Author Archives: Amy Proal

Interview with Resia Pretorius: how bacteria, viruses and their inflammatory products can impact blood clotting in chronic disease

August 6th, 2020 by Amy Proal

Resia Pretorius is both the Department Head and a Research Professor in the Physiological Sciences Department, Faculty of Science at Stellenbosch University in South Africa. Her team uses super-resolution and electron microscopy, together with flow cytometry and thromboelastic analysis of clot structure, to characterize inflammatory biomarkers (inflammagens) created by bacteria in human blood. She also studied how viruses like COVID-19 can drive similar clotting processes. Her team has published dozens of papers showing that bacterial inflammagens are increased in the blood of patients with a range of chronic inflammatory conditions, including Parkinson’s disease, Alzheimer’s disease and Type II diabetes. They have further detailed how such inflammagens interact with receptors on red blood cells, and bind or interact with the fibrinogen protein. This can impact the blood clotting cascade, resulting in hypercoagulation and chronic inflammation that negatively impacts surrounding blood vessels.

Here are some terms Resia mentions in the interview:

Platelets: component of blood whose function (along with the coagulation factors) is to react to bleeding from blood vessel injury by clumping, thereby initiating a blood clot.

Coagulation: also known as clotting, coagulation the process by which blood changes from a liquid to a gel, forming a blood clot. Coagulation involves the activation, adhesion and aggregation of platelets, as well as deposition and maturation of fibrin.

Fibrin: an insoluble protein formed from fibrinogen during the clotting of blood. It forms a fibrous mesh that impedes the flow of blood.

Fibrinogen: a soluble protein in the plasma that is broken down to fibrin by the enzyme thrombin to form clots.

Inflammagens: Molecules, often tied to bacterial activity, that play a role in activating clotting cascades in blood. These inflammagens include:

  1. LPS: part of the bacterial cell wall that can act as an endotoxin
  2. gingipains: toxic proteins secreted by certain bacteria
  3. lipoteichoic acid: a major constituent of the cell wall of gram-positive bacteria
  4. cytokines: inflammatory molecules generated as part of the immune response to bacteria and other pathogens

At the beginning of the interview, Resia explains why her lab started studying bacteria in the blood of patients with Parkinson’s and Alzheimer’s disease. When she started the research, most of the scientific community did not think bacteria were capable of persisting in human blood. In fact, that’s what Resia and her students also believed. However, two of her students were trying to perform studies on Alzheimer’s and Parkinson’s blood and, to their surprise, kept finding bacteria in the blood samples. At first, they assumed that the bacteria must be contaminants (they assumed the bacteria in the samples were derived from the lab or the external environment as opposed to the human body). But, as they performed an increasing number of sterilizing approaches in an effort to prevent this bacterial “contamination,” nothing worked. Finally, they were forced to consider the possibility the bacteria in their samples might not be contaminants, but actual organisms present in Alzheimer’s and Parkinson’s blood.

In order to confirm that this might be possible, they began to talk to other research teams studying blood, all of whom were increasingly open to the possibility that the bacteria were indeed “real.” Resia also started to work more closely with Douglas Kell and team in the UK to better understand how bacteria can enter the blood via the gut and mouth. Her team also read this paper by the research team I worked with at Autoimmunity Research Foundation. Our paper put forth a model of how bacteria in tissue and blood may contribute to chronic inflammatory disease. Resia and team found the paper informative. All of the events jump-started dozens of research projects on the topic, and further work on how identified bacteria and their inflammatory product can impact the blood clotting cascade, blood iron levels, and even the shape (or deformability) of red blood cells.

In fact, since that time, Resia and team have found that minuscule concentrations of LPS and other bacterial inflammagens can produce a domino effect of soluble fibrinogen in the presence of thrombin in blood. This can further trigger the formation of extensive pockets of amyloid protein aggregates. They have performed hundreds of experiments on the topic, and found that a level of just 0.03ng/L of LPS can trigger such changes in fibrin and amyloid formation.

Key to Resia’s microscopy work is her ability to image bacteria in different states. Bacteria in the human body can persist in a dormant state, in which they are not active and replicating. However, under episodes of stress, or other inflammatory insults, the same bacteria can change their activity to drive a range of inflammatory processes, including clotting issues. One factor Resia and team have found can cause bacteria to shift from a dormant to active form is changes in blood iron levels.

Resia and team also study how bacteria and their inflammagens can cause red blood cells (RBCs) to change shape (red blood cell deformability). They have found that in the presence of bacterial inflammagens, RBCs can commit “eroptosis” – a type of programmed cell death. The figure to the right was photographed by Resia with a microscope. It shows bacteria and RBCs in Parkinson’s/ Alzheimer’s blood. The red blood cells display various abnormal shapes, likely due to the fact that inflammagens have interacted with their membranes, causing the membranes to lose their elasticity. The RBCs cannot reform to the correct disc shape, even when they travel through tiny capillaries. The team has also found that increased ferritin (iron) levels cause RBCs to stay elongated.   

Resia also explains how her team recently identified toxic gingipain proteins created by the bacterial pathogen P. gingivalis in Parkinson’s blood. In a series of experiments, they further showed how the gingipain proteins could increase hypercoagulation, the presence of amyloid formation in plasma, and profound ultrastructural changes to platelets. The findings are particularly exciting because P. gingivalis and its gingipain proteins were also recently identified in the Alzheimer’s brain by a different team. Taken together, the two studies suggest that P. gingivalis (which can enter the blood from the mouth/oral cavity) may play a much greater role in contributing to neurodegenerative/neuroinflammatory disease than previously believed.

Resia and team also recently published this amazing paper detailing how viruses can secrete products and proteins that also modulate platelet function and clotting in blood. They explain how, during infection, an onslaught of inflammatory and virus-derived stimuli can evoke and challenge platelets, leading to inappropriate activation, immunological destruction, and sequestration. They also just released this paper with data showing that the blood of patients with COVID-19 carries a massive load of pre-formed amyloid clots. These clots can be easily imaged in a clinical setting to provide a rapid, early detection test for clotting severity in COVID-19 patients.

Some other highlights from the interview include these comments from Resia:

  1. “I think that pathogens play a more prominent role [in contributing to chronic disease processes] than most clinicians and researchers can imagine .”
  2. “The focus of research on Parkinson’s disease has been very immunocentric. We think it should shift to focus on more prominently including the role of lifestyle and environmental factors. Because otherwise, to address the condition, where a mind-boggling number of people are suffering, we are missing something.”


A conversation with Mike VanElzakker: how his research team studies neuroinflammation

July 18th, 2020 by Amy Proal

Michael VanElzakker, Phd, is a neuroscientist affiliated at Massachusetts General Hospital, Harvard Medical School, and Tufts University. He conducts his imaging research at the Martinos Center for Biomedical imaging. We discuss how he uses fMRI and PET imaging to study neuroinflammation in patients with chronic disease, including the condition Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS).

One of the topics Mike talks about is microglia, which are immune cells in the brain. Mike uses the imaging technique PET with a PBR28 radioligand to detect where microglia may be activated in the brain of a living patient. If you want to hear Mike talk more about activated microglia in ME/CFS watch this talk he gave on the subject. Mike also mentions perivascular spaces – fluid filled spaces surrounding blood vessels that penetrate from the skull into the brain, and are enlarged during neuroinflammation. If you want to hear Mike talk about preliminary data his team has collected on perivascular spaces in ME/CFS watch this talk.

Ken Kwong (left) Creator: Smitha Jacob, Copyright: MGH/REMS 2012, IG: @mghmartinos

One of the members of Mike’s ME/CFS neuroimaging team is Ken Kwong. Ken co-discovered the fMRI BOLD response three decades ago in 1991. The picture to the right shows him using that early machine. Mike is also working to set up a 7-Tesla imaging study with Jon Polemeni at the Martinos Center. Jon develops 7Tesla sequences, and took the beautiful picture on the left (an image of blood vessels in a living patient’s brain).

Jon Polemeni, brain blood vessels IG:@mghmartinos


A conversation with Mike Lustgarten: Bacteria, viruses and the microbiome in aging and chronic disease

July 11th, 2020 by Amy Proal

Michael Lustgarten PhD is research scientist at the Tufts University Human Nutrition and Research Center on Aging. He studies how bacteria, viruses, and other organisms that persist in the human body can contribute to aging processes and diseases of aging. Several of his research projects focus on the role of the gut microbiome and blood metabolome (microbial metabolites) on muscle mass and function in older adults. Dr. Lustgarten has been a guest lecturer at the Friedman School of Nutrition Science and Policy and other Organizations on topics such as the gut microbiome, serum metabolome, oxidative stress, exercise, and sarcopenia. Learn more about Mike’s research at his YouTube channel, or follow him on Twitter at @mike_lustgarten.

(scroll below the video for more information)

Here is more context on some of the terms Mike and I use in the video:

HSV1 = Human herpes virus 1

HHV6 = Human herpes virus 6

CMV = Cytomegalovirus

Pathobiont: an organism (bacteria, virus, fungi etc.) in the human body that can be present in a healthy person, but may also change the way it expresses it genes to act as a pathogen under conditions of immune suppression, imbalance, or inflammation. You can listen to me talk more about pathobionts and chronic disease development here. 

Polymicrobial: “Poly” means “many.” A polymicrobial disease is one in which different organisms (bacteria, viral, fungal etc.) interact together to collectively disable the human immune response or drive other pathological processes. The word “polymicrobial” is also sometimes used to describe the fact that entire communities of microbes and viruses can evolve together towards a state of pathology or imbalance. This microbiome and/or virome “dysbiosis” is increasingly being documented in patients with a range of chronic inflammatory conditions.

Virome: The word virome refers to the ecosystems of viruses that persist in human tissue and blood – along with bacteria, fungi and other organisms. The virome includes DNA viruses, RNA viruses, and a large number of bacteriophages (viruses that infect bacteria.)

Here are some highlights from our conversation and some additional clarifications:

Mike’s funded research focuses on how metabolites (discussed more below) created by microbes in the gut and blood may impact muscle mass in older adults. On the side, he’s also interested in optimizing fitness and health by blood testing and tracking diet. He also wrote a book several years ago called “Microbial Burden“, with the goal of educating the public about the how microbes and viruses in the human body can play a role in health and disease. In the book he talks about the gut microbiome, but also explains how pathogens and/or communities of organisms capable of persisting in human tissue and blood can contribute to chronic disease and aging. He also discuses strategies for optimizing our microbiomes to delay aging and aging-related disease… to hopefully help people live as long as possible! 

I (Amy) have always loved the title of Mike’s book Microbial Burden. That’s because while research teams focus on how “good” microbes in the human body (and especially the gut) might promote health, Mike and I share an interest in better understanding how many of these same microbes can change their activity under conditions of immune suppression or imbalance to drive chronic disease. If and when that happens, the microbes that live in and on us can become more burden than benefit, a dynamic that the title “Microbial Burden” captures well. Many of the microbes (and viruses) that can become a “burden” in chronic disease are now understood to be capable of persisting in blood or other areas of the body previously regarded as sterile – such as brain or placenta.

