at dealing with being told she had the “yuppie flu” and other misconceptions. This is a bright, motivated person and I could see her devastated by the illness.

At the time I was a University of Colorado undergraduate student. My research focused on stress/memory in PTSD (still my second life!). But I had friends doing neuroimmunology research. I would go to those friends’ presentations and talk to them about neuroimmunology. I also found myself brainstorming about my sick friend. I formed the basis of my Vagus Nerve hypothesis for ME/CFS. Then I chatted with Linda Watkins, a professor in the Department of Psychology and Neuroscience. She’s an esteemed researcher who’s done great work on the intersection of the immune system and the nervous system. She even won the Spanish version of the Nobel Prize. I spoke with her and asked, “What would happen if a neurotrophic virus got right into the Vagus Nerve? Could that look like ME/CFS?” She’s not a hyperbolic person but she seemed really stunned and told me, “Oh my God, all it took was for someone to put it together.” That moment has carried me through a lot of frustration and disappointment as I tried to get people to listen to the idea and follow up.

Me: I love how you listen to your friend and to other patients and use their feedback to help inform your research

Mike: Yes, there’s an obnoxious strain of elitism that often impacts ME/CFS patients. It centers on the idea that patients are fooled by their own silly brains. I feel the opposite way. For example, I have great appreciation for my friend with ME/CFS. I constantly ask her very personal questions about her body/symptoms, and she’s totally willing to give me feedback. To act this way your have to be willing to step outside typical institutional roles in which people like me are the real experts. You have to be willing to think, “This patient is more than likely just as smart as I am. I’m going to interact with this person as a thoughtful, critical human who has real insight into their condition.”

Me: Yes! Before we go on, could you explain the ME/CFS hypothesis you’ve published? It centers on infection of the Vagus Nerve…

Mike: Sure. So when an otherwise healthy person gets sick with pretty much anything, many of the symptoms they experience will be similar no matter what specifically is making them sick. For example, people with both Strep and the flu feel extra tired, achey, and have problems with lack of concentration, loss of appetite, reduced sex drive, etc. This is true despite the fact that the flu is  a virus and Strep is a bacterial infection. These similar symptoms occur as part of the body’s general “sickness response:” a response driven by the innate immune system (the more ancient branch of the immune system that first recognizes and combats infection).

These “sickness response” symptoms overlap with important primary symptoms of diseases like ME/CFS. This suggests that a sustained and exaggerated, “sickness response” may be a core component of ME/CFS. How might this come to pass? When the innate immune system detects pathogens (microbes causing disease), it generates cytokines (signaling proteins) in an effort to target and draw attention to the infection. These cytokines are created locally at the site of infection (they don’t always make it into the general bloodstream). Still, the brain is able to perceive and respond to this cytokine activation. So how does this work?

Cytokines are relatively large lipophobic polypeptide molecules, so they don’t easily cross the blood/brain barrier. Instead the brain senses changes in cytokine activation via a nerve that conducts signals from the body to the brain, the Vagus Nerve. The Vagus Nerve is an extremely important conduit between the nervous system and the immune system (especially because it densely innervates parts of body in contact with outside world like the lungs and stomach).

A number of key pathogens such as the herpes viruses and the bacterial species Borrelia burgdorferi (Lyme disease) particularly like infecting nerve tissue (they are neurotropic). The hypothesis I put forward in my paper posits that, in ME/CFS, a number of different possible pathogen(s) may directly infect the Vagus Nerve. Resulting cytokine signals relayed to the brain then cause a sharp rise in “sickness response” symptoms. Because the signaling is directly on this sensitive nerve, the brain “overreacts” to these signals and sort of perceives that the entire body (and not just the Vagus Nerve) is infected with pathogens. If this is the case, these “sickness response” symptoms will be exaggerated. In addition, the signaling may not stop correctly, and could induce a snowball effect “feed forward” loop that sustains chronic symptoms. This would be similar to the way a war veteran might still sense pain in an amputated toe (inflammation has triggered a cascade reaction that can sustain itself).

If I were to update the hypothesis today, I would clarify that the Vagus Nerve also plays a large role in relaying information about the human microbiome to the brain, and adapts signaling based on microbiome composition/activity. I would also add rat/mouse studies showing that a pathogen doesn’t have to be fully “active” for nerve and glial tissue to sense its presence. Many viruses persist in latent, chronic forms that aren’t detected well on blood tests but could still be contributing to symptoms.

Me: I love the emphasis on infection of nerve tissue. I’m not sure many people realize how easily nerves can become infected. But question: is it possible that, in ME/CFS the Vagus Nerve is infected, but other chronic pathogens are also infecting other areas of the body (immune cells in the blood, etc.). In that case, the inflammation that triggers “sickness response” by the brain via the Vagus Nerve might not be exaggerated, but actually correct?

Mike: That’s totally possible and something we should also be considering. In order to test that possibility we could look for glial cell activation in the periphery (areas farther away from the central nervous system). Maybe we could add LPS (molecules that trigger a response towards infection) into the periphery and see how Vagus Nerve signaling is impacted. But those are early ideas, and we’d have to sit down more seriously to really tease things apart.

Me: Aren’t most microbes in the body technically “latent” in that microbiome populations are acquired in the womb and often persist with us throughout our lives?

Mike: I was talking more about acquired pathogens. But I agree that the microbiota count as organisms that survive for long periods in the body. And if components of the microbiota begin causing inflammation then the nervous system will likely detect it, relay it to brain, and trigger “sickness behavior” and other related responses.

Me: I see. What factors made you decide to formally publish your hypothesis?

I was a grad student at Tufts working studying PTSD when my advisor went to Korea for a few weeks with her family, so I had a little extra time. I thought, “Why don’t I just write this up?” – I had put a lot of text together from my previous life when I was working in rat labs. But at the time I didn’t intend to get into the ME/CFS field. I thought that if I wrote up my hypothesis, and better explained some info on how cytokines work etc., another research team might take the idea and run with it.

Me: I take it that didn’t happen?

Mike: No. A lesson I learned is that if you want something done you kinda have to do it yourself. Other people might become organically interested in your hypothesis but are unlikely to pursue it as doggedly as someone personally invested. Now I find ME/CFS very interesting to work on, but it’s very different than studying PTSD. In the PTSD research community there exist differences in opinion but most of us are pulling on the same rope. Of course there are controversies, but the atmosphere is not as politically charged as with ME/CFS, where there is broad, controversial argument about what the disease even is. And with ME/CFS I spend a lot of my energy doing patient advocacy work, communicating with patients, etc.

I actually think that part of what I’ve tried to contribute to ME/CFS is being able to talk about this condition while having fancy institutions (Mass General Hospital etc.) listed next to my name, which seems to help ME/CFS legitimacy. It’s a little crazy that thanks to the building I sit in, I can get people to listen to some of the things patients have been screaming for decades.

Me: I think it’s great you were willing to form a solid hypothesis about what causes ME/CFS. When I publish on ME/CFS I also tie my insight to a specific hypothesis. I think doing so makes what I put forward easier to follow, test and even discredit if necessary. But many research teams seem nervous about publishing hypotheses. Why do you think that is and should that mindset change?

Mike: Scientists generally ought to be at least trying to tie their data to a hypothesis. I do wish the field would put more effort into looking at how their data relate to existing hypotheses. Most papers are currently published as phenomenology (aka “this is happening in people’s bodies”), but many lack a framework that attempts to explain why things are happening. That makes it much harder to decide what direction to move in next. In ME/CFS we’ve known for years that metabolism, the immune response, the neurological system are off. It’s time to get more into the specifics of why this might be happening.

Me: Your specific hypothesis aside, I also like the way you wrote your recent ME/CFS paper. You use “simple” language that patients can understand, and went out of your way to define difficult terminology. 

Mike: Yes, in the original draft I was writing largely for patients. I actually included way too much background and it got too long, so I dialed it back. But my writing was very much intended for people who didn’t already know the stuff. When I look at the ME/CFS research community almost everyone involved with the disease is personally impacted. So they didn’t set out to formally study ME/CFS from the get-go. This leads to situations where some orthopedic surgeon with a sick cousin decides to research ME/CFS. Such people may need more context for areas outside their training.

That being said, a lot of the simplified language in the paper is a result of the peer-review process. It was the most contentious review process I’ve ever had – some of it was really condescending and smug. The responses had “ou” spellings so I wondered if one of my reviewers was a UK-based psychiatrist. I had to lay stuff out so this reviewer would understand. For example, I created the “terms table” in the paper as a response to the reviewers seeming to not know some of the terms.

I also got a comment from a reviewer commenting on a perceived misuse of an anatomical term stating, “The author seems to have a lack of medical schooling.” And I had to respond, “The reviewer may be unfamiliar with the spinal cord literature” because I was using the term correctly. The reviewer even said they ended up reading an enormous amount of extra literature to follow what I was saying. I appreciate that they did that, but the whole thing took a lot of time.

Also, my original draft didn’t mention the PACE trial. But I got some feedback from a psychiatrist who convinced me to write a section about it. At the time I didn’t really appreciate the depths of the problems in that study, most of which are not visible from only reading the actual publication. I saw it was published in the Lancet (a very highly regarded journal) and assumed it had undergone a rigorous peer review. Now I regret that.

Me: In your paper you mention possible treatment options that fit your hypothesis. How has that been received?

I wanted to be careful talking about treatments because I know that desperate patients sometimes run out and try new things based on very scant evidence. I mentioned antivirals and I have seen some people improve by taking them. But treatment is probably going to require critical thinking and a personalized approach. I don’t think there will ever be an ME/CFS pill – instead we’ll have to think about mechanisms and what’s going on with individual patients. Looking at a patient’s history is important (for example one patient might have had bad chicken pox as a teen, another Mono, another may have gotten sick after traveling). It will probably have to be systems that we target. That can make clinical trials super messy, with some treatments hard to test in a standard randomized placebo controlled trial in which all patients receive the same exact intervention.

We may also need separate treatment interventions (or treatment cocktails): treatments that attempt to get rid of possible infectious agents and others that could help patients manage the putative excess inflammation itself. When it comes to therapies that target the Vagus Nerve, Transcutaneous Vagal Nerve Stimulation is promising. The treatment targets the branch of the Vagus Nerve that comes close to the outer ear and allows action potentials to be sent down the nerve. This stimulates the normal anti-inflammatory reflex of the Vagus. I know a handful of ME/CFS patients who’ve been playing around with this Vagal stimulation. Some have felt better, some have noticed no effect, and others have suffered from side effects. So there’s a spectrum of responses but it’s one arrow in the quiver to think about.

