Oral health status in historic population: Macroscopic and metagenomic evidence

Abstract

Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.

Oral microbiome diversity in chimpanzees from Gombe National Park

“…Although we did observe differences in abundances between MetaPhlAn2 and MALT both showed low abundance of T . forsythia in chimpanzees, which was also shown in a previous study of human dental calculus to be in very high abundance (using MALT) 24 . Additionally, for degraded material, MALT (using BLASTn) was found to be the most accurate method for determining taxonomic information from shotgun sequences 25 .

Figure 6Box plots of normalized species abundance from MEGAN for all three red complex bacteria across Neanderthals, anatomically modern humans, and chimpanzees.

…”

In vivo Microbial Diversity Analysis on Different Surfaces of Dental Restorative Materials via 16S rDNA Sequencing

“…These differences between bacteria species have played a role in oral diseases, which cannot be ignored. The increase in Firmicutes has been confirmed as being closely related to dental caries in many studies [ 20 , 25 , 28 , 29 ], Streptococcus are Gram-positive bacteria and are often presented in the supragingival plaque; they are associated with the occurrence of dental caries [ 30 , 31 ]. Porphyromonas species is a Gram-negative bacterium that is often found in the subgingival plaque and is often associated with periodontal disease [ 8 , 32 , 33 ].…”

Effect of silver diammine fluoride on micro-ecology of plaque from extensive caries of deciduous teeth - in vitro study

“…The end products of its fermentation are formate, acetate, butyrate, caproate, and hydrogen [41]. It can cause periapical infection [42][43][44], it often found in deep dentin caries [30,45] and infected root canals [41]. Similarly, Fusobacterium is often detected in deep dentin caries [30,45] and infected root canals [43,44,46].…”