Mike and I are both very interested in studying how intracellular pathogens contribute to chronic disease. Intracellular pathogens have evolved the capacity to infect and enter a human cell. They often persist in the nucleus, or center, of the cell they infect. Once in the nucleus, they gain access to the DNA of the human cell, allowing them to dysregulate or modify the way the human cell decodes and expresses its DNA (transcription and translation). Intracellular pathogens may also  dysregulate the epigenetic environment, or interfere with DNA repair. They can even hijack the metabolism of the cells they infect (all virus modulate host cell metabolism in order to replicate). Overall, in simple terms, intracellular pathogens can “hack” how human cells express and control their own genes and metabolic programs. In this way, intracellular pathogens can drive many chronic disease processes and symptoms, and both Mike and I think this topic is very understudied. You can listen to me talk more about how intracellular pathogens “hack” human cell function here.

We also talk about how many persistent viruses and bacteria drive disease by creating proteins/metabolites that are very similar in size and shape to human proteins/metabolites. This overlap between pathogen and host proteins is sometimes called “mimicry.” I point out this study as an example: certain viruses can create proteins similar in size & shape to human insulin proteins. Those viral proteins can then bind into human insulin receptors, which can dysregulate downstream insulin signaling in a manner that might contribute to diabetes. Mike recently submitted a grant that, if funded, will test if metabolites created by gut bacteria can enter the blood and impact the muscle mass of older adults.

Mike and I both agree that studies of microbiome/virome imbalance or pathogen activity in chronic disease must go beyond documenting just “what’s there.” In other words, identifying the presence of organisms in a microbiome community is only a first step. The real key to understanding how such microbes might contribute to chronic disease is to use other tools and technologies to study “what they do” (their activity). Studies of microbe activity include what genes they are expressing, but also studies of the proteins and metabolites they create under different conditions (these include virulence factors, biofilm quorum sensing molecules etc).

One reason this trend matters is that the same organisms & pathogens can be harbored by both healthy and sick people, but in a person who develops chronic disease these organisms may start acting in a new way. For example, almost half of all people harbor Herpes Simplex Virus 1 (HSV1). But, in patients who develop certain chronic symptoms, a virus like HSV1 might change its gene expression, causing it to make different proteins than it would in a healthy person. HSV1 might also infect a different tissue, nerve, body site, or cell type in a sick individual. The virus may also begin to persist inside the cells of the immune system, or it may begin to interact with other organisms in the body in a detrimental, polymicrobial fashion.

Mike and I are both interested in immunotherapy – treatments that stimulate or support part of the human immune response, so that a patients’ own immune system may better manage a persistent infection and/or microbiome/virome dysbiosis. For example, cancer immunotherapies that activate T cells to target tumors are showing great promise as therapeutics. Because a growing number of viruses and bacteria are being identified in human tumors, cancer immunotherapies may allow the immune system to better target tumor-associated pathogens. If that’s the case, similar immunotherapies could be extended to the growing number of chronic conditions tied to viral & bacterial activity.

Mike and I also agree on the following: while nearly every chronic disease is now tied to “inflammation” or “inflammatory processes,” the key to better understanding this trend is to always ask, “what is driving the inflammation!?” That’s because there is almost always a root cause or a reason for inflammation (for example, inflammation is generated when the immune system targets pathogens). Although this sounds obvious, Medicine is currently more focused on palliating inflammation to temporary lower symptoms, rather than performing extended testing or research to figure out the root cause of the problem.

When Mike mentions Cosmo he’s talking about our friend and very smart scientist Cosmo Mielke. You can read more about Cosmos’ work on how viral infection contributes to the development of aging, obesity, and other metabolic issues here.

When Mike brings up “toxo” he means Toxoplasma gondii – a parasite that can persist in the central nervous system, where it is capable of driving psychosis. He mentions Lena Pernas’ work on Toxoplasma and mitochondria, with a focus on this paper her lab published in the journal Cell. Dr. Pernas shows how Toxoplasma gondii can compete with the mitochondria of the cells it infects for access to nutritional fatty acids. 

Overall, both Mike and I think bacteria, viruses and other organisms are dramatically understudied as drivers of chronic disease. We dream of a global effort in which a tremendous amount of funding, resources, and brain power are dedicated to the study of the human pathogens and pathobionts already implicated in chronic disease. We should be studying pathogens like Epstein Barr Virus, HHV6, and Pgingivalis etc., with the same urgency and funding as COVID-19. However, such a global effort (similar to the Moon Shot or Manhattan Project) would require a paradigm shift in how the scientific & medical communities think. At the moment, too many PhDs and MDs were educated by textbooks that (incorrectly) claim the blood and brain are sterile. Science education must be updated to include more recent data on organisms’ activity in body sites outside the gut. Mike and I hope that younger researchers are willing to become “warriors” in pushing this paradigm shift forward.

When it comes to implicating persistent pathogens in chronic disease, a barrier that both Mike and I note is that many such pathogens are not easily identified in the blood. Consequently, we need to keep perfecting tools and methods that allow identification of these pathogens in other body sites, including tissues and nerves. Also, persistent pathogens are often present in low quantities (low biomass) but may still drive chronic disease processes. In other words, “quality” (what a pathogen does) often matters more than “quantity” (how much pathogen is present). A good example of this is how oral pathogen P.gingivalis can drive periodontitis progression even when it’s present in very low amounts in an oral biofilm.

Mike and I talk about COVID-19, and both of us are somewhat frustrated that most drug development and attention is focused on late-stage COVID-19 (when patients are already in the ICU). We hope that efforts grow to better combat the virus in early-stage disease, when viral load is lower. We are even interested in strategies – both pharmacological and nutritional – that might prevent people from getting a bad case of COVID-19 in the first place (preventative medicine).

In fact, we both think that disease prevention (predictive and preventative medicine) is the future. Mike hopes that one day, most of the pathogens and organisms capable of contributing to chronic disease processes can be “mapped” along with other associated immune parameters, diet metrics, and aging biomarkers. We would have personalized testing that can indicate what pathogens/microbes might become problematic for a given person over time. Then we could intervene early with immunotherapies, antivirals, antimicrobials, vaccines, or other therapeutics to stop many chronic diseases processes from occurring in the first place – possibly allowing people to live longer and healthier lives.





Interview with Dharam Ablashi: On the discovery of Human Herpes Virus 6 (HHV6) and its involvement in chronic inflammatory disease

June 28th, 2020 by Amy Proal

Dharam V. Ablashi is an American biomedical researcher born in India. He is best known for his co-discovery of Human herpesvirus 6 (HHV-6), an immunosuppressive and neurotropic virus that can cause encephalitis and seizures during a primary infection or when reactivated from latency in immunosuppressed patients. He spent 23 years working at the NIH while additionally serving as an adjunct professor at Georgetown University School of Medicine. Ablashi’s research has also helped clarify the pathogenic role of HHV6-A and HHV6-B in neurological disorders such as multiple sclerosis, epilepsy, ME/CFS, and in tumors such as Hodgkin’s disease lymphomas and other brain tumors. He has co-authored 96 articles on HHV-6 and co-edited three books on HHV-6. He is also internationally known for his research on Human and Simian herpesviruses and has also been a major contributor to research on HIV, Epstein Barr Virus (EBV) and the field of immunovirology. He has served as the Scientific Director of the HHV-6 Foundation since 2004.

How did you discover HHV6? What led you to begin studying the virus?

It was late 1984 when I met Zaki Salahuddin and Dr. Robert Gallo at the National Cancer Institute (NCI). At that time, I was a member of another branch of NCI working in the same building where Dr. Gallo’s laboratory was located. They had found EBV in two-thirds of B-cell lymphomas of HIV patients. Gallo suspected there must be another herpesvirus causing cancer in the rest of the patients and asked us to look for it.  So, that was the beginning of our discovery.

We cultured the spleen cells and lymphocytes and stimulated with PHA from the B-cell lymphoma AIDS patients, and we saw very large cells (juicy cells-see image) appearing. When we sent these cells to get electron microscopy, we found that there was a herpesvirus. I thought I had isolated an EBV virus, but none of the monoclonal antibodies from other human herpesviruses were positive. At that time, we named it human B lymphotropic virus and determined that it was highly cell associated, spreading from cell to cell.  Of 8 isolates from HIV patients with AIDS lymphomas, all were HHV-6A, not HHV-6B.

NIAID investigator Dr. Paolo Lusso, who also was in Dr. Gallo’s lab as a post-doc, tested these cells and showed that these infected juicy cells were T-cells. That is when we changed the name to HHV-6 in 1987. Then in 2013 HHV-6 was reclassified as HHV-6A, and HHV-6B.

We also discovered HHV-7. However, we decided to characterize it more before publishing and, and Dr. Niza Frankel beat us to publication.  Dr. Gallo was very upset on that one!

What was it like to work with Robert Gallo? Do you have any interesting stories about working in that lab?

Visualization of HHV6B DNA by radioactive in situ hybridization in an immune cell of the myocardium (PMID: 23473961)

My relationship with Dr. Gallo developed quite well.  In fact, I considered him to be my mentor, and he respected my training and knowledge working with herpesviruses.  He was very hard to please but respected those who produced solid data.  He expected us to work very hard and would often call for meetings on weekends.

Ironically Bob Gallo helped kill funding for HHV-6 research in the early 1990s. At that time, HHV-6A was suspected as a possible co-factor in AIDS progression, because HHV-6 also infects CD4 T cells and a co-infection was thought to hasten the depletion of CD4 T cells in AIDS. Then a vocal AIDS activist and publisher of the New York Native started claiming HHV-6A was the primary cause of AIDS and that Gallo was covering up this “truth.”  Gallo became irritated and started proclaiming HHV-6 to be a benign virus, even though he knew it was not true, in order to get them to stop. He admitted to me years later that he feels guilty about this. It is a great example of how uninformed activism can be quite damaging. This individual is still accusing Gallo and myself of a cover-up, threatens protests outside our small scientific conferences, and accuses our speakers of “covering up the true cause of AIDS.”

You earned degrees in India, the UK, and the USA. Do you think this international education had an impact on how you approach research challenges?

My education in India was based on British teaching, so I had my DVM, and then when I came to the US, the education system was completely different.  I did all the work for a Ph.D., but could not pass the language requirement at the time, so gave up. That same institution, University of Rhode Island, recently gave me an honorary doctorate which was very kind of them. Most of my education came from long hours of hard work in the laboratory.

You’ve received many awards for your HHV6 research. Which are you most proud of and why?

In 2006, at the International Conference on HHV-6 and HHV-7 held in Barcelona, Spain, the keynote speaker said he was very proud to present me with the Lifetime Achievement Award on behalf of the HHV-6 Foundation. This award was named the Dharam Ablashi Lifetime Achievement Award, and I was the first recipient.  I am very proud of this award.  There have been many other ones, and I remember one given to me on the Rudy Perpich Memorial Achievement Award for Chronic Fatigue Syndrome (CFS) research.

What has been the greatest challenge you’ve faced in pushing research on HHV6 forward?

