A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus

Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain

“…To minimize contamination, samples were processed in an ultra-sterile, specialized ancient DNA laboratory and underwent a decontamination protocol, as previously published 39 . Samples underwent an in-house, silica-based DNA extraction, as previously described 20,57,58 . Extraction blank controls (EBCs) were incorporated throughout to monitor laboratory and reagent contamination at a ratio of two EBCs to ten samples, as well as no template controls (NTCs) during the amplification process 59 .…”

A Journey into the Evolution of Human Host-Oral Microbiome Relationship through Ancient Dental Calculus: A Scoping Review

“…The NGS method has contributed also to overcoming many limitations in the use of other molecular methods of pathogenic identification by enhancing investigative potential with meaningful data regarding genetic mutations, genomic rearrangement, and, more generally, the evolution of pathogens [11,12,14,19,20]. The ability to clarify eating habits, lifestyle, and health status through dental calculus, dietary microfossils, or calcified bacterial cells has been integrated through the NGS method, defining the microbiome that in ancient times contributed to the delicate balance between health and disease, as it does today [20][21][22][23][24][25]. This experimental genetic approach identifies ancient dental calculus as the preferred oral substrate because, despite the small quantities from archaeological finds, it has proved to be the best reserve of microorganisms associated with high-quality biomolecules to advance our knowledge on the bacterial/oral health status, mainly related to periodontium [26].…”

“…It is found in the common microbiota associated with primary endodontic infection [26]. The P. micra is a Gram-positive anaerobic coccus isolated from multiple polymicrobial infections such as periapical and endoperiodontal lesions, periapical abscesses and periodontitis [25], while P. alactolyticus, is an anaerobic Gram-positive rod considered by some authors as a good candidate for participation in the etiology of different forms of periradicular diseases. Moreover, it is amongst the most frequently identified microorganisms in the root canal of necrotic teeth associated with acute periapical abscesses [26].…”

“…In contrast, gingivitis is associated with high levels of anaerobic bacteria, especially the Gram-negative proteolytic species belonging to the genera Fusobacterium, Prevotella, Treponema, Prophyromonas and Tannerella (the last three known as the "red complex") detectable in periodontal pockets [30]. The "red complex" acts synergically secreting virulence factors, leading to the inflammation of the host periodontal tissue, bone immuno-inflammatory resorption and chronic periodontitis and other forms of periodontal disease [25,26]. The current state of knowledge on oral microbiology and on the role of the microbiome in favouring or protecting the host from the onset of the most common oral diseases, such as caries and periodontitis, leads us to consider a much more varied population of microorganisms which, in the form of organised colonies, act on the state of health and disease of the oral cavity [31,32].…”