How scientists are reconstructing ancient human microbiomes to understand health evolution and modern diseases
Imagine if, instead of bones and artifacts, the most telling story about our ancestors came from the trillions of invisible microbes that lived in and on their bodies.
What if the bacteria in the gut of a Neolithic farmer could speak across millennia to tell us about their diet, their health, and even why we get sick today? This isn't science fiction—it's the cutting-edge field of bioarchaeology of the human microbiome, where scientists are reconstructing our ancestral microbial selves to understand everything from the rise of modern diseases to what it truly means to be human.
Our bodies contain at least as many bacterial cells as human cells
Key Insight: We are not singular organisms but complex walking ecosystems, with the collective genetic material of our microbiome forming what's known as the "hologenome" .
The human microbiome comprises bacteria, archaea, viruses, and eukaryotes that reside within and outside our bodies 9 . These organisms impact human physiology, both in health and in disease, contributing to the enhancement or impairment of metabolic and immune functions 9 .
Often called "calcified plaque," dental calculus is an exceptional preservation medium that forms incrementally throughout life and can survive for thousands of years in the archaeological record 8 .
As one researcher aptly noted, "Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome" 8 .
Palaeofaeces (ancient human feces) provide an even more direct window into the ancestral gut microbiome.
A landmark 2021 study published in Nature successfully reconstructed 498 microbial genomes from 1,000-2,000-year-old palaeofaeces samples from the southwestern USA and Mexico 4 .
| Body Site | Relative Microbial Density | Dominant Microbial Types | Preservation Potential |
|---|---|---|---|
| Gastrointestinal Tract | 29% (highest) | Anaerobes (Bacteroides, Prevotella) | High (palaeofaeces) |
| Oral Cavity | 26% | Facultative anaerobes (Streptococcus) | Very High (dental calculus) |
| Skin | 21% | Aerobes (Staphylococcus, Corynebacterium) | Low |
| Respiratory Tract | 14% | Aerobes | Very Low |
| Urogenital Tract | 9% (lowest) | Lactobacillus | Low |
Recovering genetic material from ancient samples requires specialized approaches because ancient DNA is typically highly fragmented and contaminated with environmental DNA 4 .
Researchers must first establish that samples are truly ancient and human-derived, using multiple methods including damage pattern analysis and host DNA identification 4 .
Samples are collected under controlled conditions to prevent modern contamination, followed by specialized DNA extraction protocols optimized for fragmented ancient DNA 3 4 .
Unlike targeted approaches that only identify known microbes, this method sequences all DNA fragments in a sample, allowing researchers to reconstruct complete microbial genomes—even from previously unknown species 4 .
Ancient DNA exhibits characteristic damage patterns at molecule ends, which helps distinguish genuine ancient sequences from modern contaminants 4 .
Sophisticated computational tools assemble the millions of DNA fragments into coherent genomes, binning them by species and assessing their quality and completeness 4 .
Discovery: This comprehensive approach has revealed that a staggering 39% of the reconstructed ancient microbial species represent previously unknown taxa 4 , highlighting how much of our microbial heritage has been lost or transformed.
In 2021, a groundbreaking study published in Nature successfully reconstructed ancient gut microbiomes from 1,000-2,000-year-old palaeofaeces samples from the southwestern United States and Mexico 4 . This research provided unprecedented insights into how the human gut microbiome has changed between pre-industrial and modern societies.
The team began with 15 potential palaeofaeces samples but excluded 7 that showed evidence of soil contamination, poor DNA preservation, or non-human origins. The remaining 8 samples underwent rigorous authentication, including analysis of DNA damage patterns and identification of host DNA to confirm their human origin 4 .
Using specialized protocols for ancient DNA, the team extracted and sequenced genetic material from the samples. The DNA fragments were notably short (averaging 174 base pairs), which is characteristic of ancient DNA 4 .