Detection of HHV6 in human astrocytes and in T lymphocytes (PMID: 16014907)

One reason was due to the confusion caused by chromosomally integrated HHV-6. Once physicians saw occasional asymptomatic patients with extremely high viral loads (not understanding that this was an inherited condition), they assumed that the virus must be benign. Ironically Bob Gallo also admitted to me that he helped kill interest in HHV-6 research. HHV-6A was suspected as a possible co-factor in AIDS progression (working with HIV to deplete CD4 T cells) but when AIDS activists started claiming it was the primary cause of AIDS, Gallo started saying that HHV-6 was unimportant, just to get them to stop accusing him of covering up the “true” cause of AIDS.

The other challenge is that HHV-6 is very difficult to grow because infected cells will die very quickly. It is much more difficult than other herpesviruses, and as a result, there are very few laboratory scientists currently who understand the right techniques to even grow the virus.

HHV6 infection is connected to a range of chronic conditions that are deemed “autoimmune” or “of unknown cause.” Do you think that’s accurate? Do you think the scientific community needs to take HHV6 infection more seriously in many of these disease states?

Several researchers from diverse fields have found a connection between HHV-6A and Multiple Sclerosis (MS) as well as autoimmune thyroid disease. HHV-6B reactivation occurs in most severe DRESS/DIHS cases, and many of those patients go on to develop autoimmune diseases such as diabetes type 1. HHV-6A has been found in over 80% of Hashimoto’s thyroiditis patients vs 10% of controls, and HHV-6 is found at high levels in the islet cells of patients with diabetes type 1. The mechanisms require further study.

DRESS expert Chia-Yu Chu in Taiwan believes that IP-10 may be the link between HHV-6 reactivation in DRESS and subsequent autoimmunity. A group in Italy has found that HHV-6 infection of thyrocytes and T cells alters the expression of miRNA in a pattern similar to that of autoimmune thyroiditis. The scientific community needs to follow up on these important potential associations.

What research team do you think is currently doing the best research on HHV6, and why?

The Japanese have led the way in molecular biology. Virologist Koichi Yamanishi was the first to associate HHV-6B with roseola in 1998, and his protégé Yasuko Mori has contributed enormously to basic science, including valuable data on cell entry, and identifying CD134 as the receptor for HHV-6B.  Transplant specialists such as Masao Ogata in Japan have also done valuable work in characterizing HHV-6B encephalitis, and Japan is the first country in the world to have a drug approved specifically to treat this condition (foscarnet). Japanese dermatologists have done valuable characterizing of frequent HHV-6B reactivation in drug-induced hypersensitivity syndrome, a phenomenon that has been mostly ignored in the US. Finally, Kazuhiro Kondo has recently published a study tying HHV-6B latency protein to a 12-fold increased risk of depression as well as increased activity of the HPA axis.

In the US, very little research has been done on HHV-6 compared to Europe and Japan. Over the past several decades, only one investigator at NIH has consistently studied HHV-6 in neurological disease (Steve Jacobson, NINDS) who showed that HHV-6A accelerates neuroinflammation in a marmoset model of MS.  The only academic center that has demonstrated a sustained interest in HHV-6 has been at the University of Washington led by Danielle Zerr (Seattle Children’s Hospital) and Michael Boeckh, Keith Jerome, Joshua Hill, and Alex Greninger (Fred Hutch). They have characterized HHV-6B in children, found increased CNS dysfunction in transplant patients with HHV-6 reactivation, revealed increased graft vs host disease in stem cell transplant patients with HHV-6 reactivation, as well as with chromosomally integrated HHV-6.

What are the top mistakes that research teams can make when trying to study HHV6?

In situ PCR for HHV-6 in inflammatory sites of Kawasaki’s coronary arteritis (Luka et al, Cell Vision, 1995)

Many groups studying HHV-6A/B in chronic conditions want to look in the plasma or cerebrospinal fluid (CSF), and fail to understand that HHV-6 DNA appears in those compartments only briefly and typically only during acute reactivations. These are low copy number viruses that spread cell-to-cell. They also generate potent chemokines and cytokines, even in latency.

There may be low-level DNA detectable by nested PCR in a chronic case, but generally, qPCR, ddPCR, and RNA sequencing techniques are not able to detect low level central nervous system infections of HHV-6A/B in plasma in ME/CFS and MS patients. HHV-6 DNA levels can be extremely high in the brain, liver, or lung, with barely a trace in the plasma. So biopsy analysis is extremely important. Also, HHV-6A/B viral infections have scattered foci, multiple samples per biopsy are necessary to get a true understanding of prevalence in any organ.

Another mistake is to look at DNA in whole blood, where viruses like HHV-6B and EBV can be found in latent form. For HHV-6, this is too simplistic. It is more important to identify organ tissues where there might be active infection, or a smoldering infection – a latent infection that is still throwing off inflammatory cytokines and chemokines.

Finally, many studies fail to rule out inherited chromosomally integrated HHV-6, which occurs in 0.86% of the US population controls and 1.5 – 2% of patients. These patients will always be positive for HHV-6 DNA in the plasma and CSF, even if asymptomatic, so this condition needs to be determined. (This is easy to do by measuring HHV-6 DNA in whole blood by qPCR because there is one genome per nucleated cell, so the viral load is typically in the millions per mL.)

What role do you think HHV6 plays in the illness myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)?

We don’t think ME/CFS is triggered by a single pathogen; we believe it can be triggered by a number of intracellular pathogens including enterovirus, parvovirus B-19, mycoplasma pneumonia, chlamydia pneumonia, EBV, Cytomegalovirus (CMV), and HHV-6A/B and HHV-7. After the Dan Peterson and Paul Cheney first discovered HHV-6 in patients with the outbreak of ME/CFS in Incline Village Nevada in the 1980s, Dan Peterson, Anthony Komaroff, and Deidra Buchwald came to see Dr. Gallo to discuss whether HHV-6 played a role in ME/CFS.  At their request, we tested the antibodies of sera or plasma from ME/CFS patients.  During this process we found a subset of samples with very high antibody titers to HHV-6.  Buchwald, Komaroff, and associates published a paper in 1992 that found used primary cell culture to determine that 70% of ME/CFS patients but only 20% of controls showed signs of active replication.  Later in 2001, I published another paper that showed an increased level of IgM antibodies to an HHV-6 early antigen protein in ME/CFS patients. This was an assay based on a reagent produced at Gary Pearson’s lab at Georgetown, and unfortunately, this reagent is no longer available. Recently Dr. Bhupesh Prusty in Germany has shown how persistent HHV-6 infection can cause mitochondrial dysfunction, which may play a role in ME/CFS.  Also, Dr. Kondo recently published very interesting data showing that a neurovirulent HHV6 latency protein plays a pathogenic role in both depression and fatigue. He previously determined that HHV-6 builds up in the saliva when the body is fatigued and says this virus finds its way to the nasal passages and then on to the olfactory bulb and brain. A latency protein he calls SITH-1 then causes hyperactivation of the HPA axis and subsequent depression and fatigue.

What are your thoughts on HHV6 and Alzheimer’s disease?

Again, we believe that infections are the most logical explanation for the inflammation neurodegeneration associated with Alzheimer’s, but don’t believe that there is a single pathogen responsible. HHV-6A and HHV-7 were identified as likely culprits in 2018 paper, using RNAseq analysis by Readhead and team. Two subsequent studies did not find an increase in HHV-6/7 using the same data, but at the same time did not find a significant presence of ANY herpesviruses in the brain, which we know is not the case. Dozens of careful studies have identified a high prevalence of low-level HHV-6 and HSV1 DNA in brain tissues. This tells us that RNAseq and ddPCR methods employed to date are not sufficiently sensitive to really answer the question of whether these viruses play a role in Alzheimer’s. Future studies should be done with both extremely sensitive assay as well as multiple samples from each brain region to answer the question of HHV-6A/B prevalence in Alzheimer’s samples vs. controls. In 2002, Ruth Itzhaki’s group looked for HHV-6 and HSV1 by nested PCR and found HHV-6 DNA in 70% of Alzheimer’s brains vs. 40% of controls. They found HSV1 at high levels in both AD patients and controls. Old-fashioned nested PCR is time-consuming and complicated because measures must be taken to prevent contamination, but this old-school technique may still be a better approach than newer techniques (such as RNAseq analyses) that can find little to no herpesvirus in these brains. The other issue is that infections may be early triggering events that disappear over time. It will take a lot of time and a solid investment in research to find any answers.

Are there any key experiments that you think should be conducted on HHV6 that haven’t happened yet?

The NIH has dedicated several hundreds of million dollars each toward the study of CMV, HHV-8 and EBV over the past 20 years, but almost nothing for HHV-6. As a result, we have a long way to go in understanding much of the basic science behind HHV-6 that would allow more sophisticated analysis. For example, a great deal of effort has gone into characterizing EBV early and immediate early proteins, and there are assays that can measure EBV early antigen and EBNA antibodies. We don’t have those tools for HHV-6. This is a complicated virus, and it will require significant funding to unravel disease associations.

One simple clinical study that is at the top of our list is a clinical trial to determine if antiviral treatment would benefit infants with HHV-6B induced febrile status epilepticus (FSE). A large study in 2012 confirmed that 32% of infants with FSE have active HHV-6B, yet for reasons we don’t understand, these infants are not given an antiviral and are treated only with anti-seizure drugs. Around 30% of these infants eventually develop epilepsy, and many of them suffer from cognitive dysfunction.

You describe HHV6 as an immunosuppressive virus. Can you explain why you’ve come to that conclusion and describe some key research findings that led to that understanding?

All three roseoloviruses (HHV-6A, HHV-6B, HHV-7) are immunosuppressive, and animal homologues such as murine and porcine roseolovirus are immunosuppressive as well. HHV-6 preferentially infects CD4 T lymphocytes and is associated with delayed engraftment in transplant patients. HHV-6 reactivation in transplant patients is also associated with bone marrow suppression, graft rejection and increased bacterial and fungal infections. Transplant patients with HHV-6B reactivation are 15X more likely to develop a CMV infection after reactivating with HHV-6. Severe cases of primary HHV-6B infection are tied to neutropenia.

Do you think that HHV6 can act along with other pathogens to drive chronic disease processes? If yes, how might this happen (for example can HHV6 support HIV survival and vice versa)?

Yes, but the mechanism is likely to be indirect, and not due to active replication. HHV-6A/B can generate inflammatory cytokines, chemokines and virokines even in latency. This causes chemoattraction of leukocytes which in turn triggers inflammation. In addition, there appears to be a state of abortive infection wherein some early proteins are expressed in the absence of full replication. HHV-6 is actually likely to reduce HIV patient survival by accelerating the depletion of CD4 and CD8 T cells. HHV-6A was shown to accelerate AIDS progression in macaques.  Macaques co-infected with simian HIV and HHV-6A died quickly and showed a dramatic depletion in both CD4+ and CD8+ T cells, whereas those infected with only simian HIV never progressed to full blown AIDS.

What advice do you have for young researchers starting to learn about and study HHV6?

For decades scientists have avoided HHV-6 research because the NIH was not funding HHV-6 related grants. As a result, there is a lot of opportunity to make important clinical and scientific discoveries, with very little competition. My advice is to be courageous and aim for a major discovery in an emerging field, rather than making a marginal contribution to a well-studied pathogen.




