Photo by Meg Jerrard on Unsplash

Did you know the plaque on your teeth holds a treasure trove of information about your oral microbiome, which will endure for thousands of years after your death? Oral bacteria are frozen in dental calculus, much like a prehistoric insect preserved in tree sap. Thanks to calcified plaque on teeth, we have a record of not only ancient humans dating back more than 10,000 years, but also the microbes that coexisted with them. Find out what key historical events permanently changed our mouth bacteria and set us on a path of more cavities and gum disease. You might be surprised to learn how modern-day humans measure up to our ancestors in terms of oral microbial diversity and what are the worst foods for teeth according to the fossil record. Connecting the dots with anthropological, microbial DNA, and skeletal evidence, we know what key events changed the course of oral health for our ancestors and how to reverse them for better health today.


A Fossilized Superorganism

We are superorganisms. Go ahead, put a cape on, and own it. 😊 We are not purely human. Microbes living in and on our bodies – at numbers equal to our human cells or more- make up an organ that is vital to our health and physiology. The bacteria, fungi, parasites, and viruses that inhabit our bodies are known as the microbiome.

“Together with our symbiotic microbial residents, we form a ‘superorganism,’ or holobiont,” state Kilian and colleagues.1

We have been superorganisms, coevolving with our microbial companions, for at least 1.5 billion years.1 Scientists have figured this out because so many other mammals share the same microbiomes. In fact, using the bacteria Helicobacter pylori, you can map out the differences between human populations better than using genetic markers. You can map the migration of early human beings out of Africa to other continents using this single oral bacterium.

Exciting research suggests that ancient teeth can serve as a fossil record of the early oral microbiome. This may be one of the few microbial records that persist in ancient human remains.2 Studying ancient teeth is called paleodontology.

When bacterial biofilms on our teeth (called plaque) harden and combine with a tooth mineral called calcium phosphate, they turn into something called calculus. Crystalized, calculus is a structure much like bone. Calculus does a great job of preserving bacteria over thousands of years. Bacteria in calculus are essentially frozen in a time capsule; just like an ancient fly fossilized in tree sap. Does this conjure images of Jurassic Park, anyone? It should.


What Can We Learn from Ancient Fossil Teeth?

Paleontologists, who study ancient remains, love teeth. The value of teeth isn’t lost on any of us who watch TV or read murder mysteries. Teeth are extremely hard and durable, more so than bones. They can take a beating and still stick around so that paleontologists and forensic scientists can get their questions answered. Teeth can help identify unrecognizable human remains. They give information about a person stretching back to before birth.

Teeth can also reveal the roots of humankind. They serve as an ancient record of the oral microbiome and even can tell us about the kinds of foods humans were eating around the same time. Oral bacteria found on ancient teeth provide an evolutionary record going deep into the past. They can help track family members and relationships because oral bacteria are inherited from parents early in life, and transferred among family members later in life.2


Historical Events that Changed the Oral Microbiome1

Based on anthropological and evolutionary records, there were key turning points for the oral microbiome in human history. Mouth bacteria coexist with us and they eat what we eat. They are exposed to chemicals and medications that we are exposed to. They change with our oral hygiene habits. Here are some of the changes in history that packed the greatest punch for our ancestors and their oral microbiota. 

  • Use of fire1
  • Shift from hunter-gatherer to agricultural societies1
  • Introduction of refined sugar with the industrial revolution1
  • Industrial revolution leading to heavy metals, disinfectants, biocides, and antibiotics1
  • Access to processed foods1
  • Worldwide campaign to brush and floss teeth in 1890
  • Antibiotics1
  • Modern-day acidic drinks, cigarette smoking, and high amounts of refined sugar1


Bushman cave paintings in Cederberg

When Our Diet Changed 12,000 Years Ago, Our Mouth Bacteria Changed, Too

From about 2.6 million BC until about 10,000 BC (during the Paleolithic Era), humans were traveling nomads, getting their food from nature as they went. When these hunter-gatherers settled down into agricultural communities in the Neolithic Era, they started eating more foods high in carbohydrates from domesticated grains (wheat, barley, corn, rice).

Prehistoric European hunter-gatherers didn’t have as many problems with cavities and gum disease, according to their skeletons. It’s shocking, isn’t it? They also didn’t have the pathogenic bacteria that are characteristic of cavities and gum disease.2 However, after humans switched to agricultural communities, there was a noticeable uptick in the oral microbiota associated with gum disease and cavities. This is probably due to eating softer, carbohydrate-rich foods. At the same time, ancient human remains show that these Neolithic farmers were prone to more cavities and periodontal disease. The Neolithic age runs from 10,000 BC until 2200 BC. This pattern of oral health problems and bad oral bacteria was maintained until about the Medieval age (~400 years ago), likely because food processing methods remained similar through those years.2

