Alternative and Complementary TherapiesVol. 26, No. 3 Free AccessFunctional Medicine-Based Dentistry: A Clinical Conversation with Mary Ellen S. Chalmers, DMD, and Robert Rountree, MDMary Ellen S. Chalmers and Robert RountreeMary Ellen S. ChalmersMary Ellen S. Chalmers, DMD, is a dentist practicing integrative and functional dental medicine, in Santa Rosa, California, USA, and a faculty member for the Institute for Functional Medicine.Search for more papers by this author and Robert RountreeRobert Rountree, MD, practices family medicine in Boulder, Colorado, USA.Search for more papers by this authorPublished Online:10 Jun 2020https://doi.org/10.1089/act.2020.29274.mecAboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Mary Ellen S. Chalmers, DMD, is a dentist in Santa Rosa, CA, practicing integrative and functional dental medicine. Dr. Chalmers received her dental degree from Tufts University School of Dental Medicine in 1980 and became a Board-Certified Naturopathic Physician (BCNP) in 2010 by the American Naturopathic Medical Certification Board, with training from the American College of Integrative Medicine and Dentistry (IBDM). She is a faculty member for the Institute for Functional Medicine (IFM).Robert Rountree: Is it fair to say that you are not a typical dentist?Mary Ellen S. Chalmers: No, I am not a typical dentist. I think more dentists need to practice this way, and frankly I think the future of my profession depends on it. The more I view the ways in which conventional dentistry manages problems, the greater benefit I see for a systems biology, functional medicine approach.There are many very good biological dentists and evidence-based dentists in practice. What I believe sets me and the handful of dentists who have achieved Institute for Functional Medicine (IFM) certification apart is that we think about the root cause. It is not about fixing the tooth, it is about getting to the source of the problem. Why are we seeing oral disease? Nothing makes this oral–systemic connection better than functional medicine. We have been talking about and making the oral–systemic connection for 10 years now at the IFM.Dr. Rountree: When you went into dentistry, was this what you envisioned your future would look like?Dr. Chalmers: I did not. I entered with no preconceived notions. I was fascinated by the mouth. I was fascinated by dentistry. But what really grabbed me early in my freshman year at Tufts University, where I went to dental school, was when the head of the Department of Oral Diagnosis and Oral Medicine, Dr. Stanley Schwartz, stood in front of the class and said to us, “You have to develop the mindset of a physician of the mouth.” That was the first time, and it was more than 40 years ago, where I heard that term, that you really needed to behave and think like a physician of the mouth.He said, “There are very few MDs, except neurosurgeons and ear, nose and throat specialists, that know more from the clavicle up than dentists.” Dr. Schwartz also said “We should never take a back seat to our medical brethren, because over 100 systemic diseases manifest in the mouth.” Bottom line, we really needed to pay attention and look deeper than just what is wrong with that tooth.I did not do a residency coming out of school. At the time, it was not typical to do one, as it is now. I went right into private practice. I liked everything about dentistry. I liked doing root canals. I liked doing oral surgery. I could not choose one specialty to go into.My overwhelming feeling within a year of being out of school was that I had squandered my time at Tufts, and really did not learn all that I could. So I began this drive for continuing education, always learning, which is culminating at this point in my career with the master's at University of Southern California (USC) in oral medicine and orofacial pain.Dr. Rountree: Never stop learning.Dr. Chalmers: Never stop learning. Lifelong learning is foundational.The first major shift in the direction of my practice was when I began to recognize by the late 1980s that, frankly, mercury was a problem. A patient, I believe it was an electrician who was working with mercury, found that it had caused toxicity and created some health problems for him. He came to my office saying, “You know, I have all these fillings, and I do not think it is smart that we are storing a heavy metal in our head.”The light bulb went on, and I thought, “You know, he may be right about that.” Then a few years later the problems with mercury amalgam were followed up by the 60 Minutes exposé in 1990.Dr. Rountree: That was 1990, and yet today the American Dental Association (ADA) still says that mercury is fine, right?Dr. Chalmers: It does. Although I think at this point, the ADA does not have a choice but to maintain that position. I think the science with respect to the issues with amalgam is getting better and we are understanding the many manifestations of mercury toxicity