Abstract
The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.
Highlights
Palaeomicrobiology is an important and growing area of archaeological [1] and microbiological [2] research
The promise of palaeomicrobiology has been tempered by the uneven quality of research; the field has been plagued, so to speak, by high profile controversies [15,16,17,18,19], and bold claims made on the basis of modest, incomplete, or problematic evidence have been met with scepticism, doubt or outright rejection by the broader ancient DNA community [20,21]
The hard tissues of the teeth provide two microbial habitats, one above and one below the gingival margin, resulting in two distinctive plaque communities known as supragingival and subgingival plaque, respectively [63,64]. These two habitats differ in redox potential and nutrient sources, with supragingival plaque forming in a more aerobic environment fed by nutrients of primarily salivary origin and subgingival plaque forming in a mostly anaerobic environment fed by gingival crevicular fluid (GCF), an inflammatory exudate of the gingiva
Summary
Palaeomicrobiology is an important and growing area of archaeological [1] and microbiological [2] research. A major recent advancement in palaeomicrobial research has been the discovery that dental calculus acts as a long-term reservoir of high-quality biomolecules from human-associated microorganisms [35,36,37,38,39] While this substrate was previously recognized to contain calcified bacterial cells [40] and dietary microfossils [41,42,43,44], and was later shown to preserve host mitochondrial DNA [36] and biomolecules from a few select bacterial species [36,37], the application of high-throughput sequencing has allowed the recovery of entire ancient microbial communities [35,39], known as the native human microbiota or ‘microbiome’ [45]. This paper will discuss the potential of ancient microbiome research, as well as current methodological challenges
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