Leaving behind a hunter-gatherer diet and switching to domesticated grains coincided perfectly with the arrival of Streptococcus mutans and other cavity-causing pathogens on the scene. Streptococcus mutans is one of the main mouth bacteria implicated in cavities. With so many more carbohydrates to eat, Streptococcus species were able to grow and thrive in the mouth. Evolutionary genetics suggests that these bacteria exploded in growth and genetic diversity. It is no coincidence that cavities accompanied humans from the rise of agriculture all the way to the present day.3 


Industrial revolution

The Industrial Revolution Harmed the Oral Microbiome

The Industrial Revolution presented a historical event for the bacteria in our mouths, on par with the transition from hunting and gathering to farming. The processing of food and the availability of refined sugar that arose during the Industrial Revolution permanently changed the oral microbiome. There were far more cavity-causing bacteria in our mouths after the introduction of farming, but even more fluorished after the Industrial Revolution, which began about 200 years ago. Industrially processed flour and sugar was the largest change to food production since the shift to farming and it completely changed the landscape of the oral microbiome. It put cavity-causing bacteria on center stage. In contrast to early humans and even Medieval agricultural humans, the modern human’s oral microbiome is dominated by bacteria that contribute to cavities.2


Woman smiling

Diversity Equals a Healthy Oral Microbiome

Diversity is usually a measure of a healthy microbiome. We typically want a variety of species, many species, and differing amounts of each. More biodiversity means that an ecosystem is stronger. It can bounce back after stress or imbalance, such as after an infection.2 Think of a microbiome as a village. You need lots of people of all kinds, all ages, and all skills to have a healthy and thriving village.

When a microbiome becomes less diverse, it is not as effective at warding off infection and disease. It can’t perform all of the healthy activities it is supposed to do for the host (you or me).

Today, our oral microbiomes are not as healthy or diverse as those of our hunter-gatherer ancestors. When compared to ancient humans, even the ancient farmers from the Neolithic period, modern humans have much lower oral microbiome diversity. We have fewer healthy oral bacteria, more disease-causing oral bacteria, and higher amounts of pathogens. Our diet of grains and refined carbohydrates decreased oral microbiome diversity in early man over 10,000 years ago and its effects can still be seen today.

“…Over the past few hundred years, the human mouth has become a substantially less-biodiverse ecosystem.”2


Various types of bread

The Worst Foods for Teeth

A diet rich in bread, corn chips, corn tortillas, cake, cookies, and pasta is not only bad for our oral microbiome, causing cavities and gum disease. It is also bad for blood sugar, heart disease, metabolism, weight gain, and cancer. What a coincidence! 😊 Perhaps the change from hunter-gatherer diets to farming communities around 10,000 BC had more negative side effects on our health than anyone could have predicted.

There has never been a better time to focus on whole foods. Ultra-processed foods starting with the Industrial Revolution harmed human health, oral health, and they also pushed the microbiome completely off balance. I feel sure the oral microbiome is not the only microbial population that took a hit. Gastrointestinal, lung, vaginal, and skin microbiomes also likely felt the negative ramifications of a diet high in processed flour and sugar.


Man exploring ice cave

Oral Pathogens Found in 5,000-year-old “Iceman” Mummy

Fossilized teeth of the 5,300-year-old “Iceman” showed bacteria Treponema denticola and Porphyromonas gingivalis, both commonly associated with gum disease. Also known as Otzi, the Iceman is the oldest natural European mummy from the Copper Age (born 3275 BC). His remains were found in a melting glacier in the Italian Alps near Austria.

Iceman was from a farming community and he had the telltale signs of it. At about 45-years-old, he had extensive alveolar bone loss (the bones that support the teeth), suggesting that he had gum disease.

The Iceman may also be an example of the oral-systemic connection. Treponema denticola was not only found in Iceman’s mouth. It was found in his bones. There is no way to know if Iceman had oral pathogens in his bones during his lifetime or only at the time of his death. However, it’s possible that these oral pathogens had made their way beyond his mouth and into his bones. They had already damaged the bones in his jaw. He also showed arteriosclerotic disease, or plaque buildup in his arteries. Heart disease has been linked with gum disease and gum-disease-causing bacteria.4


Scientist pipetting a DNA sample into a multi well plate ready for genetic testing in a laboratory

DNA Analysis Techniques Measure the Oral Microbiome Today and Yesterday

Molecular methods made it possible for us to measure the gut microbiome and the oral microbiome in a way that had never been done before. These same techniques can also tell us about the oral microbes that our ancestors carried over 10,000 years ago!

What we know about bacteria and microorganisms is only as good as the tools we use to measure them. In 1885, the first bacterium was cultured. In 1969, scientists learned how to grow bacteria in the absence of oxygen, making it possible to study bacteria that had been invisible beforehand. But in 2000, molecular methods for studying bacteria became available. These DNA analysis techniques would make it possible to see 50 percent more microbes than we had ever seen before5-7 and this technological breakthrough would later be called a “molecular revolution.”8

Molecular techniques fall in two large categories that measure the DNA code to identify organisms: polymerase chain reaction methods or sequencing methods. Because they use DNA, they are more accurate than previous ways of studying microbes. They also can detect very small amounts or a huge variety of microbes.

