Archaeological dental calculus reveals patterns of dietary shifts related to the farming transition in Africa

Abstract: Archaeological dental calculus represents a depositional environment that entraps oral microbes, and debris of dietary, environmental, and cultural material that entered the mouth throughout the host’s life. Hence, they represent valuable archives of information about the host’s lifestyle, health, and environment. The aim of this study was to identify if the farming transition and its’ associated change in diet composition, may have influenced species composition in the oral cavity. To shed some light into the evolution of ancient oral microbiomes from Africa, 3 novel Iron Age dental calculus metagenomes together with a comparative dataset of 18 archaeological dental calculus metagenomes from North African Upper Palaeolithic, Later Stone Age, Iron Age, and 18th-19th century populations where analysed. Shotgun sequencing data was used to reconstruct 21 oral metagenomes from the past 15,000 years. This study found an oral microbiome that has been maintained from the Upper Palaeolithic (North Africa) to the 19th Century. However, closer examination to the relative abundance of three keystone species of the subgingival plaque, portray a chronological evolution that reflects that of its host during the major dietary and cultural transition that occurred during the farming revolution in the Iron Age.