Ever-changing Diversity of the Microbiome of the Mouth
Hailey Ragan – HUBI-B400
Dr. Micheal Wasserman
13 December 2021
Introduction:
As humans, everything in our body works together synchronously to produce energetically favourable functionality, especially microbes. The microbes in our body and on our body work together to form an important organ, or superorganism, that functions as a whole (Dewhirst, Chen, Izard, Paster, Tanner, Yu, Lakshmanan, Wade.) More specifically, our mouth is home to the second more diverse microbial site that coats the teeth, gums, tongue, and oral cavity to ensure the strength we need to chew. Throughout human evolution, we have continuously reconstructed the composition of the human microbiome (Verma, Garg, Dubey.) These changes not only come from the refinement of processed sugars and heavy dyes in foods and beverages but from human evolution itself. Recent studies have collected data representing dental plaque samples of hunter-gatherers, Neolithic societies, and pre and post industrial revolution proposing a rather large declining shift of the diversity in dental composition from the hunter-gatherers to now (Yates et. al.) These findings are important to provide truth to the harmful chemicals humans use daily. For example, refined sugar was introduced to our diets in early agricultural times and our oral microbes have now been able to adapt to these changes when before, these microbes had not genetically evolved to this diet (Weyrich.) Adaptations of this nature have led to an increase in the number of microbes able to handle a more orally acidic environment. Today, humans are more exposed to heavy metals, dyes, disinfectants and more that have the potential to harm or alter the microbes in our body. This included the changes to oral health introduced to the modern world of brushing regularly and flossing that have altered the microbes in our oral cavities (Deo.) More recently, the human population is facing an excessive consumption and usage of drugs that has further altered the ecosystem of our oral cavity and the microbes that live in our mouths to carry resistance for us. Because of the war with drugs and oral health, studies have shown a prevalence of increased cases of dental caries (cavities) and periodontal disease.
As an undergraduate seeking to become a dental professional in my future, I have shadowed multiple doctors where I have witnessed what drugs and harmful sugars/dyes can do to oral health. These dentists are highly trained and can answer the question that I will be asking – What differences in the oral cavity have you noticed in those who are healthy but still have poor oral health, have genetic loss of teeth or chronic tooth decay or noticeably large changes in diet such as going vegetarian, etc. What is the patient’s diet like? Do living conditions and location alter the microbiome of the mouth? What kind of habits do these doctors see that alter and deteriorate the oral cavity and otherwise breakdown the microbes in our mouth? What habits do the patients take part in such as drugs, alcohol, etc?
To answer these questions, I will be interviewing multiple dentists around the Bloomington, IN and Indianapolis, IN areas. I will be asking each doctor the same questions and go into detail about the most common habits these doctors encounter and how it affects the oral health of the patient. Because my results will not be something measurable and instead credible from doctors, I will be taking a journalistic approach to my findings as well as using research done regarding the shift of oral microbes from hunter-gatherers to humans today.
Entry 1: Background
An important aspect of what we already know about the microbiome of the mouth demonstrates that it is composed of a variety of microbial residents that have coevolved with us over millions of years. The relationship between oral microbes and the host, being humans, has evolved and now reflects our modern aspects of life such as diet, tobacco/drug use, geography, genetics, and evolution (Kilani, Chappel, Marsh, Meuric, Pederson, Tonetti, Wade, Zaura.) In my first journal post, I will be discussing various primary research over the research done on the oral microbiome, what we know about the evolution of bacteria in the oral cavity, and the effects on oral health (Weyrich.)