Me: I’m a big fan of how you share information on Twitter. In fact, you recently asked for brain scan donations in a Tweet. I think that’s awesome. It helps people donate money towards a specific goal with an outcome that’s easy to follow

Yes, so far my salary as a post doc has been paid by donors. These donations are sent to Mass General and are enormously helpful. I’m really appreciative. But it’s also so hard to start a research position from scratch. Normally as a post doc I would enter an already-established lab that’s already doing the kind of work I want to do. But I’m starting something totally new with my ME/CFS research. It’s a stupid amount of work:) For that particular project I want to run a handful of brain scans to get good pilot data. Just five scans would be enough, so that’s what I am trying to raise. And even if donations trickle in slowly, when I reach $5900 I can do the scan immediately. That’s opposed to applying a formal grant for millions of dollars and waiting long periods for a decision.

It’s a bit of a Catch-22 because it’s hard to apply for big money without data, and hard to get data without money. If I do the scans with private funding I can use my pilot data to hopefully get a larger government grant. I want to call the NIH’s bluff and see if they really are willing to fund research here. Francis Collins and the NIH seem earnestly invested in helping ME/CFS. So I’m gonna get good pilot data and say, “Here you go!” Now really fund this:)

Me: I’m changing the subject a little, but since you work with PTSD, what do you think about the use of psilocybin as a treatment? I’ve read several fascinating articles on early trials of psilocybin in cancer (it dramatically improved patients’ emotional health)

In the PTSD field, psilocybin research has not advanced as far as MDMA research (MDMA is also called ecstasy). For patients with PSTD, MDMA can certainly help them feel good and help them talk/open up. But it seems as though that’s not the only mechanism at play. It’s also been shown to enhance fear extinction learning in rodents. It’s very worth studying but it’s important the drug is administered in a safe context. Both psilocybin and MDMA are fascinating areas of research. It’s too bad the USA still has a strong drug war mentality that makes conducting studies with these drugs much harder to do.

Me: Can you test for prions in patients with ME/CFS? In my last blog post I wrote about their antimicrobial activity (a topic I find fascinating).

Mike: No unfortunately my lab isn’t set up to detect prions. But I’ve been chatting with some folks about prions, here and at MIT. The antimicrobial activity of both prions and amyloid beta is kinda a million dollar idea. I’ll also send you a recent study showing that bacteria themselves can create prions.

Me: Aw too bad you can’t test for prions but send me that study!

Mike: OK

Me: I should probably let you go…you have lots of work to do! Thanks so much for taking the time to talk.

Mike: No problem. Take care:)

Antimicrobial activity of amyloid beta and PrP in neurological disease: a paradigm shift

November 17th, 2017 by Amy Proal
Amyloid beta (brown) forming near a nerve cell (pink) of a patient with Alzheimer's (Graeber et al)

Amyloid beta (brown) forming near a nerve cell (pink) of a patient with Alzheimer’s (Graeber et al)

Many neurological conditions are characterized by the formation of proteins or “plaque” in brain tissue. Two such proteins are amyloid beta and prion protein (PrP). Amyloid beta forms the “plaque” associated with Alzheimer’s disease. PrP has been detected in the brain/nervous system of patients with Parkinson’s Disease, schizophrenia, bipolar disorder, and even major depression.

Most of the scientific community currently regards both amyloid beta and PrP as drivers of neurological inflammation and disease. In Alzheimer’s, amyloid beta “plaque” is believed to be a useless substance that promotes symptoms and degeneration. PrP is best known for its association with Mad Cow Disease. In Mad Cow Disease and related “prion disorders” PrP protein is believed to fold incorrectly. This “misfolding” allows PrP to better access brain tissue, where it is also believed to cause symptoms and dysfunction.

However, several recent studies by researchers at Massachusetts General Hospital (Harvard) and Lund University Sweden challenge the above assumptions. In fact, their groundbreaking research calls for a complete re-evaluation of the role amyloid beta and PrP play in neurological disease. The Harvard/Lund studies demonstrate that both amyloid beta and PrP have a previously undiscovered function: they are potent antimicrobial peptides. Antimicrobial peptides are natural, broad spectrum antibiotics created by the body that destroy bacteria, enveloped viruses, fungi and even transformed or cancerous cells.

How does this change the game? If amyloid beta and PrP are antimicrobial peptides, they serve a protective role in patients with Alzheimer’s, Parkinson’s, and other conditions. Both proteins almost certainly form as part of the immune system’s response to infection in patients with these conditions.

Amyloid beta

The antimicrobial activity of synthetic forms of amyloid beta and LL-37 were determined as minimal inhibitory concentrations against 12 microorganisms (Moir et al)

The antimicrobial activity of synthetic forms of amyloid beta and LL-37 were determined as minimal inhibitory concentrations against 12 microorganisms (Moir et al)

Amyloid beta’s potent antimicrobial activity was first characterized by Moir and team at Massachusetts General Hospital. In 2009 they reported that, in the laboratory, amyloid beta inhibited the growth of eight important pathogens screened by the study (see chart to the right). These included the bacterium S. pneumoniae: the leading cause of bacterial meningitis.

The pathogen that Moir and team identified as being most sensitive to amyloid beta is the fungus Candida albicans. Indeed, Moir and team found that the antimicrobial activity of amyloid beta was so strong that in some cases, its activity exceeded that of LL-37 – one of the body’s most potent and broad-spectrum antimicrobial peptides.

Infection-induced amyloid beta deposits co-localize with invading S. Typhimurium cells in 5XFAD mouse brain. (Moir et al)

Infection-induced amyloid beta deposits co-localize with invading S. Typhimurium cells in 5XFAD mouse brain. (Moir et al)

In a second 2016 study, Moir and team showed that amyloid beta protects against fungal and bacterial infections in mouse, nematode, and cell culture models of Alzheimer’s disease. In fact, when mouse brains were infected with the bacteria Salmonella Typhimurium, amyloid beta formed rapidly in response to the infection (with amyloid beta deposits closely associated with invading bacteria)

The team concluded:

..our finding that amyloid beta is an antimicrobial peptide is the first evidence that the species responsible for amyloidosis (accumulation of amyloid beta) may have a normal function. This stands in stark contrast to current models, which assume amyloid beta deposition to be an accidental process resulting from the abnormal behavior of an incidental product of catabolism (breakdown). Our data suggest increased amyloid beta generation, and resulting Alzheimer’s pathology, may be a mediated response of the innate immune system to a perceived infection.

PrP protein

Around same time that Moir and team characterized amyloid beta’s antimicrobial activity, a Swedish team at Lund University reported that PrP protein is also an antimicrobial peptide. The team found that synthetic PrP peptides killed the bacterial species Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus. PrP also displayed potent antimicrobial activity against the fungus Candida parapsilosis.

Expression of PrP as an antimicrobial peptide in wounded skin (Schmidtchen et al)

Expression of PrP as an antimicrobial peptide in wounded skin (Schmidtchen et al)

The team further reported that PrP “breaks up” microbial membranes in a fashion similar to “classical” human antimicrobial peptide LL-37. They also showed that PrP is created as a response to wound healing in human skin. Indeed, in human skin cells, PrP protein induced production of TGF-α, a cytokine the body creates to target infectious agents.

Other independent studies support PrP’s role as an antimicrobial peptide. A team in Germany found that PrP expression was increased in patients with H pylori-infection, and not in non-infected controls. PrP levels decreased to normal after successful eradication of the H pylori bacteria. The team concluded that, “H pylori creates a milieu for enhanced propagation of prions in the gastrointestinal tract.”

Another study demonstrated PrP formation in skin cells removed from patients with psoriasis, contact dermatitis, squamous cell carcinomas, and viral warts (conditions tied to infection/skin microbiome imbalance). In these skins cells, cytokines associated with a response towards infection increased PrP production. A different team found that sheep with scrapie (an infectious condition) and lentiviral mastitis secrete prions into their milk (these prions were not created in sheep without the viral infections).

Alpha-SYN production is also promoted by toxic insult, local inflammation, and oxidative stress: conditions all associated with the presence of chronic infection.

Factors contributing alpha-SYN creation in Parkinson's (Melki et al0

Factors contributing alpha-SYN creation in Parkinson’s (Melki et al0

PrP’s ability to act as an antimicrobial peptide is particularly relevant in light of research connecting Parkinson’s Disease to prion creation. This October, the Journal of Neuroscience published two articles implicating alpha-SYN (a form of PrP) in Parkinson’s Disease. While this association between alpha-SYN and Parkinson’s has been reported for decades, the papers clarify the latest thinking on the topic. The authors of each paper debate details of how alpha-SYN accumulates in the Parkinson’s brain, but both conclude with a common belief: alpha-SYN proteins CAUSE or drive Parkinson’s disease progression.

Key to the above assumption is that both research teams do not appear to have read the Lund University study showing that PrP is an antimicrobial peptide. Or if they have, they didn’t cite the paper in their references, or refer to the findings anywhere in their writing.

The Journal of Neuroscience published two articles on prions in Parkinson's this October

The Journal of Neuroscience published two articles on prions in Parkinson’s this October

This is a major problem, because just like in Alzheimer’s, alpha-SYN is very likely not causing PD, but is instead accumulating in response to an as yet uncharacterized infection, or communities of infectious agents. In fact, the discovery that amyloid beta and PrP are antimicrobial peptides IS A GIANT CLUE suggesting that infectious agents in the brain are contributing to both disease states.

What infectious agents might these be? There are many possibilities. Researchers at the University of Alberta recently detected an ecosystem of chronic microbes in the autopsied brains of patients with HIV and a range of other medical conditions associated with severe neurological dysfunction. They detected 173 bacteria and bacteriophage-derived samples. Many of these microbes were identified inside macrophages, astrocytes, microglia, and other cells of the immune system.

Several microbes identified in the brains were pathogens associated with specific human diseases. They included Delfia acidovorans, a pathogen implicated in endocarditis, bacteremia, and urinary tract infections. Delfia acidovorans has even been identified as part of the bacterial community in the arterial wall of patients who have aortic aneurysms. Viruses (including various herpes viruses) were also identified in many of the brain samples.

Another study by researchers a the Universidad Autónoma de Madrid studied the brains of patients with Alzheimer’s. All eleven Alzheimer’s brains studied were infected with a range of fungal organisms.

These preliminary findings suggest that we should greatly prioritize new studies that search for microbes in brain tissue and the central nervous system. If more microbes are identified, the data may transform current models of Alzheimer’s, Parkinson’s and other neurological conditions.

Alzheimer's disease may cost $1 trillion dollars by 2050 (Image: Benny De Grove, Getty Images0

Alzheimer’s disease may cost $1 trillion dollars by 2050 (Image: Benny De Grove, Getty Images0

Progress in this area is stymied by the fact that most members of the scientific/medical communities are not aware of the findings discussed in this post (amyloid beta and PrP’s antimicrobial activity and/or the latest studies on microbes in the brain).

This may explain why, since 2002, 400 Alzheimer’s drug trials have been run and all 400 have failed. Many of these drugs have attempted to remove amyloid beta from the Alzheimer’s brain. But if amyloid beta is an antimicrobial peptide such treatments are removing a result of the disease process rather than the cause. No wonder they don’t work!