My favorite recent papers that impact the study of chronic inflammatory disease

December 30th, 2018 by Amy Proal

2018 was a great year for science. The following article summarizes findings from my favorite studies published this past year. Many of the studies shed light on how persistent infection can contribute to chronic inflammatory disease processes. They also clarify how activity of the human microbiome + virome + mycobiome (fungi) influence health and disease processes. Topics discussed include the maternal microbiome, the gut-brain axis, brain infection, bacteriophage activity, the circulatory microbiome, novel human structures/pathways, pathogen survival mechanisms…and more. There is also a section on potential novel treatments and treatment-based paradigm shifts (especially relevant to neurological disease).

I broke the article into “areas of study” so that it’s easier to read. Please note that despite the many studies listed below, I could still have added more findings to the list! After reading the article, please respond with other important 2018 studies that you think I might have missed.

1. Studies on chronic inflammatory disease and the human microbiome move WAY beyond just species composition:

The human microbiome (Image:

Several times this past year I’ve been told that studies connecting microbiome dysbiosis (imbalance) to chronic inflammatory disease “haven’t moved beyond association.” I disagree. In fact, for years now, teams have been using computer modeling, metabolomics and a range of other methods to dissociate “cause from effect” in microbiome-based analyses. These three 2018 studies are excellent examples of the trend (while they involve the gut microbiome, similar studies have been also been conducted on microbiome ecosystems in other body sites):

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

Lead author: Rinse K. Weersma, University of Groningen and University Medical Center Groningen

The team characterized gut microbiome dysbiosis in patients with IBD/IBS using a computer-based tool called shotgun sequencing. BUT, they also analyzed bacterial taxonomy, metabolic functions, antimicrobial resistance genes, virulence factors, and growth rates. Thanks to this extra information, they were able to identify key bacterial species that may be involved in both disorders.

Pathogenic Functions of Host Microbiota

Lead author: Marius Vital, Helmholtz Centre for Infection Research, Germany

Co-occurrence analysis of individual pathofunctions (Vital et al)

The team studied the gut microbiome, and found that different groups of bacteria often exhibit redundant pathogenic functions (they called them “pathofunctions”). These pathofunctions include the production of common metabolites (like trimethylamine, secondary bile acids, and hydrogen sulfide). This functional redundancy has implications for the study of chronic inflammatory disease tied to microbiome dysbiosis: it suggests that metabolic dysfunction driven by different groups of organisms can result in similar clusters of inflammatory symptoms. 

Distinct Microbes, Metabolites, and Ecologies Define the Microbiome in Deficient and Proficient Mismatch Repair Colorectal Cancers

Lead author: Nicholas Chia, The Ohio State University College of Veterinary Medicine

The team combined tumor biology, metagenomics, metabolomics and modeling approaches to study the impact of the gut microbiome on colon cancer. They demonstrated distinct roles for microbes and their metabolites in colon cancer mismatch repair status. For example, highly influential microbes included many butyrate producers.

Continue reading

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

November 28th, 2018 by Amy Proal

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

Please watch this video of our interview/conversation:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

George: Absolutely. I agree with you.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

George: Yes. 

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

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

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

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

Amy: And bacteria can also modulate phage activity right?

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

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

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

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

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

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

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

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

Amy: OK what’s next for you? 

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

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


Interview with David Paez-Espino (JGI): Identifying novel viruses on Earth and in the human body

June 12th, 2018 by Amy Proal

Hey readers!

Viruses are the most abundant life form on the planet

This blog and my peer-reviewed papers explore how the human microbiome can impact chronic inflammatory disease processes. It is well understood that an extensive microbiome persists in the gut (hundreds of trillions of microbial cells in total!) In addition, extensive microbiome communities have been identified in every other human body site – from the brain, to the liver, to the lungs, to the bladder, to the placenta and beyond. We now realize that no part of the human body is sterile. This includes human blood, which is now understood to contain a microbiome (even in healthy individuals).

However it’s very important to understand that even when all this new human microbiome knowledge is taken together, the global research community has still not yet identified, characterized or studied many of the microbes and viruses in the human body. In fact, almost every new human microbiome study turns up new species of bacteria, viruses and fungi that were previously unknown to science. For example, just a few months ago, Stephen Quake identified thousands of species of bacteria, viruses and fungi in human blood that were simply not known to exist before the study was performed.

Viruses are the most abundant life forms on the planet, but we know particularly little about human viruses. In other words, there are an incredible number of viruses in the human body that have not yet been identified. This is especially true of bacteriophages (viruses that infect bacteria). A recent study estimated that 31 billion bacteriophages traffic the body on a daily basis. The human body also harbors double stranded DNA viruses and RNA viruses. Most of us are familiar with double-stranded DNA viruses like the herpes viruses. We are also familiar with RNA viruses like polio, measles and influenza.

But these well-known RNA/DNA viruses comprise just a tiny fraction of all the viruses capable of persisting in the human body. Many other related viruses are still in the process of being discovered!

It follows that we cannot study human chronic inflammatory disease without understanding that viruses we have not yet identified may play a role in many human disease processes. To do so would be like going to the rainforest, studying only 2% of the animals, and coming to conclusions about how the entire rainforest functions off that information alone.

Despite this fact many doctors have been taught to test for only 10-20 well-known viruses in their human patients. If these viruses are not identified in the patient, it is assumed that a virus (or group of viruses) cannot be driving or contributing to the patient’s disease. We must work hard to change this assumption, because it greatly prevents the medical/research communities from looking at a much broader picture of what might be going on.

David Paez-Espino

In order to best make this point, I interviewed David Paez-Espino. David works at the Joint Genome Institute in Walnut Creek California, in the Department of Microbial Genomics and Metagenomics. He and his colleagues have created new, complex computational technologies that help identify both novel and known viruses. In fact, they have started a project called “Uncovering the Earth’s Virome” (viral communities). This project searches for novel viruses not just in the human body, but in ecosystems across the planet – including the ocean, the soil, the air, and in other animals. These viral sequences are stored in the world’s largest public viral database: IMG/VR.

Over just the past few years, Paez-Espino and team have identified and sequenced many, many new viruses. In a 2016 Nature paper, they unveiled more than 125,000 partial and complete viral genomes, which boosted the number of known viral genes in the world by 16-fold. By the time they published a follow-up paper in 2017, the contents of the IMG/VR database had doubled from the figure referenced in 2016. By January 2018 the database had tripled in size. At that point Paez-Espino stated the following:

“Among the million viral sequences predicted, we have now identified over 34,000 of them targeting several microbial taxa for the very first time, we’ve associated new viruses to known microbial genomes (culturable and unculturable), and the vast majority of the gene content (over 21 million genes in total) remains hypothetical or unknown, meaning that there is tremendous potential for new discoveries out of that gene pool.”


In this interview, David and I talk more about these findings. We talk about how his team has identified all kinds of viral entities and how they focus on the identification of less-studied viral groups, e.g. giant viruses, and virophages (viruses that co-infect eukaryotic cells along with giant viruses). These giant viruses were not previously known to persist in the human body. We also talk about how the study of novel viruses holds incredible potential to improve our understanding of chronic and rare inflammatory conditions.

Here is a short video clip of part of our conversation. The full interview is below and has been edited for accuracy purposes:

Amy: Tell me about your job at JGI and what projects you’re working on now.

David: Over the past four years here at JGI I’ve started working on a project called “Uncovering the Earth’s Virome” – a very ambitious name, I know. We are trying to get a sense of what viruses are out there. To do that we are generating a comprehensive list or viral catalog of viruses from samples everywhere on Earth. I work in the Microbiome Data Science group (lead by Dr. Nikos Kyrpides), where we look for novel or known viruses in environmental samples…all kinds of samples: we have metagenomes, we have metatransciptomes. We also have some isolates. And we don’t just look for viruses – we also try to link the viruses to their specific habitats and to their specific hosts. Everything is computational. But then we try to validate our findings by working with other groups here at Berkeley or beyond.

Amy: Where do get your initial viral data from (that you then use to identify novel viruses)?

David: The JGI sequences many of these samples through collaboration projects (CSPs and FICUS programs). But we also have part of our public repository database (called IMG/M) represented by other groups’ data. We developed a virus prediction pipeline to identify viral sequences directly out of those samples, and have created IMG/VR (the largest virus repository integrated by isolates and microbiome-derived viral sequences). And everything is public. We are mining millions and millions and millions of nucleotides. So we have terabytes of sequences. And this collection of viral data in IMG/VR is very diverse – it includes marine/aquatic samples, terrestrial samples (like soil), human microbiome samples, and even microbiomes from mice, ruminants, air, arthropods etc.

Amy: So let’s say I sent you a blood sample. When it comes to identifying new viruses in this sample: What is your technology able to identify versus what a technique like PCR could identify?

David: If you’re using PCR to identify viruses you’re using an approach where you already know what you’re looking for (you are biased towards viruses that are fully characterized and have been entered in known databases). So PCR is useful if you have a well-known virus already understood to be a human health threat. For example, we could identify Zika virus that way.  

But in our case, we have different approaches. The first is a general global viral discovery pipeline. It does not only rely on genes from known viruses. Instead, we use the genes from known viruses to identify novel viruses from environmental samples: think of these novel viruses as, let’s say, the cousins of viruses already in a known database (their genomes are similar to known viruses but with a certain degree of difference). It’s a homology-based pipeline, but one that’s more sophisticated than the usual BLAST approach. 

A T4 bacteriophage

Our second approach is to target very specific groups of viruses that are unique. These include specific families from single stranded DNA viruses, double stranded DNA viruses, single stranded RNA viruses etc. In fact, we have developed specific tools that can identify hallmark genes associated with many types of viruses. These even include giant viruses. Giant viruses are eukaryotic viruses that have long genomes (sometimes 1 megabase, 2 megabases, even almost 3 megabases in size!). They also have very unique capsid proteins that can’t be found elsewhere. So we can develop and use these unique viral characteristics to create specific models for identifying similar viruses. This same process of identification goes for virophages.

Amy: What exactly is a virophage?

David: A virophages is a virus that co-infects a eukaryotic cell along with a giant virus. In the majority of cases the virophage is a parasite of a giant virus. But in some cases it seems that virophages only use part of the giant virus machinery to replicate within the final host (a eukaryotic cell that is often an algae or protozoa -as currently known). The infectious process is kind of like a Russian doll. There are many different levels of infection.

Amy: Where are you finding these giant viruses and virophages?

David: They seem to be everywhere. We are submitting a paper in which we found virophages in all kinds of environments including the human gut. Finding them in the gut was something people had speculated about but we finally proved it is true. Because most people don’t have the right tools to mine for virophages, or they don’t have the right tools to mine the database, or they don’t have samples from the right habitats or styles of life in the database. So a luxury we have here at JGI is that we can apply novel tools to a very wide variety of different samples – and we can pretty much find everything everywhere:)

Amy: Yes. It seems very important to stay up to date on the latest technologies for viral identification. Because if you don’t know HOW to look for a new virus you probably won’t find it.

David: Yes, if you only study already known viruses you may be missing part of a larger unexplored picture.