Understanding the oral microbiome is important to recognize the functional and metabolic alteration of the mouth that gives rise to disease as well as identifying key molecules in the mouth to treat periodontal disease (Deo, Deshmukh.) The oral microbiome describes an ecological community of bacteria living in the mouth in a symbiotic and commensal fashion. In the mouth, there is a couple places that bacteria can colonize on including the hard tissue (teeth) and oral mucosa which contain the lips and cheeks (Deo, et al.) Other places associated with the oral cavity provide warm, soft/hard palates where these bacteria are able to flourish. The human oral cavity is composed of multiple different habitats including the teeth, sulcus, tongue, cheeks, hard and soft palate, and tonsils that is colonized by over 600 prevalent taxa of bacteria (Dewhirst, et. al.) Where these surfaces are coated with these bacteria are referred to as the bacterial biofilm of the oral microbiome. Before tooth eruption, the mouth has limited bacteria. The surface acquires microflora and some initial bacteria such as streptococcus salivarius. Once the teeth erupt, the oral cavity is evaded with many bacterial forms such as Streptococcus, Lactobacillus, Actinomyces, Neisseria andVeillonella (Deo, et al.) These organisms colonize the teeth and allow for establishment of colonization of these bacteria in multiple places within the mouth. As adult teeth erupt, we see gingival crevices that allow for the colonization of periodontal microbes and plaque accumulation at different sites of the tooth. At a bacterial equilibrium, bacteria are available at correct amounts and are beneficial to the host. However, certain imbalances allow for disease. In this process, periodontal diseases, cavities, and high amounts of bacterial species diversity can be noted (Weyrich.) But, when comparing what we know now of the human oral microbe today, how does that compare with the hunter gatherer area? How has the oral microbiome evolved? And, are these changes beneficial to us as homosapiens?
Research conducted in the evolution and changing ecology of the oral microbiome has detected a core microbiome which consists of predominant species not only found at different sites on the body but in overlap with African hominids genera (gorilla, pan, homo) and howler monkeys (Yates, et al.) Whereas a variable microbiome has evolved in response to unique and genotypic determinants exclusive to an individual (Deo, et al.) This research compared the evolutionary history of the African hominid oral microbiome by analyzing dental biofilms of humans, Neanderthals, chimpanzees, gorillas and howler monkeys and comparing the results. In total, it was found that 10 core bacterial genera had been maintained within each and play key roles in the oral biofilm. Among the findings, it was concluded that the different bacteria associated with bad bacteria leading to periodontal diseases and cavity formation was not specific to modern human suggesting that the increasing rate of cavity and oral diseases are a result of a related imbalance between the host (human) and the oral biofilm (Yates, et al.)
These findings indicate that evolutionary traits, diet, cultural behavior and more have been key in understanding the modern human oral microbiome (Zaura, Nicu, Krom, Keijser.) Investigating ancient oral microbes has the potential to unlock information about how major events in human evolution and history have shaped our microbial ecosystem and how it still affects us. Understanding evolutionary aspects of the oral microbiome can be important in analyzing why dental caries and disease have become so prominent in today’s culture and we can start by analyzing bacteria present in different foods, drinks, drugs, and alcohol most associated with oral disease. This research presented underlines the importance of the rapid changes in composition within the oral microbiome and how they change dynamically with each host (Deo, et al.)
The modern day diet has impacted the oral ecosystem and microbiome of the mouth in immense ways leading to disease such as cavities and periodontal disease. Cavities are damaged areas to the hard surface (enamel) of your teeth. Untreated cavities typically form openings or holes that cause pain and lead to disease. Certain foods interact with the bacteria that the microbiome produces in your saliva, gums, and plaque on your teeth to produce different acids (Zaura et. al.) These acids are what is responsible for dissolving the enamel and biofilm of the mouth that creates the holes in your teeth otherwise referred to as a cavity. Furthermore, the smallest imbalance of the oral microbiome can induce the formation of dental caries (Kilani, et al.) Increased cavity and dental disease can lead to various cancers including kidney, pancreatic, oral, blood, and throat cancer (Siani, Gupta, Prabhat.) It can also lead to brain and heart infection from the infections spreading through your blood and to other parts of your body. It’s even more important to understand the microbiome and ecosystem as a doctor to be aware of trends and how habits can alter the oral cavity and what bacteria in these products can do to the body.