Meanwhile, Alzheimer’s disease is the sixth leading cause of death in the USA, with a new case diagnosed every 66 seconds. Without treatment, these numbers are predicted to explode to 16 million Americans with the disease, at a cost of over $1 trillion dollars by 2050. Then, factor in patients with Parkinson’s, schizophrenia, and other conditions tied to PrP and the impact of the discoveries described in this post is TREMENDOUS.

For example, Bill Gates just announced a new mission: He is investing $50 million of his own money into the Dementia Discovery Fund, a private-public research partnership focused on Alzheimer’s research. However, the research teams he is funding do not seem aware of Moir and team’s findings on amyloid beta and/or the paradigm shift in Alzheimer’s research that the discovery warrants.

We cannot pour this kind of money into research going in the wrong direction. There is too much suffering, too much debilitation, and far too great a cost to society.  Please, if this post speaks to you, share it with as many members of the medical community as possible.


Note: It’s possible that amyloid beta and PrP play a “dual role” in chronic disease. They may combat infection initially, but cause problems if their levels become very high. For example, Moir and team point out that LL-37 (the most well-studied human antimicrobial peptide) can become cytotoxic to host cells at very high concentrations.


A final consideration: could prions (PrP) play a role in ME/CFS?

In 2008 I watched prion researcher Adrianno Aguzzi speak at the “Days of Molecular Medicine Conference” in Karolinska Sweden. His team reported that activated B lymphocytes play a critical role in facilitating prion formation.

Norwegian researchers have reported that the immunosuppressive medication ritauximab can alleviate ME/CFS symptoms. Rituximab “knocks out” B lymphocytes. If prions play a protective role in ME/CFS, their inability to form in the presence of Ritauximab would decrease patients’ ability to fight infectious agents. This would result in decreased immunopathology (less of a battle between immune cells and microbes). Inflammation and symptoms would subsequently drop, although infectious agents driving the disease would be able to spread with greater ease.

Interview with evolutionary biologist Paul Ewald: infection and chronic disease

November 11th, 2017 by Amy Proal

Paul W. Ewald is an evolutionary biologist, specializing in the evolution of infectious disease. He received his Ph.D. from the University of Washington, in Zoology, with specialization in Ecology and Evolution. He is currently director of the program in Evolutionary Medicine at the Biology Department of the University of Louisville.

Below is an interview I conducted with Ewald in 2008. What he describes is as relevant today as the day we spoke:

Screen Shot 2017-11-11 at 11.31.26 AMHow do the concepts of evolutionary biology support the idea that pathogens are to blame for most diseases?

When we consider the possible causes of disease, it’s important to make sure that at our starting point, we put all categories on the table. I believe the most useful way to do this is to think in terms of three main categories:

  • inherited genes
  • parasitic agents (this includes bacteria, viruses, fungi, protozoa)
  • non-living environmental factors (too much or too little of a particular substance, radiation, exposure to a chemical etc.)

Once we have this spectrum of categories in mind we ask, “Have all three areas been investigated?

At this point scientists tend to make an error. They decide that if they have found enough evidence for categories 1 or 3, that category 2 is not playing a role. This is a fundamental problem that has led the medical community to misunderstand the cause of most debilitating chronic diseases.

So, which of the three categories is overlooked? Category 1 certainly isn’t – once scientists figured out the structure of DNA and the nature of mutations they were extremely eager to show their relationship to disease. Category 3 hasn’t been overlooked, largely because of the fact that we can sense environmental causes of disease. We suffer from a stomach ache after eating contaminated food or feel the pain from a sunburn.

But, if we look back at every decade, there has been a lack of research on category 2 relative to its actual importance in causing disease. Our track record shows that we have consistently failed to fully understand the role that pathogens play in causing disease and this trend has continued up until 2008.

There are many examples of how we have continually overlooked the category of infectious disease. I’m not talking about acute infection – researchers were essentially able to work out the mechanisms of acute infection from 1880 to about 1920. I’m talking about chronic infection, and thus the role of pathogens in causing chronic disease.

Take the case of peptic ulcers. The idea that bacteria cause peptic ulcers was first solidified in the 1940s, then independently investigated and solidified again by Marshall and Warren in the 1970s. It took over 20 more years before the relationship was finally accepted by mainstream medicine. Now, when people look back on previous theories about the cause of peptic ulcers they think, “Oh, isn’t it surprising that we didn’t understand the cause for so long!” or “We should have known better!” But when they proceed to hypothesize about the cause of other diseases, they go right back to the dogma. They haven’t learned the lessons from the peptic ulcer story.

Instead, they should think in an opposite fashion. If we find that one disease has an infectious cause, we should learn from that information and seriously consider the same possibility in other diseases.

Think about syphilis. In 1913, it was discovered that the disease resulted from infection with the bacterium Treponema pallidum. Soon, the disease was dubbed the “Great Imitator” because its symptoms often resembled those of other diseases, particularly in the later stages. I think syphilis should be called the “Great Illustrator,” because it’s a disease that imitates a whole spectrum of other diseases. This suggests that we should be actively looking for a pathogenic cause in these other diseases as well – especially since so many illnesses are still considered to be of unknown cause. Back in the day, the psychoses associated with syphilis and schizophrenia were grouped together into a single category of illness. But as soon as syphilis was found to have a bacterial cause, we separated syphilitic insanity from what is now called schizophrenia, and assumed that schizophrenia was not caused by infection. Rather than just separating the two diseases we should have actively pursued the hypothesis that schizophrenia also has an infectious cause. The information we can gain from these kinds of relationships is far more enlightening than any genetic data.

That’s one of the realities of medicine – researchers tend to deny associations. Denial plays a major role as scientists love to hold on to the current dogmatic explanation. This suggests that in order for pathogens to be fully tied to chronic disease we will have to wait until the current powerful people pass away and a sufficient number of young people entering the arena without these vested interests mature into positions of influence, to tip the balance of expert opinion. This is something that Charles Darwin, Max Planck, and Thomas Kuhn all agreed with.

That’s because powerful people tend to hang on to the opinions that made them powerful even if there is no longer sufficient evidence to support their views. It’s a social problem that relates to the weakness of the mind. Human beings didn’t evolve to be scientists. Instead they evolved to be competitive – to grab and hold onto what is theirs. Hence the name calling often observed among the medical community and the resistance among scientists to fund or support ideas other than their own, ideas that question the validity of current dogma.

From an evolutionary perspective is it possible that current diseases of unknown cause could all be genetic diseases?

No. Take schizophrenia again. Evolutionary biologists understand that if an allele (a sequence that codes for a gene) were to code for a disease it would slowly get weeded out of the population, particularly since people who are sick are much less likely to reproduce (especially people with a severe disease like schizophrenia). Yet a person’s chances of getting schizophrenia are 1 in 100. The reality is that faulty genes cannot maintain this frequency. If schizophrenia was a genetic disease, then according to the rules of mathematics, it would only occur in about 1 in every 10,000 people. The current frequency of the disease is just far too high.

Some might try to rationalize the 1 in 100 number by saying that schizophrenia is influenced by environmental factors, but if this were the case the environmental factors would have to be widespread and consistent across much of the world which is highly unlikely. Yes, some populations do have a higher incidence of schizophrenia than others, but that variability is much better explained by the idea that some populations harbor more of the pathogens that cause schizophrenia then others.

This highlights another issue. The fact that illnesses tend to run in families does not mean that only faulty genes are at work. Family members could just be passing each other pathogens. If one member of a twin pair has schizophrenia, there is a 35-60% chance that the other member of the twin pair will have it. However, this may be just a reflection of the fact that both twins were exposed to the same pathogens in the womb.

Pathogens also possess the ability to evolve and adapt at rapid rates, meaning that even if the host acquires a defense against them they can often find away around it. As previously mentioned, genetic disease would gradually be weeded out of the population. But as soon as you hypothesize that a disease has an infectious origin, and that the pathogens causing it can adapt and evolve, it is possible to explain how diseases can be perpetuated indefinitely in quite severe forms.

So you support the idea that the genetic mutations picked up on by many scientists may be induced by pathogens?

Yes, it’s possible. We know that some viruses and bacteria mutate and damage DNA. Similarly, the compounds created by the body in order to continually combat pathogens are often potent molecules that can also cause genetic mutations.

Give me some examples of diseases in which an infectious agent is certainly to blame.

Cancer is really a special case of the problems we have discussed. The same dogma has been driving how the disease is viewed for so long. But if people are able to recognize the dogma for what it is, they can take a better look at definitive evidence about the disease. Taking a look at the track record of cancer researchers is a good way to decide whether the consensus view is right or wrong.

Back in 1975, mainstream medicine agreed that about 0.1% of human cancer cases were caused by pathogens. When it came to the rest of cases, their view was that they were probably caused by a combination of inherited predispositions and mutagens. Then in 1985, the percentage of cancer cases they tied to pathogens was 3%, and they continued to make the same argument about the remaining cases. In 1995 the percent of pathogen-induced cancer cases was accepted to be around 10%. Now, we’re at 20%. Still, mainstream medicine contends that the other 80% of cases do not have an infectious cause, but the questions is – do you believe them anymore? In this sense, the clarity of hindsight can help a lot. Between evolutionary instinct and plain common sense we can view the issues of pathogens and cancer much more effectively.

Or, take a disease like atherosclerosis in which noting patterns of infection is unavoidable. There are bacteria in the lesions of people with the disease and all kinds of inflammatory markers. What we need to do is take a step back, divorce ourselves from our predispositions, and look at these ideas together.

Modern medicine has done a poor job looking for clues of continued infection. This may be partly explained by the fact that in many cases, it’s hard to link a pathogen to a disease because the pathogen grows and spreads so gradually. So the time at which a person becomes symptomatic may be years after the onset of infection.

Recognizing these patterns requires thinking broadly and deeply, but medical professionals and researchers have been trained to think narrowly. They’ve tried to follow a model that resembles a NASA undertaking for a great moon mission in which every person brings his or her own particular specialty to the table. But that model doesn’t work for medicine. Instead medical professionals need to work together with a unified theory in mind. But at the moment, they don’t have a unified theory, and without a conceptual model to guide them, researchers are only able to determine risk factors for disease rather than come to an understanding of the overall cause.

Evolutionary biology is the most synthetic area of biology. It asks why things are the way they are, and integrates knowledge of how things work mechanistically. Evolutionary biology promises to be the most synthetic area of medicine for the same reason.

While we’re on the subject of cancer, it and heart disease are now considered to be inflammatory diseases. Wouldn’t the presence of inflammation be a red flag that pathogens are to blame?

Yes. And the immediate questions researchers should be asking is “What causes inflammation?” One thing that we clearly know causes inflammation is the presence of an infection. So, as soon as I hear the word inflammation I think, “What infectious agents are at play?”