Amy: I’m interested identifying novel viruses that might play a role in the disease ME/CFS. Let’s say I had blood samples from patients with ME/CFS. Can I send them to you so that you can use your technology to search for new viruses in the samples? How would that kind of collaboration work?

David: We have two ways to collaborate. First we have official calls for research. About 40-60% of those projects get accepted. But those projects are more along the lines of the DOE (energy, carbon cycling, and environmental viruses rather than human viruses). 

But for identification of novel human viruses: We are developing new tools for the discovery of RNA and DNA viruses. And we need validation of these tools. So we want to apply them to all kinds of samples as opposed to just those from the environment. Also because everything is connected we sometimes find environmental viruses in humans and vice versa. So if you’re interested in human viral discovery we don’t have official calls for that research. But you can talk to me and say, “Hey I have these samples and I’d like to know if your RNA viral pipeline could work for my samples.” Then I can talk to my boss, and if we all have this common interest or a common outcome (a paper, a patent) we can hopefully find a way to collaborate.

Amy: What are some of the most interesting viruses you’ve identified in the human body? Do you mostly have gut microbiome samples?

David: So as I mentioned before, all the data we get is deposited in the interactive IMG/VR database. On the database website you can access the habitat of the samples to see where our human viral samples come from. At the moment IMG/VR includes viruses found in five different human body subtypes: skin, urogenital, salivary, gut, and the respiratory tract. 

One interesting thing we’ve found is that viruses are very specific to their habitats. That means if you find a virus in a marine environment it’s very unusual to find it somewhere else. You can find it across the globe in different oceans but, if it’s a marine virus, it’s a marine virus. The same is true of human viruses. If you have a human virus it’s probably going to be only found in the human body. And if it’s a human gut virus, only in the human gut. So, we saw very few connections between the different body subtypes. The findings are similar to those reported in a separate recent paper: The healthy human phageome. In that study, healthy humans were found to have a certain pattern of viruses always present in the gut. We also found that to be true – there seem to be marker viruses that could indicate the health status of a person. Probably because such viruses are maintaining a balance with the bad bacteria.

Amy: And in disease there might be shifts away from that core viral state?

David: Yes, definitely. For example, we have a very recent paper (in editorial status) where we compare the virome of IBS mice to that of healthy mice. And we found a certain core pattern in the gut virome of the healthy mice and a very stochastic pattern in the gut virome of the IBS mice. Basically, totally different virome patterns identified between the two groups. And those patterns may give us some leads as to what happens in human IBS. Hopefully the paper will be out soon.

Amy: Wow, you have some great papers coming out.

David: Yes. We are also doing work related to phage therapy. We are trying to predict certain phages and then predict their bacterial hosts. And of course, many of these bacterial hosts are harmful to humans. That gives us the opportunity to engineer the phages in ways that might allow them to best kill the bad bacteria.  

So, we predict phages in the human body and then say “This viral (phage) sequence is probably infecting this particular bacterial host.” But we are collaborating with other groups here at Berkeley on the project because, if we do identify a bacterial host, we need to know if we can culture it in the lab. Culturing the bacterium allows us to test it. We need to do that because our computer-based predictions are pretty robust – but we must be 100% sure that what we predict computationally holds up in the lab. Also, we need to confirm that the phage sequences we predict are perfect before attempting to use them as therapeutics.

Amy: That’s great. That’s what the phage therapy community needs right now. Much more information on verified phage/bacteria relationships (that can be easily accessed in a database). It’s also great for our general understanding of the microbiome. Because if we fail to account for the phages in any microbiome ecosystem, we’re unlikely to really understand the community dynamics. 

David: Yes. For example, if you study cell biology there’s another layer beneath that knowledge. You also need to understand molecular biology, because you need to understand molecules in order to understand cells. Similarly, if you want to understand bacteria in a microbiome community, it’s important to understand that the way the bacteria behave is based on their relationship to the phages. For example, there is a theory called “kill the winner.” Sometimes a bacterium grows exponentially in an environment. If its levels come back to equilibrium it’s usually because there is a phage that’s killing it. This equilibrium is built into the foundation of the ecosystem. And without understanding viruses you can’t fully understand that equilibrium. So yes, it makes sense to think that way.   

Amy: Yes that’s even true of an intervention like a probiotic. It would be helpful to understand how the bacteria in a probiotic might be modulated by neighboring phages.

So give me some numbers. I know it’s a ridiculous request. But about how many viruses are you finding in just the human samples you have so far?

David: So, starting with only DNA viruses…we have around a million sequences but some are redundant. So, if you only take the unique viral entities, we have about 400,000. Of those 400,000 about 30,000 or so are unique viral sequences coming from the human body.  

When it comes to RNA viruses, that’s a new ongoing project that we haven’t published on yet. But so far, we have around another 100,000 novel predicted RNA viral genomes. And about 20% of them are coming from human samples.

Amy: Do you see an end in sight?

David: There must be an end in sight, right? But the problem with viruses is that they also recombine. It’s complicated because it’s very hard to define a viral species. For example, there are cases where two closely related viruses are trying to avoid predation by bacteria, and to do that they recombine and create a third virus. Then…that third virus can recombine with another virus. Another example is that two viruses infecting the same host, at the same time, can also recombine. So, I think that the possibilities are countless and it’s going to be very complicated. We are definitely not even close to scratching the surface at all.

Growth rate of virus identification and microbial host prediction for the new release of IMG/VR database. Growth over time in the total and unique number of viral sequences in IMG/VR. (Image composite by David Paez-Espino).

Amy: It’s daunting but also exciting. Because we understand very little about the human microbiome and most ecosystems. So it’s great to realize there’s so much more we can learn about what might be going on.  

David: Right. We have a collection of ~21 million different genes from the viruses we’ve collected so far in IMG/VR. And 80-90% of these viral genes are hypothetical or have unknown functions. 

This same pattern is even true with E. coli. People have been studying E. coli for decades but we still don’t know the function of ~30% of E. coli’s genes. So, imagine how little we know about these novel viruses that are predicted from fragments here or there. It’s very complicated to make any kind of estimation.

Amy: It’s mind-blowing. To clarify: E. coli is one of the most well-studied bacterial species and we still don’t know a great deal about it.

David: Yes. E. coli is so well-studied that you’d think all the metabolic pathways are perfectly covered. But if you actually look at the databases, people still have no idea about what 30% of the E. coli genome is doing. So, these are exciting times, yes.

Amy: It’s clear that no matter what you’re studying related to the human body, you need to account for these viruses and other microbes. Whether you’re an immunologist, a neurologist etc. We need to account for their DNA/RNA and metabolites.

David: We have advanced a lot in science. Especially thanks to early studies of the microbiome that created reference genomes. But, for example, I recently went to a conference that discussed the drinking water microbiome. And they were not even testing for viruses (phages) in the drinking water. They are looking at 16S RNA sequences from about 20 known pathogens. And we’re are able to drink apparently safe water with just that knowledge. The basic necessities are covered. But – if we could understand even more about what microbes/viruses are in that water we could develop even better solutions.

This is especially true when it comes to human rare diseases. The majority of them could be caused by something we are not controlling. Medicine is doing a great job, but still – new knowledge about viruses can add to the picture. For example, now we understand that even some forms of cancer are caused by human microbiome dysbiosis accompanied by proliferation of a certain virus. So many of these novel or rare diseases could be better explained if we understand more about viruses and other microbes. 

This is also true for therapeutics (treatment). Now we can think about phages killing bacteria in a more precise way than antibiotics. Or we can use viruses that can be delivered to specific human tissue along with something that can access your immune system. You can design the virus to deliver something to the immune system “a la carte.” This precise medicine needs to evolve along with the new technologies.

My ideal job is applications. But I am also very pro basic science. For example – the CRISPR/Cas system. We are now engineering human cells from the use of bacterial genes that are designed to be a defense system against phage. So, the tremendous repertoire we have of novel genes can give us many new tools and technologies that we can manipulate at our will in the near future. We have been doing that for years, but the pace of discovery is now way, way faster. It’s a catalytic process: we are speeding up the different steps. 

Amy: Yes. The pace of discovery is incredible. I recently submitted a paper to a journal. They wrote back and asked me to give specific numbers for how many bacterial and viral species persist in the human body. I had to explain this wasn’t possible, and even if I made an estimate the number would change by the next month…or even the next day. 

David: Yes, for example, we have the largest viral database in this field. But even then, we’re only operating with assembled sequences larger than 5 KB. That represents less than 2% of all the sequences we have. Which is pretty much nothing. So, it’s not just the discovery pipeline that’s important. We can also go back and analyze metagenomes from 15 years ago. Because now we have different sequencing technology, we have different assembly technology, we have new binning algorithms, we have more robust models for gene annotation and functional predictions. And everything is still getting improved and improved and improved. So yes, as you said, there are no magic numbers. 

Amy: Definitely no magic numbers:) David thanks for speaking with me. I’m fascinated by your research and very excited to see where your findings lead. 














Re-thinking the theory of autoimmunity in the era of the microbiome

April 16th, 2018 by Amy Proal

Antibodies are Y-shaped molecules that target pathogen antigens

Hey there! Last podcast I mentioned the “theory of autoimmunity” and the range of immunosuppressive treatments that have stemmed from its promotion. I stated that the theory needs to be re-evaluated to account for the discovery of the human microbiome. Today I will go into even more detail on why that’s the case.

First, let’s talk about how the theory of autoimmunity gained popularity and widespread acceptance in the first place. Around the turn of the century, scientists began detecting Y-shaped molecules called antibodies in patients with a range of “acute” infectious diseases: diphtheria, tuberculosis, polio and pneumonia among others. Researchers (like the famous immunologist Paul Ehrlich) soon realized that these antibodies play a key role in helping the human immune system correctly target the bacterial and viral pathogens driving these and related diseases. They came up with a model of antibody activity that still largely holds up today. It contends that:

  1. Antibodies are released by B cells and T cells of the human immune system in response to an infectious threat: most commonly a bacterial or viral pathogen
  2. Antibodies target/neutralize these pathogens by recognizing the shape/size of unique protein molecules on the pathogen’s surface. These pathogen proteins are called “antigens.”
  3. When a human antibody correctly recognizes a pathogen antigen, the two molecules bind together. This “tags” the antigen and associated pathogen for further attack by other cells of the immune system (like white blood cells).
  4. The immune system begins to rapidly produce or “clone” more versions of the antibody that correctly “tagged” the pathogen. As more and more copies of this antibody pour into human blood/tissue, the immune system increasingly recognizes and kills the pathogen.

Today, almost every infectious disease is tied to antibody production. For example, when you get the flu, your immune system releases a range of antibodies in response to the flu virus. If all goes well, the antibody that best “tags” the virus’ specific antigens is “cloned.” More copies of this targeted antibody enter your bloodstream and the recovery process begins.

These same antibodies form the basis of the flu vaccine and related vaccines. In simple terms, a vaccine is made by taking an antibody already known to target a specific pathogen antigen – and injecting a small amount of this antibody into a patient. This “prepares” the patient’s immune system for the pathogen. Then, if the patient becomes infected at a later date, the immune system already knows exactly what antibody it should “clone” and rapidly release. The pathogen can then be neutralized and killed before it has a chance to spread.