The ancient microbiomes were compared to 789 present-day gut microbiome samples from both industrialized and non-industrialized populations across eight countries, providing crucial context for interpreting the findings 4 .
Rather than just identifying known microbes, the team used advanced computational methods to reconstruct complete microbial genomes from the fragmented DNA, enabling the discovery of previously unknown species 4 .
The findings revealed striking differences between ancient, non-industrial, and industrial gut microbiomes:
| Characteristic | Ancient Microbiomes | Modern Industrialized Microbiomes | Health Implications |
|---|---|---|---|
| Diversity | Higher overall diversity | Lower diversity | Reduced diversity linked to immune and metabolic disorders |
| Specific Taxa | Enriched in Spirochaetes, Prevotellaceae | Enriched in Bacteroidaceae, Akkermansia | Loss of fiber-degrading microbes may affect digestive health |
| Functional Genes | Lower antibiotic resistance | Higher antibiotic resistance | Reflects widespread antibiotic use in modern society |
| Mobile Genetic Elements | Higher abundance | Lower abundance | Suggests ancient microbes were more genetically dynamic |
Bioarchaeological microbiome research requires specialized reagents and materials to overcome the challenges of working with ancient, degraded genetic material.
| Research Tool | Specific Function | Application in Ancient Microbiome Research |
|---|---|---|
| Shotgun Metagenomic Sequencing | Sequences all DNA fragments in a sample without targeting specific organisms | Allows reconstruction of complete microbial genomes, including previously unknown species 4 |
| DNA Damage Pattern Analysis | Identifies characteristic chemical changes in ancient DNA | Authenticates ancient specimens and distinguishes them from modern contaminants 4 |
| Metagenome-Assembled Genomes (MAGs) | Computational approach to group DNA fragments into complete genomes | Enables reconstruction of ancient microbial genomes from fragmented DNA 4 |
| Sterile Sampling Protocols | Prevents introduction of modern contaminants during collection | Maintains sample integrity for accurate analysis 3 |
| MIxS-MIMS Standards | Standardized reporting framework for microbiome data | Ensures comparability between studies and facilitates data sharing 5 7 |
| Bioinformatic Pipelines | Computational tools for processing and analyzing sequencing data | Handles unique challenges of ancient DNA including fragmentation and damage 4 |
The reconstruction of ancient microbiomes isn't just an academic exercise—it has profound implications for understanding and treating modern diseases. The "disappearing microbiome" hypothesis suggests that the loss of microbial diversity associated with industrialized lifestyles contributes to the increasing prevalence of chronic diseases like obesity, autoimmune disorders, and allergies 4 6 .
Future research aims to better understand human microbial evolution across different populations and time periods .
Researchers are working on improved techniques for cultivating and studying newly discovered ancient microbial species 4 .
Future studies will work to create clearer connections between specific microbial taxa and health outcomes 6 .
Efforts are underway to establish reporting frameworks like the STORMS checklist to improve research quality and comparability 7 .
Therapeutic Potential: Understanding which specific microbes we've lost—and what functions they performed—opens up exciting possibilities for microbiome-based therapeutics. If researchers can identify ancient microbial species that provided protective effects against modern diseases, these could potentially be developed into next-generation probiotics 6 .
The bioarchaeology of the human microbiome represents a remarkable convergence of archaeology, microbiology, and genomics, allowing us to recover a part of our biological heritage that was until recently considered lost to time.
By analyzing the microbial DNA preserved in ancient dental calculus and palaeofaeces, researchers have revealed dramatic changes in our internal ecosystems that parallel the rise of industrialization and modern chronic diseases.
This research fundamentally challenges our notion of what it means to be human, suggesting that we should view ourselves as "meta-organisms" comprised of both human and microbial components that have co-evolved over millennia 2 . As we continue to uncover the secrets of our ancestral microbes, we may find solutions to some of modern medicine's most pressing challenges—all by listening to the whispers of our microscopic past.
References will be added in the final publication.