Polymerase chain reaction (PCR) methods hone in on a specific microbial DNA signature and make many copies of it, a process called amplification. The next step is hybridization, or the binding (like a lock and key) of one single-stranded DNA segment to another complementary piece of DNA. This step is important for accurate identification of a microbe based on its DNA signature. PCR can pick up very small amounts of DNA, such as 10 bacterial cells. Quantitative PCR is the best technique for quantifying specific amounts of microbial material in a human specimen. Oral microbiome testing using quantitative PCR is available to clinicians.

Next-generation sequencing technologies are DNA or RNA sequencing methods that use PCR to get enough DNA to work with, but then they determine the order of nucleic acids in a DNA molecule and count them. They can sequence an entire genome. These methods are great for exploring a microbiome A to Z and understanding the relative abundance of all players. These DNA analysis tests of the oral microbiome are also available to test your mouth bacteria in today’s modern world (see link below).

Scientists used next generation sequencing and PCR to learn about the Iceman’s oral bacteria. Sequencing is particularly helpful for working with damaged and short segments of DNA, such as those found in mummies or other ancient specimens.


happy man smiling

Lessons from the Ancient Oral Microbiome

The oral microbiome not only lies at the foundation of oral health, it is also strongly tied to the health of the heart, brain, joints, fetus, metabolism, and gastrointestinal tract. As if that weren’t enough, the oral microbiome, preserved like an insect trapped in amber, can tell us treasure troves about prehistoric humans and the microbes that have coevolved with us over millennia. Teeth coated in dental calculus are one of the few records of the human microbiome and they reveal pivotal turning points in human history that set us on a path toward more oral disease and systemic disease. Let’s take a lesson from our prehistoric ancestors and put our microbiomes back on track to fight off cavities, gum disease, brain aging, inflammation, and more.

Increase Your Oral Microbiome Diversity with These Tips from Our Ancient Ancestors

  • Eat a hunter-gatherer diet rich in whole foods, plants, fiber, nuts, and seeds
  • Eat a wide variety of colorful foods
  • Avoid the worst foods for teeth such as pasta, bread products, corn flour, cakes, cookies, chips, sweets, all packaged/processed foods, and sugar
  • Take oral prebiotics
  • Take oral probiotics
  • Test your oral microbiome diversity with Bristle (use this link for $15 off!)


Reference books in library


  1. Kilian M, Chapple IL, Hannig M, et al. The oral microbiome – an update for oral healthcare professionals. British dental journal. Nov 18 2016;221(10):657-666. doi:10.1038/sj.bdj.2016.865
  2. Adler CJ, Dobney K, Weyrich LS, et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet. Apr 2013;45(4):450-5, 455e1. doi:10.1038/ng.2536
  3. Moye ZD, Zeng L, Burne RA. Fueling the caries process: carbohydrate metabolism and gene regulation by Streptococcus mutans. Journal of oral microbiology. 2014;6doi:10.3402/jom.v6.24878
  4. Maixner F, Thomma A, Cipollini G, Widder S, Rattei T, Zink A. Metagenomic analysis reveals presence of Treponema denticola in a tissue biopsy of the Iceman. PLoS ONE. 2014;9(6):e99994. doi:10.1371/journal.pone.0099994
  5. Wade W. Unculturable bacteria–the uncharacterized organisms that cause oral infections. Journal of the Royal Society of Medicine. Feb 2002;95(2):81-3.
  6. Rappe MS, Giovannoni SJ. The uncultured microbial majority. Annual review of microbiology. 2003;57:369-94. doi:10.1146/annurev.micro.57.030502.090759
  7. Dewhirst FE, Chen T, Izard J, et al. The human oral microbiome. J Bacteriol. Oct 2010;192(19):5002-17. doi:10.1128/JB.00542-10
  8. Rajilic-Stojanovic M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev. Sep 2014;38(5):996-1047. doi:10.1111/1574-6976.12075

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, MS, is a researcher, author, educator, and laboratory consultant. She studied medicinal plants in the rain forests of Panama as a Fulbright Scholar and then launched a career in science and natural medicine. Early on, she studied ethnobotany, ethnopharmacology, and drug discovery at the University of Georgia and AptoTec, Inc. She joined innovators at Metametrix Clinical Laboratory as a medical education consultant helping clinicians use integrative and functional laboratory results in clinical practice. She owns Health First Consulting, LLC, a medical communications company with the mission to improve human health using the written word. Ms. Nelson-Dooley is an oral microbiome expert and author of Heal Your Oral Microbiome. She was a contributing author in Laboratory Evaluations for Integrative and Functional Medicine and Case Studies in Integrative and Functional Medicine. She has published case studies, book chapters, and journal articles about the oral microbiome, natural medicine, nutrition, laboratory testing, obesity, and osteoporosis.