more. For years it was difficult to find any evidence that it created problems. However, now we are seeing in dental education that there are fewer and fewer schools requiring the placement of mercury amalgam fillings by their dental students.Dr. Rountree: I wonder whether our readers understand what you mean by saying that the ADA does not have any choice.Dr. Chalmers: The mission of the ADA is to advocate for and support all dentists and a significant number of dentists in this country still routinely place amalgam fillings. The amalgam controversy is also reflected in the positions of other national regulatory agencies. While the U.S. Food and Drug Administration (FDA) describes amalgam fillings as strong, long-lasting and the least expensive filling material, their website also warns that amalgam contains elemental mercury and releases low levels of mercury in the form of a vapor that can be inhaled and absorbed by the lungs.The Environmental Protection Agency (EPA) determined that dental offices are the main source of mercury discharge to publicly owned water treatment facilities (POTWs) and discharge approximately 5.1 tons of mercury each year to POTWs, with most of this mercury being eventually released to the environment. In July 2020, the EPA is requiring the placement of amalgam separators in all dental offices, to filter out the mercury before it enters public sewer systems to reduce mercury pollution. So, fillings that are “safe” in our mouths become hazardous waste once they are removed.In the Functional Medicine community, we recognize the links between endothelial damage, autoimmune disease, cognitive decline and mercury. I believe that by integrating systems biology and functional medicine into oral health diagnostic and treatment considerations, all dentists will have a different perspective to reconsider our position on amalgam fillings.Dr. Rountree: What percentage of dentists in the United States still use the same old mercury amalgams?Dr. Chalmers: I think the most recent statistic on use of amalgam dropped to 48% or 49% of American dentists. It is still more than I would like to see, as many European countries have banned the use of amalgam altogether. A good place to start to educate dentists would be to talk about cognition and how genetics, actually one of the genes in particular, affects mercury detoxification.The apo-E gene is related to cardiovascular disease and Alzheimer's risk. Patients have different versions of the e2, e3, or e4 alleles. The Journal of Alzheimer's Disease published an article in 2003 identifying an association between mercury and cognitive decline in patients with the apo-E e4 allele. So arguably, as we become more aware of ways to incorporate genetics, an appropriate question on a health history would be “Do you know your apo-E status?” A great many patients do.Dr. Rountree: So you are saying that dentists should actually have a discussion with their patient about their genetics?Dr. Chalmers: I think so. At a minimum, patients identified with the apo-E e4 allele should never have an amalgam filling, and if they have them, they must have their amalgams removed with safe amalgam removal protocols. Those precautions are standard for all patients treated in my practice and I have not placed an amalgam for >30 years.Dr. Rountree: So the first light bulb went off when you had a patient say, “Hey, think about the logic of this. We are putting mercury into people's mouths. We are putting a toxic metal in people's bodies,” and that kind of woke you up. And from what I know about you, that was just the beginning of your journey into how oral health affects the whole body.Dr. Chalmers: Yes, it was. About five years later, I had an influx of lupus patients. When we drill on a tooth, we create a transient inflammatory response. Most people whose inflammatory pathways are working and functioning well are able to manage that. It is not uncommon to have minor hot and cold sensitivity after a filling, and the body manages that transient inflammation, and the symptoms resolve.What I was seeing with these autoimmune patients was that they were not able to manage even a very small filling, that the pulp was becoming irreversibly inflamed, and they needed to have root canals on these teeth. This concerned me, because even then, I understood that a root canal was to be avoided at all costs.I happened to have a conversation about these patients with a close friend of mine who was a periodontist. Coincidentally he was seeing similar sort of problems with inflammation management in his periodontal patients with autoimmune issues that I was seeing in my patients with lupus.While we were making plans to gather data for an article, I suffered a serious auto accident in 1995, and was out of commission for about five years while I healed. It was that accident that brought me to functional medicine.Dr. Rountree: For your own healing?Dr. Chalmers: For my own healing. I