That brings us to the concept of autoimmune disease – the idea that the immune system just “goes crazy.” I think the fact that the concept of autoimmunity was developed in the first place is largely related to the fact that our brains have not evolved to think scientifically. People who have studied disease from their own point of view have recognized that the immune system is extremely important. But as we’ve learned more about the immune system, we’ve realized that it is an extremely complicated system – as complicated as the brain. Just like we can’t look at one type of neuron and infer information about the entire brain, we can’t try to understand the characteristics of only some immune cells and think we understand immune function.

So, over the years, as researchers have been daunted by the complexity of the immune system, it has seemed logical that such a complex entity has the potential to go wrong. Because they are limited by the power of their brains, they tend to simplify the issue and view the immune system in the same way they would view a truck that could break down. There are two problems with this type of thinking. For starters, we can’t trust our intuition that something complex is likely to malfunction. The fact is, the immune system functions just fine in a large proportion of the population. The only logical way to explain the immune activation seen in patients with “autoimmune disease” is to suggest that there is some sort of agent pushing the immune system off balance. This argument is only strengthened by the fact that the same evolutionary forces that would cause a serious disease to be weeded from the population would also cause those people whose immune systems are prone to self-destruction to be eliminated from the population.

The concept of autoimmune disease has progressed to the point that now even researchers who previously dismissed the possibility of infection are accepting the possibility that “autoimmune” disease could be triggered by infection. This is some progress, but it’s not enough. Especially since the concept of autoimmunity encourages doctors to prescribe immunosuppressive steroids to patients. But if persistent infection is involved these steroids may exacerbate the fire by allowing pathogens to spread.

Do you believe that pathogens could be involved in the aging process?

Aging is a super-category. We’ve gradually lumped together more and more symptoms under the category of natural aging. Many of these symptoms are the same as those caused by diseases that surely have an infectious cause. In that sense, you could view much of what we now call aging as an incapacitating illness that leads to a decrease in function. We know that inflammation and the interaction of the immune system with pathogens can destroy tissue. So it’s not surprising that the tissues of a person who harbors a lot of pathogens would age earlier and alter their biological structure earlier in life. I do believe it is inevitable that people will eventually die of old age, but I suspect that this should generally happen when they are 80-100 years old. But we are increasingly seeing signs of aging-related diseases in people who are much younger.

What does evolutionary biology have to say about psychosomatic illness?

Personally, I believe that we label an illness as psychosomatic when we don’t really know what’s going on with the patient. It’s a last resort diagnosis – a black box. If we knew more about what was causing their symptoms we could address the issue more clearly.

Looking at psychosomatic illness from an evolutionary viewpoint, you could say that those people who might exaggerate how sick they feel in order to gain attention and resources could have an evolutionary advantage. But if that’s the truth, it only accounts for an extremely small percentage of cases. It’s also true that often an illness will have both a psychological and physical component. But just because a psychological component is identified doesn’t mean the physical component should be overlooked. Plus, most mental illnesses are probably the result of infection too. Chronic Fatigue Syndrome is a good example of a disease that up until recently has been dismissed as psychosomatic just because researchers couldn’t figure out the cause. On the contrary, it’s quite a serious illness.

What role do you feel the Internet will play in facilitating acceptance of an understanding of pathogens in disease?

I think the Internet plays an incredibly beneficial role as it can provide information to anybody who is willing to put in the time to learn terminology and information presented in the literature available on the Internet. I believe it will, and already is, changing the patient/doctor relationship and also the relationship of the general public with the government mainly because we can now check up on things and check up on them quickly. I can find information in half an hour rather than spending an entire day at the library – and think about the fact that this is happening all around the country.

Of course, now there is so much information on the Internet that it’s too much for an individual mind to keep up with. Sometimes you have to read quite a bit of literature in order to extract the relevant information. That’s why we need people to team up and share information. What we need is small groups of people poring over information together. In this way they can develop a more thoughtful, broad outlook. This is in contrast to the current medical model in which doctors and researchers are trained to specialize in such a narrow area of knowledge. They know very little about issues outside their area of expertise and have trouble seeing the big picture. Thus, what we need is for the NIH to put money into grants that foster interdisciplinary insights.

Do you think that the peer review system and pharmaceutical industry are standing in the way of understanding chronic infectious disease?

I think the peer review system is becoming less important because there are so many other outlets where people can put up information. So I don’t see it as too big of a barrier.

When it comes to pharmaceutical companies, it’s important to recognize that they are very good at some things and very bad at others. What they are good at is product promotion and marketing, and working in innovative ways when the resulting product can bring in lots of money. The problem is the products that make the most money are not necessarily the products that actually help people the most.

Basic economic principles first put forth by Adam Smith show that the free enterprise system does not work well under certain situations. Writing over two hundred years ago, he argued that free enterprise cannot be expected to generate an effective national defense. For modern society, pollution control would be another example. If we want to move in that direction there needs to be a profit driven motive, or we have to get the government to do the things that do not generate sufficient profit. Otherwise, it just won’t happen.

If you think about it, there isn’t very much money to be made off a vaccine because a person uses it once or twice in his or her life and that’s it. Instead, think of the amount of money to be made off a statin when a person is going to take it every day of their life. There’s just not much motive for drug companies to invest in products that are cures or very good preventatives. We don’t have to condemn drug companies, just recognize this role that they are playing in drug development. If we want to develop a drug under a high priority situation that may result in a curative solution we can’t count on the pharmaceutical industry. In cases where the free enterprise system doesn’t result in a situation that may benefit the population the government has to step in and provide funding for the possibility at hand.

What kind of approach to research would best expedite the process of better understanding the role of infectious agents in disease?

Most experts in the health sciences advocate a building-block approach to the problem of causation. They try to understand the workings of disease at the cellular and biochemical levels, in hopes that solutions will eventually emerge. Even among infectious diseases, however, the fundamental achievements have occurred more through the testing of deductive leaps than by building-block induction. What it boils down to is that we need both types of development but we can’t have one without the other. Working incrementally can be great as long as scientists understand the big issues and the larger concepts that need to be guiding their research. But right now we have way too many scientists working in building block mode, missing what’s going on outside the box.

Why do doctors often have such a problem accepting the idea that pathogens are to blame for more diseases then commonly accepted?

Because it’s not in the textbooks. They are trained to look at a patient and try to match them with something in a textbook. These medical texts don’t consider the preponderence of evidence across the entire spectrum of possible causes of most chronic diseases. The evidence implicating infectious causation tends to be a casualty of this restricted perspective, leading to the result that consideration of infectious causation in medical texts is minimal for chronic diseases of uncertain cause.

So until infectious pathogenesis is accepted to the point that it is in the medical texts taught in medical school, they will continue to consult only the standard operating procedure. If they can’t put a label on the patient’s illness it falls into a bin of “unexplained phenomena” which goes back to what I was saying earlier about psychosomatic illness, since they have a tendency to speak dismissively about what’s in the bin.

The problem is that considering a new pathogenesis or a cause that isn’t in a textbook requires thinking hard about unknown problems. They just don’t have the time or training to think logically and deeply about such issues. This is evidenced by the fact that you can go to five different doctors, get five different explanations for your problem and be recommended five different treatment options.

What got you interested in this area of research?

My interest in evolutionary medicine began in grad school around 1977. I came down with a bad case of diarrhea and was thinking about whether I should treat the symptoms or let the illness run its course. At first it seemed like it was most logical to let the illness run its course because that seemed to be my body’s way of eliminating the pathogen. But then I thought about the fact that the pathogens might be manipulating me. If I expelled them, they might be endowed with an evolutionary advantage that would allow them to persist and infect others. I realized that my intuition couldn’t provide me with the answer. That led me on a long web-like series of connections. The more I started to consider medical problems in the light of evolution the more I realized that some diseases simply cannot be caused in a way they are explained by current dogma. So I’ve tried to look at disease in a balanced way, to put all possibilities on the table, and from there to figure out what’s feasible and what’s not.

Gut microbiome dysbiosis: The chicken/egg scenario

November 6th, 2017 by Amy Proal
The gut microbiome expresses over 9 million genes (Image: Medium Magazine)

The gut microbiome expresses over 9 million genes (Image: Medium Magazine)

Just ten years ago the human body was assumed to be largely sterile. Today, molecular technologies have revealed complex microbial ecosystems in nearly every human organ/niche. These microbiome communities persist in blood, tissue, the brain, the liver, the amniotic fluid, the placenta and beyond.

To date, the gut microbiome is the most widely studied human microbiome ecosystem. For one thing, the gut harbors a tremendous number of microbes (the gut microbiome alone expresses over 9 million genes!). Also gut microbiome composition can be evaluated by collecting fecal samples. These fecal samples are easy and relatively cheap to obtain.

When it comes to the gut, an increasing number of studies report a common trend: most inflammatory disease states is associated with imbalance of the gut microbiome. This imbalance, or dysbiosis, is characterized by decreased gut microbiome species diversity.

If the gut microbiome reaches a state of dysbiosis, a second trend is often observed: the lining of the gut becomes “leaky,” or worn down. This allows infectious agents to more easily cross the intestinal lining into bloodstream. There, increased inflammation may be generated in response to their presence.

While gut dysbiosis and “leaky gut” contribute to symptoms and chronic inflammation, the phenomena beg an important question: Is gut microbiome dysbiosis the CAUSE of chronic inflammatory disease, or does it RESULT from immune dysfunction initiated inside the cells of the immune system?

I’ll describe research on HIV/AIDS to clarify the situation. Several studies show that the gut microbiome is imbalanced in HIV/AIDS. However, the disease is also connected to an easily identified pathogen; a pathogen able to survive inside the cells of the immune system. Once inside these cells, HIV is able to “hijack” and dysregulate human pathways that control the immune response. The result: patients with the virus become extremely immunocompromised, to the point where controlling infection at other body sites (like the gut) becomes a serious challenge.

Gut microbiota alterations during HIV infection and their potential effects on the host (Elinav et al)

Gut microbiota alterations during HIV infection and their potential effects on the host (Elinav et al)

With the above in mind, gut microbiome dysbiosis in HIV/AIDS is largely believed to be a SECONDARY or downstream result of the overall disease process. In effect, immune dysfunction caused by HIV intracellular infection (often in the blood/tissues) comes first. Gut microbiome dysbiosis comes second, as immune cells in the gut progressively lose the ability to correctly target/manage the billions of microbes in their vicinity.

Does this chicken/egg situation apply to other inflammatory disease states? It might. Take ME/CFS. Several research teams have reported gut microbiome imbalance/decreased species diversity in patients with the disease. This has raised the possibility that gut microbiome dysbiosis may initiate the ME/CFS disease process.