OK. But what does this have to do with the theory of autoimmunity? In the 1930s-40s, researchers/doctors began to detect antibodies in patients with a range of chronic inflammatory conditions like lupus, rheumatoid arthritis, and multiple sclerosis. The natural next step would have been to search for chronic human pathogens whose presence could be tied to these antibodies. However, at the time (as described in my previous podcast), the human body was incorrectly believed to be largely sterile.

This confused many research teams working on the topic. How could they explain the presence of these antibodies when there were apparently no persistent microbes in the human body? They were forced to come up with their best guess as to what could be going on. They settled on a new concept that forms of the backbone of the theory of autoimmunity: the “autoantibody.” AKA, they postulated that in patients with these chronic inflammatory conditions, the immune system had somehow “broken down” or “gone crazy.” This confused immune system could then generate antibodies against antigens associated with the body’s own tissues. They named these hypothetical “self-targeting” antibodies “autoantibodies.”

Paul Ehrlich at his desk

At first the theory of autoimmunity and the idea that “autoantibodies” could exist met with resistance. Paul Ehrlich, the famous immunologist who had helped characterize antibodies in the first place, was particularly vocal. He wrote papers condemning the theory and coined the term “horror autotoxicus” to best counter it. Horror autotoxicus contends that the immune system has innate protection mechanisms that simply do not allow it to turn “against itself.”

But the scientific community wanted a consensus on the topic and needed simple guidelines on chronic inflammatory disease that could be given to doctors. Large conferences began to promote the theory of autoimmunity and detractors were increasingly pushed to the fringe. By the 1950s the theory started to be included in medical textbooks. Soon a growing number of “autoantibodies” were tied to different chronic inflammatory conditions. For example, patients with lupus test positive for an “autoantibody” that was named ANA. Rheumatoid arthritis was officially diagnosed if the “autoantibody” rheumatoid factor (RF) showed up on blood tests.

But a major question remained: if the theory of autoimmunity is correct, then what causes the immune system to fail so dramatically that it turns against the body’s own tissues? A number of theories attempting to explain this dilemma have been proposed over the years, none of which has been proven. One involves infection and is still frequently referenced today: the “pathogen/trigger” theory. It contends that certain well-characterized pathogens may infect a patient. Something about this temporary infection goes wrong and “triggers” the immune system to misfire and induce “autoimmunity.” The pathogen itself is somehow killed, but the immune system never recovers and the patient develops a full-fledged “autoimmune” disease.

The “pathogen/trigger” theory might have held more weight if the human microbiome had not been discovered around 2005. As described here, the discovery occurred when research teams started using new molecular tools to search for human microbes. The results of these new analyses were astounding: entire ecosystems of microbes were identified in the human body that had been missed by previous laboratory testing methods. Today we understand that trillions of microbes live in and on us – from the moment we are conceived in the womb until the day we die. These vast microbiome communities persist in every human body site – from the brain, to the liver, to the lungs and beyond.

This means that there are actually thousands, if not more, microbes/pathogens in the human body that could be tied to “autoantibody” release in patients with chronic disease. In other words, “autoantibodies” may just be regular antibodies created in response to pathogens that our testing methods were previously unable to detect. So, for example, when the “autoantibody” ANA is identified in patients with lupus, it could simply indicate that an unidentified pathogen plays a role in driving the lupus disease process. Also, it’s more likely that “autoantibodies” are created in response to chronic, persistent human pathogens than a temporary pathogen that the immune system somehow kills (as postulated by the “pathogen/trigger” theory.)

The possibility that “autoantibodies” are created in response to microbiome pathogens rather than “self” is strongly supported by the fact that “new” bacteria, viruses and other microbes continue to be identified in the human body. For example, Stanford researcher Stephen Quake recently detected thousands of never-before identified bacteria and viruses in human tissue/blood. In fact, 99% of the microbes he identified were previously unknown to science.

Also, for decades, “autoantibodies” have been regularly detected in patients with no signs of autoimmune disease that are instead suffering from an infection. For example, high levels of “autoantibodies” like rheumatoid factor, ANA (and others like ASCA, annexin-V and Anti-PL) have been identified in patients with bacterial, viral, and parasitic infections ranging from hepatitis A/B to Q fever to Rickettsia.

E. gallinarum under a microscope

A more recent study by researchers at Yale came to a similar conclusion. The team studied E. gallinarum, a bacteria they identified in the human gut, liver, spleen and lymph nodes. In models of genetically susceptible mice, the researchers found that E. gallinarum initiated the production of “autoantibodies,” activated T cells, and inflammation. Moreover, this “autoantibody” production stopped when they suppressed E. gallinarum’s growth with the antibiotic vancomycin and/or with a vaccine against the microbe. The team also identified E. gallanarum in the livers of patients with “autoimmune disease”, but not in healthy controls. One media headline on the study read: “The enemy within: Gut bacteria drive autoimmune disease.”

Research by Stanford’s Mark Davis supports the findings. Davis and team used a new testing method to obtain T cell sequences from the tissues/blood of patients with colon cancer, MS, Lyme disease, and ME/CFS. In all four diseases, they found that the T cells were activated and “cloned’ in a manner not observed in healthy subjects. According to the theory of autoimmunity, these cloned T cells would indicate “autoantibody” production. But Davis suggested that associated antibodies are likely formed “originally against some pathogen peptide.” This definitely makes sense since since, especially in Lyme disease, we know pathogens drive the disease process.

Interesting right!? But at this point I should bring up an important concern. Some researchers are still convinced that “autoantibodies” can target human tissue. If this is the case, the situation can easily be explained by a concept called “molecular mimicry.” Molecular mimicry refers to the fact that pathogen proteins and human proteins are often very similar in size and shape. This means that an antibody created in response to a pathogen protein/antigen might accidentally target a similarly structured human protein/antigen. This “collateral damage” could result in an inflammatory response towards that human tissue.

Think of molecular mimicry this way: Let’s say you’re a solider in an army. You and your fellow soldiers all have red uniforms, blonde hair, and stand about 6 feet tall. You confront the enemy on a battlefield only to realize that their soldiers also have red uniforms, blonde hair and are about 6 feet tall! Even though their red uniforms are shaped somewhat differently than your own, at a certain distance the shape becomes blurred. This means that when the battle begins, you have trouble telling who’s on your side and who’s the enemy. Occasionally you end up accidentally shooting a member of your own army. These two armies can be compared to similarly shaped pathogen antigens and human antigens that might generate “collateral damage” in “autoimmune disease.”

Ample research supports this “molecular mimicry” model. For example, one research team found that B cells infected with Epstein Barr Virus secrete antibodies that also react with human antigens like albumin, renin, and thyroglobulin. Another Canadian research team found that proteins created by the hepatitis C virus had a high level of structural similarity with ~20,000 human proteins. Researchers in India identified tens of thousands of possible interactions between proteins created by Salmonella, E.coli, Yersinia, and similarly shaped human proteins.

All this research strongly suggests that in 2018 we no longer need the theory of autoimmunity. It seems Paul Ehrlich was right a century ago when he argued for “horror autotaxicus.” In patients with a range of chronic conditions, activated B cells, T cells and the antibodies they produce are likely targeting newly discovered human pathogens rather than “self.” This means the concept of the “autoantibody” is incorrect. In lieu of “autoimmunity,” we should focus on better characterizing pathogens in the microbiome and better studying their activity and survival mechanisms. For example, Mark Davis is planning 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). Excellent, excellent idea!

Most of the top-selling drugs in the world are immunosuppressive

At this point you might say: “Aw, well it looks like theory of autoimmunity will die over time, no huge rush.” But unfortunately the situation is very urgent. That’s because a large chunk of the pharmaceutical industry is focused on creating drugs based on the theory of autoimmunity. These drugs shut down extremely important parts of the human immune system in an effort to stop “autoantibody” production and related inflammation. In fact, these immunosuppressive drugs are the top-selling medicines in the world, generating billions of dollars of revenue each year.

If “autoantibodies” are created in response to pathogens rather than “self”, these drugs are actually hurting the long-term health and microbiome balance/health of patients with “autoimmune disease.” This is almost certainly why patients taking immunosuppressive drugs tend to get sicker over time, to the point where they often fall ill with a second or third inflammatory condition while taking the medications. In fact, rampant use of immunosuppressant drugs is likely a primary factor driving the current epidemic of chronic disease (the incidence of nearly every “autoimmune condition” is on the rise).

That means we stand at a crossroads. This paper published just last year describes an entire new generation of immunosuppressive drugs currently being developed by pharmaceutical companies. Some of these new drugs appear to shut down the human immune system even more profoundly than the ones prescribed today.

OR, we can move in a new direction of drug/treatment discovery. We can ditch the theory of autoimmunity and instead develop treatments that SUPPORT the human immune system. And/or treatments that better target key pathogens and, in turn, promote balance, health and diversity of the human microbiome. Then, maybe…just maybe we can create a future where new treatments target the ROOT CAUSE of human inflammatory disease instead of just palliating symptoms. And then maybe…just maybe a growing number of patients with chronic inflammatory disease could reach a state of actual recovery and remission.



Antibiotics, immunosuppressive drugs and the downfall of the human immune system

March 31st, 2018 by Amy Proal

Hey! Today I’ll discuss two more factors that can debilitate the human immune system (allowing the microbiome to better cause disease). They are antibiotics (when used too frequently) and immunosuppressive drugs: two of the most common medical interventions of our time. Most of us are familiar with antibiotics. By immunosuppressive drugs I mean medications like Humira, Prednisone, Ritauximab, and Enbrel. These and similar drugs block or disable parts of the human immune response in an effort to temporarily palliate inflammatory symptoms.

It’s important to note that most antibiotics and immunosuppressive drugs were developed before mainstream science “discovered” the human microbiome around the year 2005. In other words, they were created/formulated during a period when the human body was assumed to be largely sterile. The antibiotic Penicillin was discovered by Scottish scientist Alexander Fleming in 1928. By the mid 1940s it was regarded as a wonder drug, especially during World War II when it saved countless soldiers from dying of infected wounds.

After World War II, antibiotics continued to be perceived as miracles, and it’s easy to understand why: diseases like pneumonia, scarlet fever, bacterial meningitis, gonorrhea and a range of ear, skin, urinary and throat infections could finally be treated! Life expectancy increased as antibiotics allowed patients to survive an ever-growing range of these specific bacterial infections. And since the human body was considered sterile, it was assumed that antibiotics only killed the single bacterial pathogen they were prescribed to treat. They were subsequently prescribed with increasing frequency, and for minor infections like colds or sore throats (especially in children).

Alexander Fleming discovered Penicillin in 1928

Then, in the early 2000s, new molecular tools were developed that identify microbes by their DNA/RNA rather than their ability to grow in a laboratory Petri dish. When researchers turned these new tools on the human body, they discovered thousands of microbes in human tissue/blood that had been missed by previous techniques. With each new molecular analysis, mainstream science realized that the human body is the opposite of sterile! Instead, humans harbor vast ecosystems of bacteria, viruses, bacteriophages and other microorganisms. The human gut alone harbors trillions of microbes. These complex microbial communities were named the human microbiome – the “discovery” of which marks one of the most important turning points in the history of science.