had been a dentist for 15 years, and though I had not been placing amalgams for the past 8 years, I was not removing them with precautions. I did not understand that, as a dentist, you needed to protect yourself. Fortunately, my primary care provider, Dr. Sandra Magin, had been an early student at IFM and of Dr. Jeff Bland's.Two years after the accident, when I was no better—my cognition was impaired from a head injury, along with bilateral carpal tunnel—Dr. Magin prescribed medical foods and started an active detox program and I recovered.In 1995, I had a large practice in Berkeley that I had to sell six months after my accident, and in 2000, 20 years after graduation, I was starting from scratch. However, I was so grateful to regain my health and had a new strength in my convictions about the role that dentistry plays in our overall well-being. I also knew that I needed to really study and understand functional medicine, as it had become very clear to me that our role as dentists was to create what I refer to as the mouth at peace. Our job was to make sure that how we were restoring people's mouths was not contributing to the overall systemic inflammatory load. We needed to do that by finding biocompatible materials. We needed to do that by being meticulous in our investigation of infection, our delivery of care, and paying attention to the way in which a mouth at peace looks.Dr. Rountree: How does a mouth at peace look?Dr. Chalmers: Basically it is a mouth free from inflammation. The gums are pink, firm, and healthy. There is no bleeding. There is very little plaque. So much of what I have learned is that genetics play a really strong role in what people can get away with, you know? My hygienist, whom I adore, Jessica Comaich, has also studied with IFM and taken Applied Functional Medicine in Clinical Practice (AFMCP), practices with me from a functional perspective. She makes me laugh when she says, “I am so glad we think the way we do—just had another patient who defies the laws of traditional dentistry. I just saw someone who rarely brushes and flosses between visits, and yet they are fine. Their tissues do not bleed. They have no decay.”There are many important factors beyond what traditional dentistry talks about—brushing, flossing, and not eating sugar. There is really a much bigger perspective to oral health than simply that.Dr. Rountree: Can you give me an idea of what kind of genes would influence that? We certainly see that in general medicine, that there are some people who can live the worst possible lifestyles and live to be 110, you know, they have a shot of whiskey every morning and a cigar every day, and they live to be 110. And you say, “What the heck?”Dr. Chalmers: I wonder about vitamin D—VDR single-nucleotide polymorphism (SNPs) or MTHFR, COMT and other methylation SNPs. I would like my capstone project at USC to investigate methylation and orofacial pain and oral medicine. A lot has been written about methylation in other aspects of our health. I really want to do a deep dive and take a look at methylation with oral health. I also think our CoQ10 pathways play a role.Dr. Rountree: Well, this raises a logical question. It is a little bit of a sidetrack, but if CoQ10 metabolism plays a central role in maintaining oral health, does the depletion of CoQ10 by statins have an impact on the gums?Dr. Chalmers: Absolutely. We have had patients with no periodontal pockets, and suddenly between six-month visits, we are finding 4 and 5 mm periodontal pockets in the molar areas. When we quiz these patients, often they have started statins. Our conversation next is about what statins do to the CoQ10 pathways, and we prescribe supplemental CoQ10 to those patients. Usually the pockets will return to normal 2–3 mm because fundamentally the patients are healthy and their home care is good.I think nitric oxide also plays a role in bleeding gums and I would love to begin to investigate nitric oxide synthase (NOS) SNPs. What role do they play in patients with bleeding gums?Dr. Rountree: Are you referring to problems with inducible NOS?Dr. Chalmers: Correct. In 2015, when I listened to a presentation by Dr. Nathan Bryan, PhD, talking about nitric oxide and endothelial health, it occurred to me that the first sign of any periodontal condition is bleeding gums, a representation of endothelial damage. Dr. Mark Houston, MD, talks about cardiovascular disease and the three finite responses—immune dysregulation, inflammation, or oxidative stress that manifests in endothelial dysfunction. We could extrapolate that description to the beginning symptoms of periodontal disease. I think if we observe bleeding gums in the mouth, we need to really think upstream about what is happening.Dr. Rountree: Well, maybe this is a good time to talk about nitrates—dietary nitrates and this whole notion that if you eat beets that the nitrates in the beets get converted by oral bacteria into nitric oxide. Can you