While this is possible, gut microbiome dysfunction in ME/CFS may actually be quite similar to that of HIV/AIDS. Consider that recent analyses have detected thousands of “new” microbes in human tissue/blood. Are any of these uncharacterized microbes capable of slowing the immune response by infecting the cells of patients with ME/CFS? If yes, then ME/CFS gut microbiome dysfunction may also be a downstream result of systemic intracellular infection.

Research on other inflammatory conditions supports this possibility. For example, the gut microbiome of patients with Alzheimer’s disease is characterized by decreased microbial diversity. However, central Alzheimers pathology occurs outside the gut (eg. amyloid beta accumulates in the brain in response to infection). Parkinson’s is also characterized by gut microbiome imbalance. But the disease is connected to other infectious processes, including prion build-up in the central nervous system (CNS). This led Parkinson’s researcher Haydeh Payami to ask the million dollar gut microbiome question:

“At this point, researchers do not know which comes first. Does having Parkinson’s cause changes in an individual’s gut microbiome, or are changes in the microbiome a predictor or early warning sign of Parkinson’s?”

Alzheimer's disease is characterized by gut microbiome dysbiosis (Image: Kerafast blog)

Alzheimer’s disease is characterized by gut microbiome dysbiosis (Image: Kerafast blog)

I think Payami’s first suggestion is most probable. In Parkinson’s, infection of immune cells in the brain/blood/CNS may cause a system-wide drop in immune function. Gut microbiome composition/balance may suffer as a result of this immunosuppression (it doesn’t help that immune cells in the gut can also become infected). 

Also, under these and similar conditions, gut microbiome dysbiosis CAN be a useful warning sign. Gut microbiome imbalance may serve as a predictive marker of increasing systemic immune dysfunction.

I’ll give another example. A recent study found that patients with more diverse gut microbiomes responded better to a cancer immunotherapy treatment. Based on this data, the research team concluded that diverse gut bacteria might “help” the treatment function correctly. But what if the opposite association is true? It’s very possible that subjects with higher gut microbiome diversity were simply less immunocompromised. Aka, the immune system of a person with less severe cancer would be able to better keep the gut microbiome in a state of balance. If this second possibility holds true, no wonder the patients with more diverse guts responded better to a therapy that requires the immune system to work (immunotherapy).

Gut microbiome studies should subsequently be accompanied by analyses that continue to study intracellular pathogens capable of slowing the human immune response. We must also study the numerous strategies these pathogens employ to infect host cells.  As I’ve published many times, intracellular pathogens can directly alter human DNA transcription, translation and metabolic activity. This makes them uniquely suited to drive inflammatory disease processes.

Screen Shot 2017-11-06 at 10.49.51 AMIf you follow me on Twitter (@microbeminded2), you’ll see I’ve shared many recent studies that better clarify how pathogens survive inside human cells. In fact, intracellular survival could be considered a pre-requisite for any human pathogen able to drive a persistent disease. One study found that Zika virus slows T cell activity by infecting human macrophages. By surviving inside human cells, S. aureus maintains greater control over nasal microbiome composition. Mycobacterium tuberculosis can persist for decades inside the acidic lysosomes of human cells.  A range of bacteria can use flagella (a motor-like tail) to better colonize and attack host cells. E.coli rapidly evolve to invade white blood cells in order to evade the immune response. 

E.coli (in blue) inside the phagosomes of human white blood cells

E.coli (in blue) inside the phagosomes of human white blood cells


I don’t mean to suggest that gut microbiome dysbiosis isn’t a major issue in its own right. Even if imbalance is a downstream result of intracellular infection, it still “feeds into” pathways increasing symptoms and illness progression. An imbalanced gut may begin to harbor new pathogens, or allow chronic pathogens to re-activate. This causes additional suffering, inflammation, and disease. 

So dietary interventions and other treatments aimed at improving gut microbiome function are still very important. Let’s just make sure these therapies are accompanied by research on intracellular infection, immunity, and microbial persistence in tissue/blood.     

A letter to the ME/CFS research community (+ doctors, + patients)

October 18th, 2017 by Amy Proal

Dear ME/CFS research community,

My name is Amy Proal. I am a microbiologist who also suffers from ME/CFS. I first became ill with ME/CFS in 2004, while studying medicine at Georgetown University. Almost immediately I began to research the disease from bed and wrote my undergraduate thesis on ME/CFS. Several years later, I obtained a fellowship from Murdoch University (Australia) that allowed me to study the human microbiome. I was awarded a PhD in microbiology in 2011. I’ve published many peer-reviewed papers/book chapters that discuss how microbiome imbalance can drive inflammatory disease processes (commissioned by the J. Craig Venter Institute, the NIH, and the European Autoimmunity Network among other groups).

When I fell ill with ME/CFS in 2004, few, if any, research teams were seriously studying the disease. Now I am thrilled that an increasing number of researchers across the globe are better analyzing the ME/CFS microbiome, metabolome, immune response and more. The results of these analyses have sparked new, exciting dialogue in the the ME/CFS community. By writing this letter I hope to add several of my own hypotheses/observations to the conversation.

Ample evidence suggests ME/CFS is driven by chronic infection

Most studies on ME/CFS, and the general history of the illness, suggest that infectious agent(s)/environmental exposures plays at least some role in driving the disease process. These include (but are not limited to!) early associations with EBV/HHV6, “autoantibodies”/antibodies detected in patients with the disease, and even the nature of early ME/CFS “outbreaks.” In fact, a significant number of ME/CFS patients I know have fallen ill with the disease after travel to a foreign country, or after a severe viral infection (suggesting a lack of immunity against acquired pathogens/toxins?).

The ME/CFS proteome differs from that of patients with Lyme disease and healthy controls

The ME/CFS proteome differs from that of patients with Lyme disease and healthy controls

Most of the latest findings on ME/CFS also make sense when viewed through the lens of chronic infection. Reports of cytokine activation in patients with ME/CFS clarify that the disease is characterized by a sustained inflammatory response. Montoya found this cytokine activation increased with disease severity, suggesting patients may struggle with a growing infectious burden over time. Two research teams have shown that the ME/CFS cerebrospinal proteome differs substantially from that of healthy controls. Since the vast majority of metabolites in the human superorganism are microbial in origin, the findings imply that components of the ME/CFS microbiome may exist in a state of imbalance. Mark Davis and Lab at Stanford recently demonstrated massive clonal T cell expansion in patients with ME/CFS. It’s likely these T cells are activated against an infectious threat. Indeed, patients with Lyme disease (known to be driven by infection) demonstrated a T cell response similar to that of the ME/CFS subjects. Another study analyzing the ME/CFS metabolome demonstrated a sustained hypo-metabolic response in patients with the disease. This  dour-like state is “triggered by exposure to adverse environmental conditions”, as would be expected if the ME/CFS immune system is overwhelmed by a chronic infectious burden.

The recently discovered CNS lymphatic system connects the body to the brain

The recently discovered CNS lymphatic system connects the body to the brain

Other ME/CFS research teams have detected various forms of mitochondrial dysfunction in patients with the disease. While a number of mechanisms could account for these findings, intracellular pathogens are very capable of dysregulating human metabolic pathways. Also, an increasing number of studies have detected infectious agents in the brains of patients with Alzheimers, epilepsy and other conditions characterized by inflammation/immunosuppression. It’s possible that similar pathogens in central nervous system (CNS) tissue could contribute to brain abnormalities reported in patients with ME/CFS. The recent discovery of the human CNS lymphatic system strengthens the likelihood that microbes easily traffic in/out of brain tissue.

The human microbiome persists in tissue and blood

With the above in mind, many research teams have searched for single pathogens in patients with ME/CFS. However, the discovery/characterization of the human microbiome challenges the validity of studying single infectious agents in isolation. Microbes in the human body are now understood to persist in complex communities, where they continually interact with neighboring species. Further, human microbiome ecosystems have now been shown to persist in every human body site/niche (blood, tissue, placenta, amniotic fluid etc). Indeed, just this past month, Stephen Quake and team at Stanford demonstrated the presence of thousands of previously undiscovered bacteria/viruses/fungi in human blood and tissue. These “new” microbes, along with those detected by similar analyses, allow us to study the role of infectious agents in ME/CFS with ample new data.

DNA reads corresponding to known, divergent, and novel microbes detected by Quake and team.

DNA reads corresponding to known, divergent, and novel microbes detected by Quake and team.

In addition, a growing number of inflammatory disease states are now tied to dysbiosis or imbalance of human microbiome populations. This dysbiosis is characterized by massive community-wide shifts in microbial population structure, often resulting in decreased species diversity.

Conditions associated with microbiome dysbiosis include type 1 and 2 diabetes, Crohn’s disease, ulcerative colitis, psoriatic arthritis, among many others. Dramatic, continual alterations in the microbiome were reported during the development of tumors in a murine model of inflammation-driven colon cancer. These changes were directly responsible for tumor development. Urbaniak and team identified different bacterial profiles in breast tissue between healthy women and those with breast cancer. It follows that further studies of the ME/CFS microbiome (particularly in blood and tissue) may identify similar community-wide imbalances in patients with the disease.

We must study microbiome ACTIVITY

While species-based microbiome analyses (like those described above) are extremely informative, they are unlikely to paint a full picture of the ME/CFS disease process. For one thing, the species composition of any microbiome community is complicated by a host of environmental variables; variables that also cause large shifts in the body’s microbial ecosystems. These include geographic location, food consumption, and even time of day (this is particularly true of gut microbiome studies). Many research teams studying inflammatory conditions related to ME/CFS have subsequently been unable to isolate disease-induced microbiome dysbiosis in the face of this “noise.”

To avoid this pitfall, the ME/CFS research community must also study what the microbes in any human ecosystem are doing to drive inflammatory processes. We must examine microbe activity, microbe gene expression, and the myriad ways in which microbes interact with the host immune system, the host genome, and each other.

Microbes persist in complex communities

As mentioned previously, microbes in the human body continually interact, both directly and indirectly (the proteins and metabolites they create are also in constant interplay). Microbial communities exhibit synergistic interactions for enhanced protection from host defenses, nutrient acquisition, and persistence in an inflammatory environment. These include biofilm formation and cooperative signaling via quorum sensing peptides.

Microbes often persist in complex biofilm communitites

Microbes often persist in complex biofilm communitites

Even viruses seldom act as single entities. Virgin and team found that enteric virus activity is regulated by “transkingdom interactions” — processes critical to their infectivity, disease induction, and control. For example, the virus MMTV binds lipopolysaccharide (LPS) on the surface of Gram-negative bacteria. This initiates innate immune responses that culminate in host tolerance, transmission, and viral replication.

Microbes alter their collective gene expression to cause disease

These interacting microbes often subvert the human immune response by collectively altering their gene expression. Analysis of these gene expression patterns (studies of the metatranscriptome) should be a priority for the ME/CFS research community. Time/money can be saved by studying the methods other research communities have developed to analyze these patterns. For example, Yost and team recently performed an excellent gene ontology (GO) enrichment analysis of the oral microbiome during periodontal progression.

