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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.

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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.

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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
blood

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…”

I AGREE

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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
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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
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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.

http://www.discoverymedicine.com/Amy-D-Proal/2017/01/microbe-microbe-and-host-microbe-interactions-drive-microbiome-dysbiosis-and-inflammatory-processes/

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:

http://www.biofilm.montana.edu/

The power of patient reported feedback: Part 1

January 29th, 2016 by Amy Proal
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Last year I was invited to give a speech at a scientific conference that examined the role of the microbiome in autoimmune disease – concepts I describe in this Current Opinion in Rheumatology journal article. Our research team had also developed an immunostimulatory treatment for autoimmune disease based off concepts in the paper. Doctors in at least a dozen countries were using the treatment with their patients, often with success.

I didn’t discuss this treatment in my speech, but made the following statement during the last twenty seconds of the talk: “We have developed an immunostimulatory treatment that patients are using in conjunction with their doctors. If you’re interested in any of our case histories find me later.” Continue reading

Of mice and not men: can complex human inflammatory disease be studied in mice?

January 13th, 2016 by Amy Proal
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Much of my junior year at Georgetown University was spent in an animal research facility. Along with my undergraduate thesis mentor and several fellow students, I studied the impact of a high-fat (ketogenic) diet in Sprague-Dawley rats. We had read reports in which human children with epilepsy who were fed this ketogenic diet experienced fewer seizures. Now we were attempting to ascertain whether rats eating a ketogenic chow would experience seizures at a different rate than those eating a chow rich in carbohydrates.

I graduated before the research project was complete, but later learned that some differences in seizure incidence between the two groups of rats were identified. Yet the team was never able to figure out the root cause underlying these differences.

Continue reading

Mothers and microbes, Part 2: The placental, breast milk, and breast tissue microbiomes

December 27th, 2015 by Amy Proal
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While the vaginal microbiome has received a great deal of attention from the research community, recent research also indicates that microbes persist in the womb, where they come in contact with a fetus before it is born. Studies demonstrating the presence of microbes in the amniotic fluid have now been bolstered by the discovery of a placental microbiome. Dysregulation of this placental microbiome by pathogens has also been associated with preterm birth and low infant birth weight.

Consistent with the presence of a placental microbiome, naturally-born infants often harbor microbes not commonly found in the vagina. For example, while vaginal communities are often composed of up to 80 percent Lactobacillus, the microbiomes of newborn infants contain high levels of other taxa, such as Actinobacteria, Proteobacteria, and Bacteroides. Infants appear to have acquired these microbes in the womb, and not during the birthing process. Continue reading