elaborate on that story a little bit?Dr. Chalmers: This is another area that I think is ripe for investigation and involves the health of our oral microbiome. On my reading list is Cass Nelson-Dooley's new book on the oral microbiome.1 Oral bacteria and an optimal oral microbiome could have an important role in the conversion of nitrates and production of nitric oxide.2 Basically, periodontal disease is first and foremost dysbiosis. It is a group of pathogens that form a biofilm and together can create havoc, systemic havoc.Dr. Rountree: So the idea that you are just going to go in there and drill out all the bad areas, and that is the end of the story, is kind of limited?Dr. Chalmers: It is limited. For example, we do know that Porphyromonas gingivalis and Fusobacterium nucleatum play a role in oral cancer. My first thing when examining oral cancer patients is to test them with OralDNA®. (I have no affiliation and receive no benefit from the company.) OralDNA, a commercial laboratory, has a salivary test with DNA-polymerase chain reaction (PCR) testing to determine the microbes present. I have found the results to be very consistent. Patients are treated individually depending on the pathogens found, sometimes with antibiotics. After three months we will retest. It is important to know that these many periodontal pathogens can burrow into the tissue, including P. gingivalis and Treponema denticola. In our practice, we find that if pathogens are present and not identified and the patient only receives scaling and root planning, they are less likely to fully improve.Another important bacterium to identify because of its relationship with autoimmune disease is Aggregatibacter actinomycetemcomitans. A. actinomycetemcomitans has an effect on the citrullinated proteins and the anticitrullinated proteins.Dr. Rountree: Let me take a minute to clarify this scenario for our readers. The earliest diagnostic test that you do for rheumatoid arthritis is the anti-CCP, which stands for cyclic citrullinated peptide, also called anti-CPA. The way you get that antibody starts with an enzyme called peptidylarginine deiminase (PAD) that converts an arginine residue in epithelial tissues into citrulline. PAD is produced by dysbiotic bacteria and is upregulated in inflamed tissues. The result is citrullinated proteins that look “foreign” to the immune system, and that can elicit an autoimmune response. So the immune system gets activated, and you make these antibodies. In mainstream medicine that is accepted as a standard test, but nobody asks, “Why is this phenomenon occurring?” Right? Nobody says “Hey, why is this individual making these antibodies? What is the underlying mechanism?” And you telling me that it could all start in the mouth.Dr. Chalmers: Right, and A. actinomycetemcomitans makes that enzyme. It triggers the dysregulated activation of citrullinating enzymes in the neutrophils. And my understanding is that testing for the anticitrullinated protein antibodies (ACPAs) is actually a more sensitive predictor of autoimmune disease than antinuclear antibodies.Dr. Rountree: Yes, it is more sensitive. We have primarily used it for diagnosing rheumatoid arthritis, but it turns out that it can be positive in many of other immune diseases, including multiple sclerosis. So are you making a case that dentists should be doing anti-CCP or ACPA, depending on the laboratory?Dr. Chalmers: I think we need to be identifying the presence of this particular bacterium in our autoimmune patients, and then working in concert with the rheumatologist or the primary care physician to order those tests. That is at this point in time. This is another way in which the two professions, medicine and dentistry, need to work together. I have been saying this for some time—functional medicine enriches and broadens that partnership and that conversation is really what is most important.Dr. Rountree: Functional medicine practitioners essentially need to be the matchmakers between the rheumatologists and the dentists. Because I can guarantee you that 99% of the time rheumatologists never talk to their autoimmune patients about what is going on in their mouth. Has that been your experience, too?Dr. Chalmers: Yes it has. And what is even more fascinating, as we talk about this link, are two Sjögren's patients I have examined recently. Independently, they have each seen very astute MDs who suggested that they have their third molar extraction sites evaluated for osteonecrosis—again, another very controversial topic in dentistry. Both of these patients had their maxilla and mandible evaluated by 3-D Cone Beam CT, finding areas of the bone that had never healed properly when their wisdom teeth were extracted.With the surgical treatment of these osteonecrotic areas, we are seeing some resolution of their dry mouth and other Sjogren's symptoms. Not total resolution, but significant improvement in xerostomia from Sjögren's.At the time of