Gene expression of stable sites did not change over the two-month study period. In contrast, active sites that progressed to periodontitis were easily characterized by several functional genomic signatures. At the breakdown point these active sites expressed genes associated with ferrous iron transport and response to oxidative stress. At baseline, GO terms associated with potassium ion transport and isoprenoid biosynthesis (among others) were highly enriched.

Ranked species by the number of upregulated putative virulence factors in the periodontitis metatranscriptome (Yost et al)

Ranked species by the number of upregulated putative virulence factors in the periodontitis metatranscriptome (Yost et al)

Progression was also correlated with increased expression of putative virulence factors. In addition, ciliary and flagellar motility, as well as chemotaxis genes that direct bacterial movement, were all active at initial stages of periodontitis disease progression. Viral activity was also detected in all samples, with phage and herpesvirus activity higher in progressing sites as compared to baseline samples.

The team concluded that the entire oral microbial community, and not just a few select pathogens, drives the increase in virulence that leads to periodontitis progression. In effect, under conditions of increasing imbalance and inflammation, the whole community appeared to act together as a pathogen. This was supported by the fact that, in active sites, groups of microbes not usually considered pathogens upregulated a large number of putative virulence factors. S. mitis and S. intermedius, usually associated with dental health, were especially active.

Intracellular “keystone” pathogens may drive microbiome dysbiosis

When it comes to dysbiosis, microbe quantity may be less important than microbe “quality” (what a microbe is capable of DOING). Community-wide shifts in microbiome virulence are often driven by “keystone pathogens.” Keystone pathogens can provoke inflammation even when present as quantitatively minor components of the microbiome. For example, P. gingivalis often comprises just .01% of periodontal biofilms, yet impairs innate immune activity so profoundly that it becomes a central player in biofilm growth and development.

Most characterized keystone pathogens have evolved to persist inside the cells of the immune system. By surviving in this fashion, they can directly interfere with human transcription, translation, and DNA repair processes. Their persistence in the cell cytoplasm further dysregulates the epigenetic environment. If the accumulation of errors resulting from this interference exceeds the capacity of cellular repair mechanisms, serious dysfunction/illness can result.

The millions of proteins and metabolites expressed by intracellular pathogens additionally interact with the host genome, further altering human gene expression in a manner that can promote disease. Even bacterial quorum sensing molecules can dysregulate human pathways. Wynendaele and team found that, in vitro, quorum sensing peptides created by gram-negative bacteria altered human gene expression in a manner that promotes angiogeneisis, tumor growth, and neovascularization in colon cancer. 

The byproducts of human and e.coli metabolism are very similar

The byproducts of human and e.coli metabolism are very similar

The above is complicated by the fact that microbial proteins and metabolites are often identical or similar in structure to those created by their human hosts. For example, the human body and E. coli generate the same intermediate byproducts when metabolizing glucose. The “molecular mimicry” or sequence homology between these molecules makes it increasingly difficult for the host to recognize “foreign” from “self.”

Dozens of recent studies have better characterized mechanisms by which pathogens colonize and survive inside human cells. These include reorganization of the actin cytoskeleton, remodeling of vacuole proteolitic composition, development of “zipper and trigger” mechanisms, among many others.

Different pathogens employ common survival strategies

Identification and characterization of previously undetected keystone pathogens in patients with ME/CFS marks a promising area of research. However, it is likely, and expected, that different keystone pathogens may be detected in different patients with the disease. This is because many keystone pathogens, or intracellular pathogens, employ common survival mechanisms to persist in host cells/tissue/blood. The metabolic dysfunction driven by these different microbes can subsequently result in similar clusters of human inflammatory symptoms.

The ability of different pathogens to dysregulate activity of the Vitamin D Nuclear Receptor (VDR) is an excellent example of how different microbes can drive similar disease processes. The VDR regulates expression of hundreds of genes, many of which regulate inflammatory/malignant processes (eg. metastasis supressor protein 1). The receptor also expresses several families of antimicrobial peptides. Microbes capable of slowing VDR activity subsequently facilitate their survival by slowing the innate immune response.

2014-Proal-NIH2.026Many pathogens frequently linked to inflammatory disease have evolved to survive in this fashion. When lymphoblastoid cell lines are infected with Epstein Barr virus, activity of the VDR is downregulated as much as 15 times. The VDR expresses TACO, a protein critical to intracellular survival of M. tuberculosis; not surprisingly then, M. tuberculosis has also evolved to slow receptor activity. HIVBorrelia burgdorferi, Cytomegalovirus, and Mycobacterium leprae also dysregulate VDR activity to varying degrees. The fungus Aspergillus fumigatus secretes a gliotoxin which significantly downregulates VDR expression. Because disabling the innate immune system via the VDR pathway is such a logical survival mechanism, other uncharacterized microbes may have also evolved to dysregulate receptor activity.

It follows that ME/CFS patients with similar symptoms may not always test positive for the exact same pathogen(s). This trend is likely to continue as an increasing number of analyses examine components of the ME/CFS microbiome. Instead of worrying about these “inconsistencies,” the ME/CFS research community should strive to better characterize even more common mechanisms of pathogen survival.   

Microbes act differently depending on host infectious history and immune status

Pathogens detected in patients with the ME/CFS are also regularly identified in healthy subjects. This is particularly true of studies that have searched for EBV, HHV6, cytomegalovirus and other easily characterized viruses in ME/CFS cohorts. While these “overlapping” results are often viewed as problematic, they make sense in light of research that clarifies how differently microbes can act depending on host immune status, neighboring species, and a wide range of other variables. For example, risk of HIV infection is now understood to vary based on the species composition and activity of other microbes in vaginal/penile microbiome communities.

Many microbes assumed to persist in a “commensal” state are also capable of virulent activity. Like their human counterparts, they evolve in the face of changing environmental conditions. For example, s. aureus can cause a range of illnesses, from skin infections to life-threatening diseases such as pneumonia, meningitis, and endocarditis. However, approximately 30% of the “healthy” human population harbors s. aureus as a member of the normal nasal microbiome. Krismer and team found that s. aureus virulence in these communities was determined by a number of factors, especially the signaling/competitive strategies employed by neighboring microbes.   

The same is true of Escherichia coli (E. coli), which also persists in numerous forms. One study found that “commensal” E. coli could evolve into virulent clones in less than 500 generations. For most microbes, this evolution towards pathogenicity occurs via the acquisition of new genes (a gain of function mechanism), or alteration of the current genome, including gene loss (a change-of-function mechanism). For example, in Pseudomonas aeruginosa the loss of mucA increases its ability to resist pulmonary clearance and evade phagocytosis.

Unique infectious history shapes ME/CFS disease progression

While keystone pathogens may be identified in ME/CFS, composition of the ME/CFS microbiome will likely differ between patients. Even in HIV/AIDS, where an easily detected virus dysregulates immunity, disease symptoms reflect a mix of those driven by HIV, and those driven by “co-infectious” agents able to take advantage of the immunocompromised host. No two patients with HIV/AIDS are expected to harbor the exact same mix of these other “co-infectious” agents.

Influence of chronic CMV on the immune response (Brodin et al)

Influence of chronic CMV on the immune response (Brodin et al)

This same pattern, in which unique infectious history drives symptom presentation may also occur in ME/CFS. A recent seminal study by Brodin and team demonstrates the profound impact infectious history on host immunity. The team performed a systems-level analysis of 210 healthy twins between the ages of 8 and 82. They measured 204 immune parameters, including cell population frequencies, cytokine responses, and serum proteins, and found that 77% of these are dominated, and 58% almost completely determined, by non-heritable environmental influences. Many of these parameters became more variable with age, emphasizing the cumulative influence of environmental exposure.

The team also calculated how acquisition of ONE chronic pathogen — cytomegalovirus (CMV) — conditions the immune response. Identical twins discordant for CMV infection showed greatly reduced correlations for many immune cell frequencies, cell signaling responses, and cytokine concentrations. In general, the influence of CMV was so broad that it affected 119 of all 204 measurements dispersed throughout the immune network. In fact, the lifelong need to control CMV causes approximately 10% of all T cells in CMV+ individuals to be directed against the virus. These and related findings led Brodin and team to conclude that the immune response is “very much shaped by the environment and most likely by the many different microbes an individual encounters in their lifetime.”

Could “successive infection contribute to ME/CFS?”

The above suggests that ME/CFS may be driven by a process I have termed “successive infection.” During the successive infectious process, an “initial event” dysregulates the immune system. This makes it easier for certain microbes to subvert the immune response by acting as polymicrobial entities. Pathogens alter their gene expression in ways that promote community-wide virulence. Infected human cells fail to correctly express human metabolites in the presence of the proteins, enzymes, and metabolites generated by the accumulating pathogenic genomes. Dysfunction due to molecular mimicry accumulates. Intracellular pathogens slow the human immune response, causing the host to more easily acquire other infectious agents. This creates a snowball effect in which the microbiome becomes increasingly dysbiotic as the strength of the immune response decreases.

Successive infection results from a patient's unique infectious history

Successive infection is driven by a patient’s unique infectious history

Eventually, the human host may present with clinically evident symptoms characteristic of ME/CFS or a related inflammatory diagnosis. The unique symptoms any one person develops vary depending on the location, species, and virulence of the pathogens driving dysbiosis, along with the semi-infinite number of ways in which the proteins and metabolites created by these microbes cause dysfunction by interacting with those of the host.

In some cases a specific “trigger” may jump start the successive infection process. For example, between the ages of 3-5 I was repeatedly hospitalized for no less than five severe infectious diseases: viral meningitis, double pneumonia, scarlet fever, measles and german measles (despite receiving the MMR vaccine). My twin sister suffered none of these illnesses and is still healthy today. While I can’t be sure, it’s possible that the pathogens driving these diseases states either persisted in my system, or dysregulated my immune response in ways that made me increasingly susceptible to microbiome dysbiosis over time. For example, the immunosuppressive effects of measles have now been shown to deplete host B and T lymphocytes for up to three years after “recovery.” As the study’s authors state, this profound immunosuppression “resets previously acquired immunity” and  “renders the host more susceptible to other pathogens.”

In other cases, a toxic environmental exposure or the difficulty of enduring a traumatic event may push the immune system to a critical mass such that previously subclinical infections become obvious. Reports of several ME/CFS ‘‘outbreaks’’ over the past decades, in which dozens of people have developed the illness at relatively the same time, may well represent this phenomenon at work. For example, in 2004, many cases of chronic fatigue were reported to occur simultaneously after a water reservoir in Bergen, Norway, was contaminated with Giardia lamblia. Nonetheless, of the approximately 48,000 people who were exposed to the contaminated water, only 5 % of the people went on to develop symptoms characteristic of ME/CFS.

