Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth.

Christelle Desnues,Kolawole Adekola,Gérard Chouin,Hong Huynh,Gérard Aboudharam,Yves Desfosses,Michel Drancourt,Michel Signoli,Patrice Georges-Zimmermann,Nicolás Rascovan

doi:10.1038/s41522-016-0008-8

Abstract

Ancient dental pulps are highly precious samples because they conserve DNA from humans and blood-borne pathogens for ages. However, little is known about the microbial communities present in dental pulps. Here, we analyzed ancient and modern dental pulp samples from different time periods and geographic regions and found that they are colonized by distinct microbial communities, which can be differentiated from other oral cavity samples. We found that despite the presence of environmental bacteria, ancient dental pulps conserve a clear and well-conserved record of oral microbes. We were able to detect several different oral pathogens in ancient and modern dental pulps, which are commonly associated with periodontal diseases. We thus showed that ancient dental pulps are not only valuable sources of DNA from humans and systemic infections, but also an open window for the study of ancient oral microbiomes.

Highlights

The dental pulp is the internal portion of teeth that contains highly vascularized soft tissues, which are protected by hard and mineralized structures
We analyzed 16S rRNA amplicon sequencing data sets from ancient and modern dental pulps and provide an unprecedented exploration of their associated microbiomes. We combined these samples with other data sets generated by different laboratories and grouped them in eight categories: (1) Ancient dental pulps, (2) Modern dental pulps, (3) Modern root canals, (4) Ancient complete teeth that were ground and homogenized, (5) Modern oral cavity surfaces, (6) Saliva, (7) Ancient dental calculus, and (8) Soils
A beta-diversity analysis based on the unweighted Unifrac (UU) distance showed an overlap between modern and some of the ancient dental pulp samples, which were markedly different from ancient dental calculus, modern saliva, and oral cavity samples (Fig. 1a)

Summary

Introduction

The dental pulp is the internal portion of teeth that contains highly vascularized soft tissues, which are protected by hard and mineralized structures (cementum, enamel, and dentin). A beta-diversity analysis based on the unweighted Unifrac (UU) distance showed an overlap between modern and some of the ancient dental pulp samples, which were markedly different from ancient dental calculus, modern saliva, and oral cavity samples (Fig. 1a).

Results

Conclusion