surgery, both patients had DNA-PCR testing of the bone biopsies. Trying to explain the clinical results I was seeing, I looked at the biopsy reports for evidence of A. actinomycetemcomitans. Although A. actinomycetemcomitans was not reported, both Actinomyces gerencseriae and Actinomyces israelii were found in the samples. As I reviewed the literature what is significant about these bacteria is that A. actinomycetemcomitans is usually present with them in infectious biofilms. Perhaps this explains these unusual clinical findings.Dr. Rountree: Let me clarify what you are saying, because I think this is profound. The typical course in rheumatology is that you diagnose an autoimmune disease as precisely as possible, and then you prescribe the drug that is indicated for that specific disease based on published clinical practice guidelines. For rheumatoid arthritis, you might use a disease modifying antirheumatic drug or biologic. Sjögren's is a little trickier, because there is no clear treatment protocol. The missing piece in rheumatology is asking the question, what is the driver of this person's disease? Right? What is triggering it in this particular individual?Dr. Chalmers: Right. And I do not think it is ever too late to begin to ask that question and to go on that quest. In functional medicine, that is what we do, right?Dr. Rountree: We are vigorously looking for the trigger or triggers. I know there are scenarios where practitioners say to me, “Gee, I looked at the person's diet. I found a few foods that might be a problem, like gluten or sugar, but I have not identified any major dietary triggers that directly worsen the condition. I have evaluated for environmental toxins and tested the person's GI microbiome and nothing significant showed up.” And so at that point, the practitioner steps back and says, “I'm not sure what else to do to find out what is driving this person's illness.” And your response is, “Have you considered the universe of the mouth?”Dr. Chalmers: Correct. And some of the restorative materials may be triggers, right? Like mixed metal crowns and implants. Fortunately, I think we are migrating away from metals, because we now have some really wonderful restorative materials that are metal free. We can now place a solid zirconia crown that is highly aesthetic and almost as strong as gold.We also have a direct restorative material that is completely bisphenol A (BPA), bisphenol S (BPS), and phthalate free, wears beautifully, and is very aesthetic. I have been using it for about four years. The pushback from dentistry regarding BPA is, “Well, it is only a little bit of BPA.” However, the ADA has published studies about children with sealants having elevated levels of BPA detected in their urine. It goes away after about six weeks, but for six weeks after the placement of the sealants, they were finding BPA in the kids' urine. The conclusion at the end of both of these studies was, “Well, we do not quite understand the systemic effect.” But I think those of us in the functional medicine world do have a very good understanding.Dr. Rountree: Well, we are saying that this is a child for whom you are administering a chemical with hormone-like effects. You are essentially giving a synthetic hormone to this kid. Are you okay with that?Dr. Chalmers: No, not ok. For a long time, our choice was between mercury or composites with different amounts of BPA, always trying to find the material with the lowest amount. There is no reason to have to deal with either one of those now, with the BPA, BPS, and phthalate-free materials available.Dr. Rountree: Back to this whole autoimmune issue, if you are a practitioner seeing patients with autoimmunity, especially early on in their course, what should you do? What do you recommend as a dentist?Dr. Chalmers: I would recommend that physicians look into ordering the OralDNA test. I believe this saliva test can be done in any office. It is just swish, spit, and ship. Oral DNA has several tests for HPV and Candida as well as genetic testing for periodontally relevant SNPs. We use their Perio-Path test multiple times a week to identify the pathogens. I think we are underestimating the role that some of these microbes can play in autoimmunity, in cardiovascular disease, cancer, cognitive decline, et cetera.Dr. Rountree: Let us talk about C-reactive protein and gum disease. That is a very well-established relationship, correct?Dr. Chalmers: Correct. It is an inflammatory marker and its relationship with gum disease has been shown for years. Ten years ago, when I would have an active periodontal patient in the practice, I would send them back to their physician for a vitamin D test with an hsCRP. Nearly always the vitamin D would be very low, and hsCRP would be very high. The physicians sometimes had some pushback—“Why is your dentist asking for a blood test?” Now it is better. Most physicians now are screening for vitamin D, and seeing low levels of vitamin D is not anywhere near as common as it once was.Dr. Rountree: The public is more aware of the need for vitamin D and supplementation, et cetera?Dr. Chalmers: Exactly. The level that has evidence in the literature is 50 ng/mL. The Journal of Dental Research, a well-accepted peer-reviewed journal, published an article establishing the level of 50 ng/mL as necessary for optimal healing from periodontal surgery.A friend asked, “My son is having his wisdom teeth out. What should we do to get him ready?” I said, “Check his vitamin D,” and sure enough, he was vitamin D deficient with a level of 25 ng/mL. She rescheduled the surgery for a couple of months while her son raised his vitamin D level.Dr. Rountree: That makes sense. You have got to get the bones healthy first. Do dentists these days need to be experts in osteoporosis, as well?Dr. Chalmers: I think dentists need to understand bone pathways to the degree that orthopedic surgeons do. Bone pathways are complicated and we fundamentally have to understand them. Magnesium is as important as vitamin D.A systematic review and meta-analysis just published in the Journal of Endodontics, titled “Apical periodontitis is associated with elevated concentrations of inflammatory mediators in peripheral blood,” determined that chronic infections in the bone have a significant role in the increase of inflammatory markers C-reactive protein, interleukin-6, and asymmetric dimethylarginine.3 When treating an endodontic patient, we have to be able to talk to patients about the nutritional aspects of bone health and bone healing.Dr. Rountree: Besides vitamin D and magnesium, as you have mentioned, do you have any other favorite nutrients that you think are especially good for bone health in the jaw?Dr. Chalmers: Another great local factor is plasma-rich fibrin (PRF) used by dentists who have specific training and equipment. To obtain PRF, the patient's blood is drawn, spun down in a centrifuge to extract the fibrin layer, and it is placed where needed in the bone. Dr. Valerie Kanter, DMD, a Los Angeles-based endodontist, is using the injectable form of PRF sometimes in larger endodontic lesions. It provides nutrients and scaffolding for bone health and bone repair. With tooth extraction procedures, particularly in an area where we may want an implant at a later date, or even third molar extractions, we encourage patients to avail themselves of practitioners who utilize PRF, because it improves healing.Dr. Rountree: What is your position on bisphosphonates in general? We are taught in mainstream medicine that these drugs can occasionally cause osteonecrosis, but it is not something to be concerned about.Dr. Chalmers: I would dispute that. Yes, the statistics for the development of medication-related osteonecrosis of the jaw (MRONJ) are low, with some medications being safer than others. The problem with bisphosphonates is the long half-life, and the way in which it shuts down the bone healing pathways. It becomes really problematic for patients who need to have an extraction or have an implant placed when they have been on them for a long period of time. Denosumab, a preventative osteoporosis medication that targets RANKL, can be reversed more quickly.4I had a metastatic breast cancer patient referred by her primary care provider, with active bisphosphonate necrosis. This young woman was two weeks away from having a hemimaxillectomy for the necrosis. Successful surgery on extensive cases is difficult because the root cause is altered bone metabolism and opportunistic infections. When bisphosphonate patients develop secondary infections, it is important to address the biofilm.I referred her to an oral surgeon who used ozone along with conservative debridement and was successful in treating the infection, allowing this patient to keep her maxilla. Another treatment for chronic bone infections used at USC is minocycline in Orabase, which is delivered locally. Orabase is a mucoadhesive paste that will keep the minocycline localized to the bone. This product is used with MRONJ patients and other chronic bone infections, where circulation is the issue.Dr. Rountree: What do you tell a long-term patient, who says, “My primary care doctor just diagnosed me with osteoporosis and wants to start me on a bisphosphonate once a week or once a month?” Do you have a detailed discussion about the pros and cons?Dr. Chalmers: We do. First, we make sure that there are not any emergent problems. Then we have a discussion about future needs such as implants or periodontal treatment. Optimally, we treat before bisphosphonate treatment begins. Many physicians are referring to dentists to get a clean bill of health before they place the patient on bisphosphonates.Dr. Rountree: What you just said is really profound—that you should get dental clearance before you start a person on these drugs. In my experience, it has reached a point wherein these drugs are being prescribed like