The successive infectious process may even begin in the womb. Infants are seeded in the womb, during birth, and after birth by extensive microbiome populations in the placenta, breast milk, and the vaginal canal, among others. Depending on the health of the parents, these communities may already be dysbiotic. The breast milk microbiome of obese mothers has been shown to harbor a different and less diverse bacterial community than that of healthy subjects (Cabrera-Rubio et al., 2012). The amniotic fluid microbiome can predict perinatal complications prior to infant delivery. 2014-Proal-NIH2.005

Many aspects of “modern” living can additionally drive successive infection. Antibiotic use greatly disrupts the ecology of the human microbiome. For example, C. difficile better exploits other microbes in its community following antibiotic treatment. Antibiotic resistance genes are also regularly transferred from farm animals and produce into the human food supply. The immunosuppressive medications, steroids, and supplements often (paradoxically) prescribed for inflammatory disease further allow pathogens in the microbiome to proliferate. High levels of stress depress the immune response. Electromagnetic radiation from mobile phones and cellphone towers (among other sources) has been shown to lower immunity.

ME/CFS patients should not always be grouped into subgroups

ME/CFS is a spectrum disorder: patients are required to present with four out of eight required symptoms. If successive infection contributes to ME/CFS, this variability in symptom presentation is expected. Furthermore, factoring “unique infectious history” into the disease process helps explain why patients with ME/CFS often suffer from a multitude of symptoms not included in the official diagnostic criteria.

Because patients with CFS/ME suffer from such diverse symptoms, it has been argued that they should be grouped into separately studied ‘’subgroups.’’ In some cases this makes sense. For example, studies that distinguish early-stage/late-stage patients may further elucidate how the ME/CFS immune response changes over time. However, if successive infection contributes to ME/CFS, future research should also focus on better understanding the common pathogenesis shared by all subjects.

“Autoantibodies” in ME/CFS are likely created in response to microbes

A number of autoantibodies have been detected in patients with ME/CFS. These include antiphospholipid antibodies, or antibodies directed against neurotransmitters such as serotonin, adrenals, adrenocorticotropin hormone. This has led some research teams to postulate that ME/CFS may be an “autoimmune” disorder.2013-Proal-Spain.001

However, autoantibodies are notoriously polyspecific. The autoantibodies detected in ME/CFS may actually be created in response to pathogens and possess a high degree of molecular mimicry. In effect, when the immune system generates antibodies in an effort to target pathogens, a proportion that are polyspecific may collaterally target human proteins. For example, Lekakh and team found that autoantibodies with polyspecific activity in the serum of healthy donors were able to cross-react with DNA and lipopolysaccharides (LPS) of widespread species of bacteria including Shigella boydii, E. coli, Salmonella, and Pseudomonas aeruginosa. Another analysis found that B cells infected with Epstein Bar Virus secrete antibodies capable of reacting with dozens of self and non-self antigens including albumin, renin, and thyroglobulin. 

If the above is true, there is no need to “lump” ME/CFS into a category of “autoimmune disorders.” This is especially true in light of the fact that the “theory of autoimmunity” is being called into question by an increasing number of research teams.

What about the human genome?

Mycobacteria alters expression of PTPN22

Mycobacteria alters expression of PTPN22

The discovery of the human microbiome has forced science to redefine the human condition. Our bodies harbor more microbial cells than human cells, and the millions of genes expressed by the microbiome dwarf the approximately 20,500 genes expressed by our human genomes. Humans are subsequently best described as superorganisms, in which the human and microbial genomes continually interact to regulate metabolism. For example, the gene PTPN22 has been connected to rheumatoid arthritis, lupus, and diabetes mellitus. However, PTPN22 expression is also altered by the bacterial metagenome — it is upregulated as part of the innate immune response to mycobacteria.

Under normal conditions, components of the gut microbiome and its corresponding metabolites oscillate in a fashion that exposes them to different gut regions across the course of a day. The host interprets the microbial signals resulting from these interactions and alters its gene expression in a manner that promotes rhythmic homeostasis.

Summary of the dynamic relationship between circadian rhythms, intestinal microbiota, and immune response (Rosellat et al)

Summary of the dynamic relationship between circadian rhythms, intestinal microbiota, and immune response (Rosellat et al)

The above suggests that studies of the human genome in isolation are unlikely to paint a full picture of the ME/CFS disease process.

The ME/CFS metabolome/proteome

Studies of ME/CFS proteome/metabolome may further clarify metabolic dysfunction in ME/CFS. However, data from these analyses must be interpreted to account for the “molecular mimicry” between byproducts of host/microbial metabolism.

As previously mentioned, many human/microbial metabolites share similar structure/functions. Kusalik and team found that 19,605 proteins from the hepatitis C virus (HCV) polyprotein have a high level of similarity to the human proteome. This remarkable similarity persisted even when the team used longer peptide motifs as probes for identity scanning. Another study reported tens of thousands of protein-protein interactions between the genomes of E. coli, Salmonella, Yersinia and the human genome.

This means proteome/metabolome studies must continually ask: “What are we actually measuring?”: aka do samples contain human byproducts, microbial byproducts, or a mix of both?

The same is true of studies that characterize DNA in human tissue and blood. Sample analysis MUST account for microbial DNA and RNA that the human microbiome exudes from infected cells. For example, Stephen Quake and team recently discovered thousands of new microbes in human blood. They derived their results by correctly separating the microbe DNA in their samples from the human DNA in their samples.

ME/CFS research must be supplemented by findings from related research communities

The ME/CFS research community struggles with funding. However, the impact of current grants can be maximized if researchers follow the work of related research communities. Most inflammatory disease states are now connected to microbiome/metabolome dysbiosis. This suggests that common underlying processes may contribute to “separate” disease states.

The high levels of comorbidity and symptom overlap between patients with different inflammatory diagnoses strengthens this assumption. For example, composition of the lung microbiome can predict the onset of rheumatoid arthritis. The figure below demonstrates the profound overlap in disease presentation among patients with a broad range of inflammatory conditions.2014-Proal-NIH2.029

It follows that “big picture” studies of the immune system, nervous system, and microbiome can directly inform ME/CFS research. For example, Davis and team reported massive T cell expansion in patients with ME/CFS. However this same trend was observed in cancer and multiple sclerosis. We can follow how the cancer/MS research communities build on these findings and extrapolate parts of this research towards ME/CFS.

Many research teams are also studying how “acute” pathogens can cause chronic symptoms by persisting in latent forms. These include groups studying Zika, influenza, and other well-characterized viruses. For example, tens of thousands of Ebola survivors have developed chronic symptoms months or years after initial infection, including joint pain, eye problems, extreme fatigue, severe pain, and a host of neurological problems. Ebola virus has even been detected in men’s semen years after “recovery.” A better understanding of these “chronic sequelae” may also benefit the ME/CFS community.

Treatment of infection often temporarily increases disease symptoms

Immunosuppresive therapies represent the standard of care for most inflammatory conditions tied to autoantibody production. Corticosteroids, TNF-alpha antagonists, and rituximab are among the many treatments routinely used to slow immune activity. These treatments often provide short-term symptom palliation but allow pathogens in the microbiome to spread with greater ease.

This pattern is recognized in the context of acute infection. For example, Earn and team recently concluded that using antipyretic medications to suppress fever (and subsequently the immune response) in patients with influenza allowed viral particles to spread more easily between people. Thus, while subjects taking the antipyretic medications felt fewer symptoms, they were actually more contagious.

2014-Proal-NIH2.036In contrast, treatments that SUPPORT or activate the immune system may allow patients to better target pathogens over time. Development of such therapies should be a priority for the ME/CFS research community.

However, most “immunostimulative” treatments are characterized by immunopathology—a cascade of reactions including inflammation, cytokine release, and endotoxin release that occur as part of the immune response to microbial death. The death of intracellular microbes is particularly hard for the host to manage, as the body must deal with debris generated from apoptosis and phagocytosis as well as the remains of the dying microbes that once inhabited the cells. The adaptive immune system may also respond to the presence of this pathogenic and cellular debris, generating antibodies in the process.

Immunopathology resulting from microbicidal treatment has been documented for over a century, with symptom presentation varying depending on the nature of the pathogen targeted. First referred to as the Jarisch–Herxheimer reaction, it was originally observed during therapy of secondary syphilis using mercury. Researchers have subsequently noted this reaction in a broad spectrum of chronic diseases such as relapsing fever, Leptospirosis, Brucellosis, and tuberculosis among others. Short-term immunopathology is also part of common acute infectious illness. When a patient develops the flu, symptoms are generated primarily as the immune system releases a host of cytokines and chemokines in response to the presence of the infectious agent.

More recently, an inflammatory syndrome similar to immunopathology has been documented in HIV/AIDS patients undergoing Immune Reconstitution Inflammatory Syndrome (IRIS) following treatment with Highly Active Antiretroviral Therapy (HAART). This condition occurs as HAART enables the once compromised host to target pathogens acquired during periods of severe immunosuppression. A number of prominent and easy-to-culture pathogens have been linked to IRIS: the herpes viruses, cytomegalovirus, hepatitis B and C, Mycobacterium avium complex, M. tuberculosis, and Cryptococcus neoformans. The presence of IRIS in culture-negative patients is common, suggesting many pathogens that cannot be detected without metagenomic tools might also be involved.

Luckily, immunopathology as a result of HAART or related treatments is temporary in nature. In most cases, immunopathology gradually subsides as an increasing number of infectious agents are eradicated. Eventually, patients often “turn a corner”, where they feel better as the body recovers.

While some ME/CFS physicians may feel uneasy about the temporary suffering induced by immunopathology, other research communities have become accustomed to treatments that cause discomfort. For example, the cancer community has developed a number of treatments that activate patient T cells. The “cytokine storm” resulting from these therapies leads to massive (temporary) symptom increases, and has even resulted in death (are infectious agents being killed!?). However, this risk is considered acceptable, as patients who survive the reaction often enter a state of remission.


PS: Hornig and team have reported distinct alterations in plasma immune signatures (including prominent activation of both pro-and anti-inflammatory cytokines) early in the course of ME/CFS. However these alterations were not observed in subjects with a longer duration of illness..

It’s possible that in early-stage ME/CFS, the immune system actively attempts to “battle” an increasing chronic infectious burden. Over time however, pathogens in the microbiome may disable the immune response to a point where “immune exhaustion” occurs. Immunopathology and cytokine production would subsequently drop. The resulting disease state could be compared to a garden, in which healthy plants become progressively stifled by kudzu vine over time.

This pattern suggests that treatments for ME/CFS should be employed as early as possible. Or, as Hornig writes, “alterations in opportunities for intervention may be transient.” This is because any treatment aimed at targeting infectious agents in ME/CFS will be most successful before the immune system becomes overly compromised.

