What Ancient Gum Disease Tells Us About Our Lost Microbial Past
We often think of archaeology as the study of grand pyramids, ancient pottery, and fossilized bones. But some of the most profound stories of our past are written in the most unexpected places: the hardened plaque on the teeth of our ancestors.
Key Insight: Recently, scientists have unlocked a new way to peer back in time by analyzing the DNA preserved in the dental calculus (calcified plaque) of Native American individuals who lived long before European contact.
What they found was a hidden world—a unique microbial ecosystem that thrived in the human mouth for millennia, a world that was dramatically reshaped by colonialism, industrialization, and modern life. This isn't just a story about ancient germs; it's a story about human history, our changing bodies, and the invisible companions we've lost along the way.
To understand this discovery, we must first reframe our perspective. Your mouth is not just a tool for eating and speaking; it is a bustling, diverse ecosystem, home to billions of bacteria, viruses, and fungi. This community is known as the oral microbiome.
A complex community of microorganisms living in our mouths, most of which are harmless or beneficial.
Hardened dental plaque that acts as a time capsule, preserving ancient microbial DNA for thousands of years.
The Disappearing Microbiota Hypothesis suggests that the microbiomes of people living in industrialized societies have become depleted compared to those of our ancient ancestors . Modern factors like antibiotics, processed diets, and improved sanitation, while beneficial in many ways, may have caused us to lose microbial diversity that was once crucial for our health.
A pivotal study, led by scientists at the University of Zurich and involving close collaboration with Indigenous communities, set out to test this hypothesis by recovering the first oral metagenomes from pre-contact Native Americans .
The process of extracting this ancient microbial story is a feat of modern science, requiring both archaeological care and cutting-edge genetics.
The research was built on a foundation of respect. The team worked directly with descendant communities and curators to gain permission to analyze the skeletal remains of individuals from archaeological sites in North America, dated to between 1000-1500 AD.
Using a sterile dental scaler, researchers meticulously collected tiny samples of calculus from the ancient teeth, taking extreme care to avoid contamination with modern DNA.
In a dedicated "clean lab" (a sterile environment to prevent contamination), they dissolved the calculus and used chemicals to extract and purify the tiny, degraded fragments of ancient DNA trapped inside.
This ancient DNA mix—a jumble of human and microbial genes—was then sequenced using high-throughput machines. This process, called shotgun metagenomics, reads all the DNA fragments in the sample without bias.
Powerful computers were used to piece the genetic fragments together like a puzzle. They compared the sequences to massive databases of known microbial genomes to identify which species were present in the ancient mouths.
The analysis revealed a oral microbiome that was both familiar and strikingly foreign.
The pre-contact oral microbiomes contained bacterial strains that are genetically distinct from any found in people of European or African descent today.
The ancient mouths harbored a high diversity of bacteria with unique gene variants not seen in modern counterparts.
The bacterium Porphyromonas gingivalis, a major culprit in severe periodontitis today, was virtually undetectable in the pre-contact samples.
Scientific Importance: This research proves that the human oral microbiome was not static throughout history. The distinct lineages found show that human populations co-evolved with their own unique microbial communities. The absence of P. gingivalis suggests that the modern "version" of gum disease may be a product of recent shifts in our microbiome .
This table shows that while the same general types of bacteria are present, their abundance and specific strains can differ dramatically.
| Bacterial Genus | Role in Oral Health | Presence in Pre-Contact Samples | Presence in Modern Industrialized Samples |
|---|---|---|---|
| Tannerella | Associated with periodontal disease | High abundance (unique strains) | Variable abundance |
| Porphyromonas | Key pathogen in gum disease | Very Low / Absent (P. gingivalis) | Common (P. gingivalis often present) |
| Streptococcus | Common pioneer species, can cause cavities | Present | Present |
| Actinomyces | Common in healthy plaque | Present | Present |
This quantifies the stark difference in the presence of a major modern pathogen.
| Pathogen | Function | Prevalence in Pre-Contact Calculus | Prevalence in Modern Populations |
|---|---|---|---|
| Porphyromonas gingivalis | Major contributor to chronic periodontitis | < 2% | ~25-40% |
This highlights the genetic uniqueness of the ancient microbes.
| Strain Source | Number of Unique Gene Variants Identified | Evolutionary Notes |
|---|---|---|
| Pre-Contact Americas | ~150 | Represents a distinct, ancient lineage not found outside the Americas. |
| Modern Global | ~50 | Shows less variation, potentially due to a recent evolutionary bottleneck. |
Visual representation of microbial diversity across different populations
To conduct such delicate research, scientists rely on a specialized toolkit designed to handle fragile ancient DNA.
| Research Tool | Function in the Experiment |
|---|---|
| Ultra-Clean Laboratory | A sterile, pressurized room with UV sterilization to destroy contaminating modern DNA, ensuring the sequences read are truly ancient. |
| Ethylenediaminetetraacetic Acid (EDTA) | A chemical chelator used to slowly dissolve the hard calculus matrix, releasing the trapped DNA without destroying it. |
| Polymerase Chain Reaction (PCR) & Enzymes | Special enzymes and techniques used to make millions of copies of the tiny, damaged ancient DNA fragments, creating enough material for sequencing machines to read. |
| Next-Generation Sequencers | High-tech machines that read the sequence of all DNA fragments in a sample (shotgun metagenomics) in a massively parallel process, generating terabytes of data. |
| Bioinformatics Software | Powerful computer programs that act as "genetic detectives," piecing together sequences, filtering out human DNA, and comparing the rest to global databases to identify ancient microbes. |
Working with ancient DNA presents unique challenges including fragmentation, damage, and potential contamination with modern DNA. Specialized laboratory protocols and computational methods are required to overcome these obstacles.
The computational analysis involves multiple steps: quality control, host DNA removal, taxonomic classification, functional annotation, and comparative analysis against modern microbial databases.
The discovery of distinct microbial lineages in pre-contact Native American ancestors is more than a historical curiosity. It provides a crucial baseline for understanding human health—a glimpse of the oral microbiome as it existed before the massive disruptions of the modern era.
This research, conducted with ethical partnership, tells a dual story: one of incredible biological diversity that has been lost, and one of cultural resilience preserved in an unexpected place.
By studying these microscopic time capsules, we are not only learning about the past but also gaining insights that could inform our future. Understanding which microbes we have lost and how they functioned could lead to new approaches for preventing and treating modern diseases like periodontitis, Crohn's disease, and even diabetes, which are increasingly linked to disruptions in our microbiome.
The story etched in ancient calculus reminds us that we are not just individuals, but walking, talking ecosystems, deeply connected to our history and our world down to the smallest microbe.