Entry 2: Methods
Because previous research has concluded that the human microbiome contains similar bacteria in comparison to the genera of African hominids and howler monkeys, the importance for understanding the prominence of oral diseases is rising (Yates, et al.) The same oral bacteria shown in historic events in comparison to the same bacteria being shown in present samples reveal that there has been a historical shift in society (Deo, et al.) Whether this is due to the war on drugs, agricultural changes, increased genetic diversity, or geographics, the question still remains: What is the difference that is causing the prevalence of oral diseases in humans today and how has the diversity of the microbiome altered in a way that is presents evidence on these differences have lead to altered bacteria in the mouth in comparison to 100 years ago or even a couple decades ago.
Moreso, we can break down the changes in the oral microbiome into a few key categories including diet/lifestyle choices, environment, and oral hygiene/health. Dietary impacts on the oral microbiota have been linked to meats, sweets, and tea consumption as well as levels of fatty acids and vitamin C (Weyrich). Diet can also come into play when analyzing environmental factors that shift the microbiome such as examining the impacts of industrial vs. modern lifestyles where research has concluded that “outdoor environmental microbes” are dwindling in industrialized populations (Yates). Lastly, the effects of oral health have obvious implications to shifting the bacterial ecosystem present in the mouth. Partly due to diet, however more seriously from an increase in the amount of flossing, toothbrushing, and use of mouthwash to overcome the steady prevalence of oral disease. In fact, mouthwashes that contain active antimicrobials such as chlorhexidine gluconate have been found to have significant effects on the oral microbiota (Verma et. al.)
The main focus of this study is to analyze previous data in a cohort fashion to recognize trends in society that give rise to altering the bacterial biofilm in the mouth. With this, I will conduct interviews among various dental professionals as well as research professionals at the Indiana University School of Dentistry about the alteration of oral bacteria and how it leads to disease and dental caries. The interviews will be conducted in a similar fashion where each doctor will be asked the same set of questions shown below. The questions will indirectly touch on the aspects of diet/lifestyle, environment, and oral hygiene to examine how doctors believe they impact oral health.
- Have you noticed a shift of good/bad bacteria in the mouths of patients that pick up and/or stop habits such as smoking/drugs, excessive sugar intake, or a drastic change in diet?
- What do you believe is the main cause of dental caries? What do you believe is the main cause for periodontal disease?
- Do you ever consider the oral microbiome and the bacteria of the mouth when accessing and determining proper treatment of patients? Do you think products such as fluoride treatment, toothpaste, and mouthwash alter the oral microbiome of the mouth?
- Do you think genetics or geography influence the likelihood or prevalence of dental disease and dental caries?
- Do you consider the bacteria in products when accessing the reason for dental caries in patients? For example, the bacteria and acidity from soft drinks and its effects in the mouth. Do you believe that it deteriorates the good bacteria in our mouth, alters the bacteria in our mouth, or disrupts the commensal relationship of bacteria we have in our oral cavity?
The results of these interviews will be composed in a journalistic fashion that will interpret the results by showing what each doctor believes is responsible for the increased account of disease as well as their thoughts on the oral microbiome. I will conduct interviews with three doctors. Two of the three will be general dentists that treat dental cavities, diagnose dental disease, and carry out procedures that assist in the prevention of disease/mouth pain. The third doctor will be an orthodontist where his main focus is treating and maintaining correct orientation of the teeth and jaw. Orthodontics mostly work with children and teenagers and are able to access the effects of sugar consumption and bacterial colonization in mouths. Together, the doctors will retrospectively give a holistic view of how we use our understanding of the microbiome of the mouth in current practice.
From data interpreted previously in the paper, we can understand that the oral microbiome is complex. Research on the oral microbiome is still lacking but new interpretations of research has helped us understand the symbiotic relationships and alteration of these relationships when discussing oral disease (Deo, et al.) While these methods have looked at what specific bacteria is at play in diseases, which we now know includes Fusobacterium, Corynebacterium, Streptococcus, Actinomyces, Porphyromonas, and Treponema (Yates, et al.) Bacteria associated specifically with Porphyromonas and Treponema are clinically significant today due to their association with periodontal disease. These bacteria are not specific to modern humans and are found across multiple primate species, highlighting the imbalance between the biofilm and modern humans leading to an increased prevalence of periodontal disease. Because we know the mouth is full of bacteria, allowing these doctors to explain their views on oral bacteria and the main causes of dental disease can give an understanding of the shifts recognized in the oral cavity (Yates, et al.)
Results:
In total, I was able to interview three doctors as well as one current dental student at Indiana University School of Dentistry. The results are shown below in separate charts for each doctor. These results will be condensed answers to the 5 questions asked in the collection of my data.
1. Dr. Ashley Lock – As a new Dentist who has just recently started practicing about a year ago, Dr. Lock reflected on her time in Dental School. She talked about how in school, they learned about types of bacteria however, the diversity of bacteria and how that may be altered was not directly touched on. Interviewing Dr. Lock was interesting because although she is a new doctor, it reflects how little is known about the diversity of the oral microbiome.
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1 |
“You can definitely tell the difference in bacteria upon looking into a patient’s mouth whether that be good or bad. I cant speak on what specific bacteria is lurking in the mouth but you have a good idea of if it’s good bacteria by whether they have healthy gums, tongue, cheeks, and teeth. Typically patients with bad bacteria in their mouths tend to have bacterial growth built up in the form of plaque on the teeth and/or calculus on the tongue and gums.” |
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2 |
“In my personal experience from what we learned in dental school and as a new dentist, I have found that most cavities come from excess sugar intake and not taking proper care of teeth which in turn reflect periodontal disease.” |
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3 |
“I don’t specifically think of the oral microbiome and the bacteria that entails when assessing a patient. I think instead I have been trained to assess the habits of the patient to try and determine why oral diseases are so prevalent in a patient. In turn, I think that reflects changes in the bacteria of the mouth that have influenced the outcome of a case. However, no, the diversity of bacteria in the mouth is not directly used.” |
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4 |
“The more I practice, the more I am able to confidently speak on how geography and genetics reflect cavities. The more that we have discussed the bacteria of the mouth has made me think of ways that I can try to use bacteria to process altered bacteria in the mouth. In terms of geography, you could say that areas of the world that are more prone to eating acidic foods show teeth that have thin enamel due to the acidic properties eating away at the teeth. I have seen this a lot in Chinese and Japanese culture. You could say the same about Americans who eat diets high in sugar and have a high prevalence of cavities and oral disease. Therefore, in relation to the microbiome, I think geography can alter lifestyle choices that will alter the bacteria in the mouth. In turn, it will reflect the outcome of different cases we see in dentistry and show trends that we are able to use to help up practice more efficiently.” |
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5 |
“Yes. Although we never learned the specifics of the microbiome, the effects of products such as sugar for example, are indicators to whether or not a patient has cavities. In that sense, you could say that we are detecting a change in bacteria based on alterations in the mouth we can directly see like tooth decay. However, I never directly think of the relationship between bacteria in the mouth and how it is altered from specific products.” |
2. Dr. Mark Vaughn – Dr. Vaughn is an orthodontist. He graduated from dental school in 2015 and went on to earn his masters in dentistry from Indiana University in 2017. He has been practicing orthodontics for around 5 years. While conducting an interview with Dr. Vaughn expressed that he is familiar with bacterial growth especially in children in teens as he works with them everyday.
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1 |
“Working with kids has given me the ability to access different types of mouths and whether they are healthy or not. In terms of your research, you could say that kids with an unhealthy amount of build up on their teeth have a bacterial imbalance in their mouth. Whether that imbalance is due to sugar intake, etc, not brushing your teeth allows for bacterial growth which leads to dental caries. Personally, I feel that I can detect whether that bacteria is good or bad only from looking at detection signs I learned in school. These signs include gum swelling, increased prevalence of cavities, or sometimes even excessive staining.” |
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“From my perspective as an orthodontist, I would have to say that most of the cavities I come across are definitely the result of sugar consumption and not taking proper care of your teeth. I typically don’t work with a lot of older adults but from experience can tell you that these habits are what lead to increased cases of oral disease” |
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“Truthfully, No. As an orthodontist I am always influencing my patients to brush their teeth and use mouthwash. Especially because having brackets increases the likelihood of food getting stuck and causing cavities which is already hard enough for teenagers and children who have braces.” |
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4 |
“Especially with braces you can see how genetics come into play. When taking X-Rays of patients, most of the time how the teeth have grown in is a direct result from genetics from mom or dad. But, the only way I personally think genes influence cavities is that when teeth come in very crooked, it affects how resistant teeth are to bacteria and in that sense, we see increased cavities and dental disease which is why it’s important to have straight teeth other than aesthetic reasons.” |
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5 |
“I actually saw this first hand. Although this isn’t specifically something we take a class on, it’s the root of all dentistry. You get cavities and disease from altered bacteria in your mouth and that comes from food, drinks, drugs, alcohol, and can even be from other reasons too. I remember in school a woman came in to get cleanings and work done at the dental school. I had him as a patient frequently and she had a dry mouth condition where glands in your mouth don’t produce enough saliva to coat your teeth and throat. Because of that, she had to have cavities filled very frequently. Saliva helps to neutralize the acidity of your mouth and because she isn’t producing enough, the acid was causing tooth decay and is just one example of how factors other than just food and drink contribute to alterations in bacteria.” |
3. Dr. Randal Christi – Dr. Christi has been my family dentist growing up. I’ve been to his office to shadow him multiple times and his insight on my topic and bacteria in the mouth has been extremely insightful in assessing how our oral microbiome has altered and changed over time.
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“Shift in bacteria can be apparent sometimes. For example, when teeth yellow its typically due to the biofilm covering the teeth deteriorating or can also just simply be from a lack of brushing and taking proper care of your teeth. When you age, the biofilm naturally deteriorates and is why older folks typically have stained teeth. However it doesn’t necessarily mean that the bacterial shift is bad but it does indicate there has been a shift in bacteria to some extent.” |
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“The most cavities I come across are from sugar intake. I could say the same about periodontal disease which is a result from lack of oral health care from letting sugar, acidic drinks, and food sit and deteriorate your enamel and can even lead to bone loss in your jaw around the root of your tooth and gum recession.” |
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“I would have to say no, not directly at least. I can tell you from experience that I have been able to distinctly tell a difference based on age which is an indication of how generations have changed. I have noticed that younger generations have more cavities, more gum recession, and I’ve noticed especially that they have thinner enamel compared to older generations. I personally believe this is from how our world has changed. For example, younger generations eat and drink way more acidic and sugary drinks and foods compared to myself at your age or my generation in general. All of those things lead to the deterioration of enamel thinning, higher cavities, and alteration of the microbiome if you would like to use those things as an indication that the bacteria has been altered, in which it has been. |
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“I don’t think geography affects the likelihood of oral disease, however genetics come into play more than most understand. Your genes are at the root for whether or not you have wisdom teeth, how your teeth grow, develop, and even if your teeth will grow in straight or not. However, these aren’t things we can predict and knowing that genetics affect the outcome of a case, it’s rarely any indication of disease.” |
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5 |
“For sure. Cavities and disease are most commonly from sugar, neglecting oral health, or can be from how teeth grow in. Crowding of teeth can cause food to get stuck and cause decay. Disease and cavities can come in many flavors, however the question is how we got from A to B meaning how did the tooth or mouth grow this disease or cavity. Typically the answer is always due to food or drinks that sit on your teeth and alter the bacteria, causing tooth decay.” |
Discussion:
Together, what my findings through the various interviews and current research has shown is that there is very little knowledge regarding the oral microbiome and the thousands of bacterial microorganisms that contribute to the ecosystem inside our body. What can be concluded is that similar to the biodiversity loss from external factors in our environment, there has been biodiversity loss within the human microbial community from similar outside factors. These include ever changing societal standards such as higher consumption of products high in acidity. Furthermore, concluding that the “abundance, diversity, and composition of the oral microbiota have been linked to changes in diet, environment, hygiene, physiology, health status, genetics, and lifestyle” have all contributed to the shift in the microbiome over time (Weyrich.)
With evolving and increasing amounts of research on the topic of oral bacteria, it can significantly influence treatments for patients. Understanding what kinds of bacteria become altered with different external factors can help doctors understand different methods and treatment plans for different patients. Mouth swabbing could become a popular method to access what kinds of bacteria are in a patient’s mouth and could be especially useful in cases concerning oral disease, gum inflammation, increased cavity prevalence, and even bone loss. To do this, future research should understand what kinds of bacteria live in the mouth and what these bacteria do as well as how they are altered when coming into contact with harmful factors. These findings can present helpful information regarding how we can halt continuous harmful bacterial growth.
The microbiome is ever-changing, there is good and bad bacteria that has evolved in our mouths that alters this diversity. Furthermore, these alterations are a result from evolving social standards, increased urbanization, and even factors such as increased use of oral health treatments. This can be shown by societal standards of each time in what we eat, products that we consume, and even how industrialised our world has become compared to 100 years or even a couple decades ago and how this has changed the bacteria that grows in our mouth. and therefore alters and contributes to helping prevent oral disease. Similarly to how humans are at the forefront of biodiversity loss on Earth, we too are responsible for the bacterial biodiversity loss we are seeing in ourselves. These ideas go hand in hand when considering the “blatant disregard for the environment entrenched in our current economic model” (Living Planet Report 4.) The rise in biodiversity loss on Earth contributes to the well-being and health of humans. With that in mind, the correlation between biodiversity loss on Earth and the bacterial biodiversity loss in humans are both contributing to the rise of infection and disease.
Future Research:
Further research should focus on understanding these bacteria and how they alter the mouth. For example, research has indicated core bacteria of the oral microbial community including Streptococcus, Lactobacillus, Actinomyces, Neisseria and Veillonella (Deo, et al.) However, instead of only identifying that these bacteria exist, research should focus on how these bacteria are altered when coming in contact with the most basic and common substances such as sugar in the form of drinks and food, acidic substances, and also drugs/alcohol. This can give a more holistic view of how and why oral diseases are increasing and how to better help disease by understanding how the microbes are modifying the oral environment in aiding it in pathogenesis (Takahashi.) Furthermore, this research can help better educate society on oral health and how we are putting our own health at risk. More specifically, we need to not only understand what is happening to the bacteria on a microbial level but as an ecohealth perspective as well where we can recognize how changing environments affect human health through examination of human interactions with the bacterial ecosystem existing in our body (Wasserman Lecture 1.) Lastly, this research should not only focus on how the bacteria alters in times of disease but also during health. This is important so doctors and researchers can educate and promote the health of the microbiome to society in order to restore and maintain proper oral health (Baker.)
Other research should investigate how these bacteria could be altered. The purpose of this research would be to be able to screen a patient’s mouth, understand the bacteria present and if that bacteria is harmful or not, and be able to alter the harmful bacteria that is deteriorating the patient’s mouth with antibacterial antibiotics or even replace the bad bacteria with a healthy form and therefore, “finely tune” the bacterial microbiome of the mouth (Campbell.) This research would be focused on how we could personalize dental medicine in ways that we alter patients microbiomes to form the symbiotic relationship that has been lost. This will be to find an equilibrium of bacteria based on each case that maintains health but is able to help fight disease (Zarko, Vess, Ginsburg.) Together, this research could significantly reduce oral diseases and therefore, increase overall health.
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