It often takes patients with ME/CFS years to receive a diagnosis. This delay wastes much of the valuable period during which the ME/CFS immune system may be most responsive to treatment. Physicians must subsequently be educated to better recognize early-stage ME/CFS. Also, the ME/CFS research community should prioritize the development of predictive/preventative treatment options.





Huge discovery: microbes in human blood/tissue vastly more diverse than previously known

September 20th, 2017 by Amy Proal

Last post I described fascinating research on the immune response by the Mark Davis Lab at Stanford. But another Stanford research team, led by Steven Quake, has published the results an equally exciting study. In fact, the team’s discovery marks one of the most important findings in modern science.

Quake and team used new methods to search for the DNA of microbes in human blood and tissue. They found that 99% of microbes identified were previously unknown to science. As this article in Stanford News describes, the discovery clarifies that “the microbes living within us are vastly more diverse than previously known.” 

DNA reads corresponding to known, divergent, and novel microbes detected by Quake and team.

DNA reads corresponding to known, divergent, and novel microbes detected by Quake and team.

To be specific, Quake and team examined microbe DNA fragments in the blood of patients with a range of conditions characterized by immunosuppression (liver transplant recipients, pregnant women etc). They collected over 1,000 blood samples, and found that they contained hundreds of never before discovered bacteria and viruses. In fact, ~3,761 of the organisms detected represent microbes not known to exist before the study was performed. 

These species include thousands of new bacteria, but also new viruses and phages (viruses that infect bacteria). The research team was forced to add new branches to the “tree of life” in order to classify many of these new microbes. Indeed, their findings literally double the total number of anelloviruses found in humans.

Quake and team conclude their paper by stating that these novel microbes “have potential consequences for human health. They may prove to be the cause of acute or chronic diseases that, to date,  have unknown etiology…”



More thoughts: I experienced several “eureka moments” while reading the Quake study.  First, I have long predicted that new microbes would be identified in human tissue and blood.  I began my microbiology career by studying the work of microbiologists/pathologists in the 1960s. The papers/textbooks published by these scientists are seldom discussed in 2017. However, their work repeatedly identified numerous microbes/pathogens in blood/tissue samples taken from human subjects.

Why are these 1960s studies seldom referenced? In the 1970s, the “theory of autoimmunity” gained hold and research on chronic microbes was largely shelved. When the 1960s microbiologists contested this mindset, their work was often dismissed on the basis of contamination (they were told that external microbes in their laboratories had “contaminated” their human samples). I’ve never believed these claims to be accurate, but most of the general scientific community has accepted them.

In fact, the possible contamination of blood/tissue samples by laboratory microbes is an ongoing concern: Quake and team were careful to include a full section in their paper called “Novel Contigs (DNA reads) are Not Artifacts or Contaminants.” There, they discuss the results of several extra experiments aimed at proving exactly that (see the study’s Methods section).

Stanford researcher Dave Relman

Stanford researcher Dave Relman

Furthermore, over the past two decades, several research teams using molecular tools have already identified numerous microbes in the blood. For example, this 2001 study by Stanford researcher Dave Relman found many bacterial species in the blood of healthy subjects. Relman is one of my greatest role models, so I’ve taken his findings and related studies very seriously.

The Quake study also hammers home a point I’ve made in every speech/paper/book chapter since 2005. Imbalances of the gut microbiome, and external body microbiomes (skin, mouth etc) can contribute to chronic disease. However, microbes in the blood reach internal human tissue, and thus may play the greatest role in driving infectious disease processes. This is especially true since many of these blood/tissue microbes persist inside the cells of the immune system. Quake and team echo this sentiment in their paper stating, “Blood circulates throughout the human body and contains molecules drawn from virtually every body tissue.” Quake also told Stanford News the following about his team’s discovery:

“I’d say it’s not that baffling in some respects because the lens that people examined the microbial universe was one that was very biased…For one thing, researchers tend to go deep in the microbiome in only one part of the body, such as the gut or skin, at a time. Blood samples, in contrast, “go deeply everywhere at the same time.”

Last but not least, the Quake team derived their results by correctly separating the microbe DNA in their samples from the human DNA in their samples. This distinction can prove difficult because microbe and human DNA are often very similar in structure. 

Many other research teams studying the microbiome ARE NOT DOING THIS (CORRECTLY SEPARATING MICROBE/HUMAN DNA).  In conjunction with my colleague Trevor Marshall I have warned about this problem in several peer reviewed papers. For example, Marshall and I state the following about correctly identifying microbe DNA in this Current Opinions in Rheumatology paper:

“What are we actually measuring? Genetic science has not yet noticed the elephant in the room – the microbial DNA and RNA that the human microbiome exudes from infected cells. This contaminates the samples of “human DNA” being analyzed.”

Well…Quake  and team noticed the elephant in the room. And doing so made a dramatic difference in the results they obtained! I am extremely excited to see how their new findings impact microbiome research in the years to come.

New Stanford University data clarifies immune dysfunction/infection in cancer, ME/CFS, MS

September 15th, 2017 by Amy Proal

Mark Davis and his lab at Stanford University are on fire! They recently released fascinating data (some unpublished) on patients with cancer, Lyme disease, MS and ME/CFS. Davis discussed this data at a recent Open Medicine Foundation meeting. The talk was recorded and I HIGHLY encourage you to watch it!

New Davis Lab Findings:

Davis starts by confirming that ME/CFS is characterized by high levels of systemic inflammation. In fact, in concert with Dr. Jose Montoya at Stanford, Davis detected elevated cytokines (inflammatory molecules) in the blood of patients with ME/CFS. First, this cytokine activation distinguished the ME/CFS patients from healthy controls: does anyone still want to argue that the ME/CFS is psychosomatic!? (please tell me no). Second, patients with more severe cases of ME/CFS demonstrated greater cytokine activation; indicating that ME/CFS disease progression is characterized by increased immune dysfunction over time. 

In another series of experiments, Davis looked at T cells responses in ME/CFS and related inflammatory conditions. T cells are part of the adaptive immune response: the branch of the immune system that creates antibodies in response to specific microbes or pathogens. Davis used a novel assay developed at Stanford to obtain T cell sequences from the tissues/blood of patients with colon cancer, MS, Lyme disease, and ME/CFS.

In all four diseases, T cells were activated in a manner not observed in healthy control subjects. To be specific, the team observed massive clonal expansion of the T cells – both in tumor tissue and in the blood of patients with MS, ME/CFS, and Lyme disease.

T cell expansion in healthy subjects as compared to patients with Lyme disease, MS, and ME/CFS

T cell expansion in healthy subjects as compared to patients with Lyme disease, ME/CFS and MS. Unpublished data by Mark Davis Lab, Stanford University.

What does this mean? In simple terms, T cell clonal expansion indicates that the T cells became increasingly activated against a “target.” This activation caused the cells to divide and proliferate. As Davis explains, this “target” could be a pathogen or dysregulated human tissue.

Davis leans towards the “target” being a pathogen, stating that antibodies driving T cell proliferation are likely formed “originally against some pathogen peptide.” In some cases, these “pathogen peptides” may cross react with similarly structured human peptides – causing the immune system to accidentally target human tissue. This is exactly in line with the new model of autoimmune/inflammatory disease I’ve described on this site.

Indeed, Davis’ next goal is to further study the activated T cells in his samples. He hopes to correlate the T cell activity with the presence of specific pathogens (and the antibodies created in response to their presence). This could lead to a better understanding of exact microbes involved in driving cancer, MS, ME/CFS etc.

CONSIDERATIONS: Davis’ data strongly suggests that in cancer, MS, Lyme disease, and ME/CFS the immune system is activated against an infectious threat. This threat could be one pathogen, or it could be many pathogens acting together (in a community).

I support the latter possibility: I suspect that T cells are activated in these conditions as part of a generalized response to microbiome dysbiosis or imbalance. However it is very possible that certain microbes in these communities play a larger role than others in driving disease processes (these microbes are often referred to as “keystone” pathogens.”)

Also, the same general pattern of T cell clonal expansion was observed in cancer, autoimmune disease, and infectious disease. This strongly supports what I have long advocated: different inflammatory conditions, commonly studied in isolation, may actually result from the same root causes. This overlap certainly explains the high levels of co-morbidity observed between patients with different diagnoses! If this is true we should be studying these illnesses TOGETHER, with an increased focus on multidisciplinary research.

Finally, the T cell activation Davis observed in patients with ME/CFS could serve as an excellent biomarker for the disease. In my opinion, we do not need to know the exact microbial species involved for the data to be useful. Nor does it matter that other related diseases demonstrate a similar pattern. For the sake of treatment, all we need to know is that patients with ME/CFS show different T cell activity than that of healthy subjects.

T cell expansion in colon carcinomas (tumors)

T cell expansion in colon carcinomas (tumors). Figure: Mark Davis Lab, Stanford University.


My new peer-reviewed paper: Microbes INTERACT to cause chronic inflammatory disease

September 10th, 2017 by Amy Proal

Hello readers!

The image above shows different species of microbes communicating inside communities called biofilms. In many instances this kind of signaling is able to drive inflammatory disease processes. For much more on this topic, please check out my latest peer-reviewed paper published in Discovery Medicine “Microbe-Microbe and Host-Microbe Interactions Drive Microbiome Dysbiosis and Inflammatory Processes.” Then come back here and ask me questions! Or give me feedback/constructive criticism! Thanks.

Abstract: An extensive microbiome comprised of bacteria, viruses, bacteriophages, and fungi is now understood to persist in nearly every human body site, including tissue and blood. The genomes of these microbes continually interact with the human genome in order to regulate host metabolism. Many components of this microbiome are capable of both commensal and pathogenic activity. They are additionally able to persist in both “acute” and chronic forms. Inflammatory conditions historically studied separately (autoimmune, neurological and malignant) are now repeatedly tied to a common trend: imbalance or dysbiosis of these microbial ecosystems. Population-based studies of the microbiome can shed light on this dysbiosis. However, it is the collective activity of the microbiome that drives inflammatory processes via complex microbe-microbe and host-microbe interactions. Many microbes survive as polymicrobial entities in order to evade the immune response. Pathogens in these communities alter their gene expression in ways that promote community-wide virulence. Other microbes persist inside the cells of the immune system, where they directly interfere with host transcription, translation, and DNA repair mechanisms. The numerous proteins and metabolites expressed by these pathogens further dysregulate human gene expression in a manner that promotes imbalance and immunosuppression. Molecular mimicry, or homology between host and microbial proteins, complicates the nature of this interference. When taken together, these microbe-microbe and host-microbe interactions are capable of driving the large-scale failure of human metabolism characteristic of many different inflammatory conditions.

Probably the most important sentence in the paper:

  1. In effect, under conditions of increasing imbalance and inflammation, the whole community appeared to act together as a pathogen.

TOP IMAGE: Property of the Center For Biofilm Engineering. They are an awesome organization, check them out: