Comparing Modern and Ancient Biomes

Recent Editor’s Note columns have discussed new findings concerning the gut and oral microbiomes of modern humans. This month, I wish to focus on the microbiomes of our ancestors, and the similarities and differences in bacteria between modern and ancient man. Compared to modern samples, studies of ancient human fecal samples by Tito et al1 found dramatic differences in the gut microbiome. These changes apparently occurred after the Industrial Revolution, and seem to be associated with the introduction of antibiotics.

Warinner and colleagues2 studied the oral biomes of four individuals who were buried in a monastic site in a medieval town in Germany. This study presented a high-resolution characterization of the oral microbiome recovered from dental calculus from these individuals, who died with mild to severe periodontitis. The researchers extracted DNA and proteins from ground samples of both supra- and subgingival deposits. Among their goals was understanding what changes, if any, might have occurred in the microbiome over time. The team sequenced the DNA using shotgun meta-genomics and identified 40 pathogens, as well as genes that have been shown to provide resistance to antibiotics. Of particular interest was their finding that bacteria associated with the development of periodontitis in modern man were present in this older group. While there are a number of similarities in the bacteria in modern humans and our predecessors, research by Adler et al3 has shown an increase in some pathogens that occurred after the onset of the Industrial Revolution, and in a fashion similar to that seen in the gut.


Warinner et al2 performed extensive sequencing of one of the bacteria from the red complex associated with periodontitis, and specifically looked at the genetic sequence of Tannerella forsythia. Interestingly, in the more ancient samples, they did not find the gene that provides resistance to tetracycline. By contrast, it was found in the bacteria taken from modern humans. This indicates an evolution of this particular bacterium to our detriment. The team attributed this genetic alteration to the widespread use of antibiotics. They also found genes that would help bacteria evade the human immune system, thus preserving the bacteria’s ability to populate and cause disease.

How do these findings apply to our patients? First, we should be aware that bacteria associated with periodontal disease have been invading human hosts for at least 1000 years or more. In so doing, they have developed resistance to antibiotics and found ways to evade the human immune system. This means the probability of removing these pathogens using current technology is slim, at best. It also underscores the need for ongoing research into ways to permanently eliminate these pathogens. As practitioners, we must continue our efforts to change human behavior to the extent that our patients will remove biofilm on a daily basis. The basic message? Magic cures and mouthwashes aside, you still have to floss.

Thomas G. Wilson Jr., DDS
Editor in Chief


  1. Tito RY, Knights D, Metcalf J, et al. Insights from characterizing extinct human gut microbiomes. PLOS ONE. 2012;7:e51146.
  2. Warinner C, Rodrigues JF, Vyas R, et al. Pathogens and host immunity in the ancient human oral cavity. Nat Genet. 2014;46:336–344.
  3. 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. 2013;45:450–455.

From Decisions in Dentistry. July 2017;3(7):8.

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