Almost every facet of human health and biology must be re-evaluated to account for the human microbiome. When it comes to antibiotics we face a stark reality: Current antibiotics like penicillin have such a broad range of activity that they kill most bacteria in the human microbiome in addition to any single pathogen they are prescribed to treat. The situation could be compared to dropping an atomic bomb on an entire continent in an effort to target a group of rebels in one small city.

What are the implications of this? Research on the topic is still in early stages. But we know two things:

  1. Health, diversity and balance of the human microbiome are key to prevention of human inflammatory disease
  2. Microbiome populations decimated by antibiotics can recover, but sometimes not to their full, previous capacity

For example, in this Ted talk, researcher Rob Knight charts how an antibiotic prescribed to treat an infant’s ear infection impacted several of the child’s early microbiome communities. The antibiotic caused “a huge change in community structure” that “set back many months of (microbiome) development.” Interestingly, the infant’s microbiome eventually recovered to a place similar to that of untreated subjects. But as Knight suggests, it’s hard to imagine that there are no longer-term implications associated with the event (especially if the infant is administered even more antibiotics over time). And, as a society, are we taking more antibiotics? We sure are! From 2000-2015 approximately 65% more antibiotics have been sold globally (accounting for 34.8 billion doses in 2015). In the USA, 47 million of these antibiotics are prescribed annually for viral infections that don’t even respond to antibiotics.

With those numbers in mind, it’s no surprise that a second major antibiotic issue has also surfaced. Antibiotics have been prescribed with such frequency that many major pathogens have developed resistance against them. As discussed in previous podcasts, pathogens can easily change their gene expression to survive under difficult circumstances. Many human pathogens have done exactly that – they have acquired genes or mutated in ways that allow them to remain alive in the face of our most commonly used antibiotics. This has created a range of antibiotic-resistant pathogens often referred to as “superbugs.” Many of these “superbugs” are deadly (Acinetobacter baumannii, Pseudomonas aeruginosa, and MRSA for example). In fact, the CDC estimates that these and related “superbugs” kill at least 23,000 Americans a year (for comparison, about 38,000 Americans die every year in car crashes).

“Superbugs” have developed resistance to most common antibiotics

The situation is regarded as a global catastrophe. According to the CDC, the rate at which new strains of antibiotic-resistant bacteria have emerged in recent years “terrifies public health experts.” Many consider new “superbug” strains to be just as dangerous as emerging viruses like Zika or Ebola. Britain’s chief medical officer, Sally C. Davies, has described drug-resistant pathogens as a national security threat equivalent to terrorism. The problem is compounded by the fact that a large number of bacteria in the human body have yet to even be characterized and named. Who knows what our overly zealous use of antibiotics is doing to these understudied bacteria! It’s very possible that heavy antibiotic use may be pushing MOST bacteria in the human body into a more virulent, resistant state.

Add to this a third major antibiotic problem. Over the past decades, farmers started feeding antibiotics to many of the animals we consume as food (cows, chickens, pigs etc). Why? Antibiotics cause the animals to gain weight, increasing the amount of meat that can be sold to consumers. Again, few people paused to consider the long-term or chronic consequences of saturating our food supply with antibiotics. Instead, approximately 80% of antibiotics sold in the United States are used in meat and poultry production. This has created an amazing atmosphere for the development of virulent pathogens that may better resist antibiotics. In addition, genes conferring antibiotic resistance are regularly transferred from farm animals into the human food supply. If ingested, these antibiotic resistance genes can theoretically be transferred and “taken up” by almost any bacterial species in the human body.

To make matters worse, antibiotics were added to the food supply during the first time in history where the average 1st world inhabitant started eating meat imported from around the world. For example, the USA imported 3.01 billion pounds of beef in 2016, from 22 countries across the globe (from Europe, to South America, to China and Thailand). Consumers are subsequently exposed to meat-associated pathogens from around the world – basically a potential cocktail of global pathogens. For example, a study by researchers in Germany found high levels of S.aureus and E.coli in pork/poultry imported into the EU, with other pathogens like Salmonella and Enterobacteriaceae present in lower amounts.

The above questions the interpretation of studies that tie meat consumption to chronic inflammatory conditions like heart disease. If a negative association between the two is identified, is the meat itself to blame? Or are pathogens in the meat to blame? (or a combination of both and/or other variables). The relatively unexplored possibility that pathogens in meat may promote chronic disease is supported by the fact that heart disease is increasingly tied to infection and microbiome dysbiosis. A recent study even found that lipids or fat molecules in arterial plaque can be created by persistent bacteria. Also, to be fair, the possible impact of food-borne pathogens on chronic disease applies to most foods – for example, what do the range of pesticides and chemicals sprayed on plants across the globe do to the microbes that live in/on the produce we consume?

Now I’ll take the topic one step further, by posing a rarely asked but extremely important question: “Where has the human immune system been during the modern era of antibiotics (1940-today)? Because, as I’ve argued in previous blogs/papers, the healthy, activated human immune system has incredible defense strategies for keeping antibiotic resistant bacteria or “superbugs” in check.

After the turn of the century, a range of chronic conditions were linked to persistent inflammation. This chronic inflammation generally results when the immune system attempts to target pathogens. However at that time (as mentioned) the human body was incorrectly assumed to be sterile. Researchers subsequently developed the “theory of autoimmunity” – the belief that in diseases like Crohn’s, Multiple Sclerosis and arthritis, the immune system “loses tolerance” and attacks its own tissues.

Most of the top-selling drugs in the world are immunosuppressive

By the 1960s-80s the theory of autoimmunity had gained incredible traction. Over 80 different conditions were deemed “autoimmune” in origin. The result? Pharmaceutical companies created drugs specifically designed to shut down key parts of the human immune system. These drugs, which temporarily palliate symptoms, have been prescribed so aggressively that today they are the top-selling medications in the world. For example, the potent immunosuppressive drug Humira is literally the top-selling drug in the world: generating more than 18.4 billion dollars in revenue in 2017.

This means we have been using antibiotics at the same time that we have deliberately compromised the immune systems of a growing chunk of the human population. In fact, it’s no coincidence that most “superbugs”  form or are identified in elderly, sick and/or hospitalized patients; patients much more likely to be on cocktails of immunosuppressive drugs/steroids. This trend escalates when severely immunocompromised patients are gathered in one place: a recent analysis found that pipes under NIH’s ICU rooms tested positive for bacterial plasmids that confer resistance to carbapenem antibiotics. The pipes were described as a “seething hookup zone for antibiotic-resistant bacteria.” Another report found that many veterans of the Iraq War suffered from antibiotic-resistant A. Baumannii infections. But the “superbug” was almost always identified in wounded veterans with complex injuries. Indeed, the report clarifies that,  “A. Baumannii  is not particularly virulent. If you’re in good health and (it) were to get into a wound it might not be a problem. It’s a problem for people who are the weakest of the weak.”

The most common treatments for “non-autoimmune” conditions are also immunosuppressive to various degrees. Opioids, antidepressants and antipsychotics dampen the immune response (especially when administered over long periods of time). Certain forms of birth control have been shown to lower immunity. Cancer chemotherapies substantially weaken the immune system. Indeed, childhood cancer survivors are prone to a wide range of health problems later in life including organ damage, cognitive deficits and high blood pressure. These long-term health issues are similar to those observed in patients administered “classical” immunosuppressive drugs. Even in animals given antibiotics for weight gain – do the overcrowded/unsanitary conditions at many farms favor “superbugs” by lowering animal immunity?

All in all, we are living in an era of mass immunosuppression. This has created a field day for antibiotic resistant and virulent pathogens! Such pathogens can easily thwart the human immune system because our drugs are “knocking it down” for them. We are greatly assisting the enemy.

Most concerning is that the “theory of autoimmunity” no longer holds up in the era of the microbiome. A growing body of research suggests that “autoantibodies” are created in response to microbiome pathogens rather than “self.” In addition, “autoimmune” conditions are increasingly linked to microbiome dysbiosis and not a defective immune response. So we are using immunosuppressive drugs to treat patients based on a failing and outdated paradigm. For more on this topic please read this paper.

To combat antibiotic resistance we must subsequently re-evaluate the “theory of autoimmunity” and the immunosuppressive drugs that have stemmed from its promotion. And we must do so NOW. We cannot afford to wait the decades it usually takes for an outdated theory to be replaced by a new, improved paradigm (Thomas-Kuhn style). Too many lives and the health of the entire public are at stake.

How else can we fix the situation? At least in the short-term, antibiotics and immunosuppressive drugs should be considered last resort treatment options. Patients should exhaust all other treatment options BEFORE being prescribed these medications. We must prioritize diet/lifestyle changes that the average doctor does not yet include in treatment plans. Although this may sound simple, it’s easier said than done when drug companies spend millions of dollars a year marketing immunosuppressive medications directly to physicians.

In the longer-term we should replace immunosuppressive therapies with new treatments that support the immune system and encourage balance + diversity of the human microbiome. This would require another major paradigm shift that I describe more here.

This last paradigm shift is essential because we NEED some antibiotics. When administered in a careful, responsible fashion antibiotics still save countless lives. Antibiotics are also a valuable tool for treating chronic inflammatory conditions that are increasingly tied to infection. For example, this article describes how a young boy with crippling OCD used antibiotics to treat a chronic strep infection. His OCD symptoms diminished to the point where he is able to function in society again.

I have several suggestions for how to best move forward:

  1. Antibiotics should be re-branded as complex, immunomodulatory drugs: Few people realize that antibiotics have profound effects on the immune system in addition to their antimicrobial properties. For example, many commonly used antibiotics (rifampin, cephradine, tetracycline, clindamycin, and penicillin among others) can bind directly into the human PXR nuclear receptor: a receptor that controls how the body detoxifies foreign substances. The PXR in turn modulates CYP3A4 – an enzyme key to controlling the human immune response. These and related interactions may explain why antibiotics like minocycline are regularly used as “anti-inflammatory” or “immunomodulatory” drugs in patients with arthritis and other rheumatic conditions. 

So imagine if every time an antibiotic was prescribed doctors were required to say: “I’m giving you a powerful medication that will impact your entire microbiome and immune system in profound ways still not fully understood by science.” This would give people pause before prescribing and/or popping an antibiotic for the common cold.
  2. We should keep this complexity in mind when developing new antibiotics: The superbug crisis has set off a wave of research aimed at creating new antibiotics. Many research teams working in this vein are trying to develop antibiotics that would target specific bacterial pathogens in lieu of the entire bacterial microbiome. This makes sense, but part of the trend involves taking parts of the human immune system and trying to make them into new antimicrobial drugs.

For example, researchers at Vanderbilt University recently made a fascinating discovery: human milk oligosaccharides (HMOs) in breast milk possess strong antimicrobial and antibiofilm activity against several superbugs (Eg: A. baumannii and MRSA). Several research teams responded to the finding by suggesting that these HMOs should be made into new antibiotics. While this makes sense in theory it also runs a large risk – any pathogen that develops resistance against these HMOs will have developed resistance against a key component of the human immune system itself.

The pathogen A. baumannii

What makes the above scenario likely to occur is that the human body constantly adapts its antimicrobial defenses to keep up with the changing nature (evolution) of virulent pathogens. For example, in this interview, Harvard researcher Robert Moir describes how the human immune system regularly changes the structure of the human antimicrobial peptide cathelicidin in response to different pathogen threats (each different form of cathelicidin is called an oligomer). The flexible nature of these oligomers means that when a pathogen mutates to survive in the face of the peptide, the peptide can change its own structure/function to “fight back.”

Human drugs based on only a single form of a human antimicrobial peptide/molecule would lack this flexibility, making resistance against them much more likely.

Ok that’s it for today. I’ll leave with the following message. Let’s not get so worried about current “superbugs” that we rush into making new antibiotics without fully considering long-term consequences. We’ve already done that once right? As the saying goes, “Fool me once, shame on you; fool me twice, shame on me!” The same goes for phage therapy – another proposed alternative to antibiotics. In this interview, Texas A&M researcher Ry Young does a great job explaining how we can move forward with phage therapy in the most proactive and responsible fashion.

Also, not everyone is surprised by the recent surge in antibiotic resistance and superbugs. Certain communities of researchers have been warning about the possibility since the 1960s. I will also do another podcast that talks about these researchers and several of their key findings – findings that should still be taken into consideration today.

The power of intracellular pathogens: how they “take down” the immune system and dysregulate human pathways

March 12th, 2018 by Amy Proal

A human white blood cell

Hey there! Last podcast I talked about how many “harmless” microbes in the human body are able to evolve to a state where they cause inflammation and illness. I explained that this “shifting” towards virulence (or disease) is much more likely to occur in people whose immune systems are compromised or debilitated. There are many factors that can negatively impact the health of the human immune system. I plan to discuss many of them in greater depth. But today I will focus on one major factor – the ability of key pathogens to slow and dysregulate the human immune system as part of their most basic survival strategies.

The most fundamental way that pathogens “take down” the human immune system is by infecting and living inside human cells – especially human white blood cells. Under conditions of health, these white blood cells traffic the body, where they engulf or digest pathogens that originate from both the internal and external environment. BUT, many key pathogens have evolved to thwart this process. They have evolved to remain alive inside these white blood cells; inside the very cells that are supposed to kill them! They can survive this way for long periods of time in a chronic, persistent state. Doing so clearly gives them a HUGE advantage or “edge” over their human host. If the situation was compared to a human war, it would be as if a soldier were able to inhabit the body of its opponent, and then make the opponent act in its own interest.

There are two main implications of this “intracellular persistence”:

1. The infected cell is unable to perform its basic immune system duties.
2. Any pathogen inside the infected cell can interfere with the way the cell “encodes” its human DNA.

Let me explain this second point in more depth. The center of every human cell has a copy of a person’s DNA. This DNA “codes” for the ~ 21,000 human genes that determine who we are and how we deal with our environment. These genes are eventually “translated” into proteins – proteins that direct our human pathways to correctly regulate the immune system, the nervous system, human metabolism and other critical aspects of human function. It follows that any pathogen able to persist in the center of a human cell can directly “mess with” the cell’s DNA and the vital human processes it regulates. The situation could be compared to a computer hacker. Imagine a hacker that not only breaks into your computer, but gains access to the programming code that directs your operating system and websites. By either directly altering this code, or changing the way the code is translated into programs, the hacker can cause your computer to malfunction in an almost infinite number of ways.

Here’s an example of how a pathogen can dysregulate a human cell in the above fashion. A research team in Louisiana studied what happens when Cytomegalovirus (CMV) infects a human white blood cell. They found that CMV significantly changed how the cell expressed its human genes. In fact, the virus “turned up” the expression of 583 human genes, and “turned down” the expression of 621 human genes. These changes were so profound that the infected white blood cells actually changed into an entirely different type of cell – an “inflammatory” cell that promoted CMV’s ability to infect neighboring cells. No wonder then that, as the paper points out, chronic CMV infection is associated with retinitis, gastrointestinal disease, hepatitis and pneumonia – but also with chronic inflammatory conditions like multiple sclerosis and atherosclerosis (heart disease).

Cytomegalovirus (CMV)

A recent study by researchers at Stanford confirms how broadly CMV can “re-program” the human immune response. The team studied identical twins and isolated cases in which one twin was infected with chronic CMV and the other was not. They tested the activity and function of 204 different parts of the human immune system in each twin. These 204 immune system “parameters” included the amount/frequency of certain immune cells, the ability of such cells to signal, and the concentrations of immune system proteins called cytokines. They found that, in general, 119 of these immune system “parameters” were altered in the twins with CMV. In fact they calculated that, in people infected with CMV, “the lifelong need” to control the virus causes approximately 10% of all T cells in the body to become directed against it. This led the 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.”

OK – but how exactly does this major pathogen interference happen? All human pathways that control the immune response, metabolism, cognition etc are regulated by receptors – protein molecules that control pathway signaling. In very simple terms, receptors function in a “lock and key” fashion. Imagine that you want to get into a very secure house. You might have to first open locks on an outside door. Then you might open or adjust a series of other locks on inner doors and/or other checkpoints before finally entering. Now, picture these locks as receptors associated with a human pathway. Under conditions of health, very specific human proteins bind into each receptor. These proteins are analogous to the keys in my house example. If the correct human protein or “key” fits into the correct human receptor or “lock,” the receptor/protein “complex” changes shape in a way that allows that part of the pathway to correctly move forward. This process happens over and over at each receptor “checkpoint” until the pathway fulfills its final, correct role in the body.

Now consider this: many pathogens have evolved to create proteins that are very similar in size/shape to human proteins (this redundancy is sometimes called molecular mimicry). If a pathogen with this ability survives inside a human cell, its OWN proteins may begin to “bind” into human receptors. Gradually, the human proteins meant to control a particular receptor may be increasingly replaced by these similar “enemy” or pathogen proteins. What happens? The slightly different shape of the pathogen proteins cause the receptor to act/signal differently than it would under conditions of health.

An excellent example of the above (that I’ve discussed in several published papers) is the ability of pathogens to dysregulate activity of the human Vitamin D Receptor (VDR). The VDR is an extremely important receptor located at the heart of every human cell. It controls the expression of almost 1000 human genes. It also controls the activity of very important parts of the human immune response. These include TLR2 (a protein the body uses to identify and target pathogens), and several kinds of antimicrobial peptides (natural antibiotic molecules the body uses against infectious threats).

It comes as little surprise then that the fungus Aspergillus fumigates has evolved to create a protein or gliotoxin that can bind into the VDR and directly slow its activity. This results in tremendous survival gains for Aspergillus – the altered VDR can no longer correctly express many of the human genes it regulates. The expression of TLR2 and the antimicrobial peptides under VDR control also diminishes. Now, Aspergillus can flourish in the face of the host’s weakened immune defenses.

In fact slowing VDR activity (and subsequently parts of the human immune system) is such a logical survival mechanism that many other key pathogens have also evolved ways to dysregulate the receptor. When Epstein Barr virus infects human B cells it dramatically lowers VDR activity. Mycobacterium tuberculosis slows VDR activity by a factor of ~3.3. Borrelia burgdorferi, Cytomegalovirus, and Mycobacterium leprae also slow VDR activity to varying degrees. HIV almost completely “shuts down” the VDR. I should be clear that some of these pathogens don’t create proteins that directly bind into the VDR. They interfere with the VDR receptor in ways a little too hard to explain here:) But you get the overall trend right!?

Now factor this in: the human body’s pathways are tightly interconnected. So any change in human signaling has “flow-on” effects that impact yet other pathways and systems. In the case of the VDR, the receptor’s activity is tied to that of related receptors that control hormone signaling (especially the estrogen-beta receptor). It follows that the “original” intracellular infection may also prevent these related receptors/pathways from functioning correctly.

But let’s go back to the immune system, and continue to use the VDR pathway as an example. Let’s say CMV infects a person’s B cells and lowers VDR activity. The person’s immune response suffers as a result. Now, it becomes easier for that person to pick up OTHER pathogens from the external environment. Or, pathogens already in that person’s microbiome find it easier to act in a more virulent fashion. These “new” pathogens may also infect the person’s cells, where the interference they cause further slows the immune response. A “snowball effect” may ensue, where each “new” pathogen begins to facilitate the survival of the next.

A successive infection “snowball” could drive many forms of disease

In many of my papers I’ve referred to this snowball effect as “successive infection.” When I think of successive infection I literally picture a snowball rolling down a hill. The snowball begins with one intracellular infection, and then grows, as more and more pathogens take advantage of the dysregulated atmosphere in the body. As more pathogens “join” the snowball, the disease state that the snowball represents pushes the human body farther and farther away from a state of health.

It’s important to realize that once the “successive infection” process has started, environmental factors besides infection can “add” to the snowball. These include chemical exposures, stress, immunosuppressant drugs, over-used antibiotics and any other factors that cause either the immune response or microbiome balance to suffer. In fact, any of these other factors can “start” the snowball too.

I realize this is a major claim, but in my mind, a successive infection snowball could drive almost any form of inflammatory disease. That’s because such wide-range of different pathogens and negative environmental exposures can contribute to the process. Pathogens are also able to infect so many parts of the human body (nerves, brain tissue, lung tissue). If the snowball represents disease, the specific illness any one person develops would stem from their UNIQUE infectious history, their unique medication history, their unique chemical exposure history, and the many, many different ways these and other variables can interact with/feed into each other.

If you think that’s a stretch, consider this: almost every analysis of the human microbiome identifies new microbes never before detected by previous studies. For example, just a few months ago, Steven Quake at Stanford identified thousands of “new” microbes in human tissue and blood. Many of them are potential intracellular pathogens we didn’t even realize could survive in humans. This led Quake and team to state that these novel microbes “may prove to be the cause of acute or chronic diseases that, to date, have unknown etiology…”

Also, research teams continue to discover new examples of how pathogens might interfere with human pathways. For example, a team in Indiana just identified viruses that create proteins similar in size/shape to the human protein insulin. They found these viral proteins could bind into human insulin receptors that determine how the body correctly regulates blood sugar levels. The viruses that create these insulin-like proteins are regularly detected in human blood and fecal samples. The team concluded that “since only 2% of (human) viruses have been sequenced, this study raises the potential for discovery of other viral hormones which, along with known virally encoded growth factors, may modify human health and disease.”

So I’ll end on the following note: never underestimate the “power” of intracellular infection. Human microbiome studies that fail to account for possible intracellular pathogens may miss part of a larger, more important picture of disease. For example, the gut microbiome dysbiosis now tied to many inflammatory conditions may be a downstream result of intracellular infection in the blood or other tissues. AKA: the widespread drop in immune system activity driven by intracellular pathogens may “set the stage” for an atmosphere that favors gut microbiome imbalance. This is certainly the case in HIV/AIDS, for example (for more context read this blog post).

Ok phew! That’s it for now. Next podcast I’ll go more into immunosuppressive drugs, antibiotics, and other factors that can also compromise the human immune system and/or the human microbiome. Talk then!