The importance of commensal microbes for human health is increasingly recognized [1][2][3][4][5] , yet the impacts of evolutionary changes in human diet and culture on commensal microbiota remain almost unknown. Two of the greatest dietary shifts in human evolution involved the adoption of carbohydrate-rich Neolithic (farming) diets 6,7 (beginning ~10,000 years BP 6,8 ), and the more recent advent of industrially processed flour and sugar (~1850) 9 . Here, we show that calcified dental plaque (dental calculus) on ancient teeth preserves a detailed genetic record throughout this period. Data from 34 early European skeletons indicate that the transition from hunter-gatherer to farming shifted the oral microbial community to a disease-associated configuration. The composition of oral microbiota remained surprisingly constant between Neolithic and Medieval times, after which (the now ubiquitous) cariogenic bacteria became dominant, apparently during the Industrial Revolution. Modern oral microbiota are markedly less diverse than historic Sequence data have been deposited in Genbank under accession ERP002107.The authors declare no competing financial interests. Europe PMC Funders GroupAuthor Manuscript Nat Genet. Author manuscript; available in PMC 2014 April 23. Commensal microbiota comprise the majority of cells in the body and play a key role in human health [1][2][3][4][5]10 . However, their evolution remains poorly understood, and detailed genetic records from commensal bacteria have yet to be recovered from the archaeological record. Dental calculus is ubiquitous in both present-day and ancient human populations 11 , and microscopic analysis has shown that it accurately preserves bacterial morphology over millennia [12][13][14] . Dental calculus develops when dental plaque, an extremely dense bacterial biofilm 15 , becomes mineralised with calcium phosphate 16 . Bacteria in calculus become locked in a crystalline matrix similar to bone 16 (Supplementary Figure 1), with deposits occurring both above and below the gum or gingiva (supra-and subgingivally) 17 . Calculus represents one of the few sources of preserved human and hominid microbiota, and genetic analysis has the potential to create a powerful new record of past dietary impacts, health changes, and oral pathogen genomic evolution deep into the past. In addition, oral bacteria are transferred vertically from the primary caregiver(s) in early childhood 18 and horizontally between family members later in life 18,19 , making archaeological dental calculus a potentially unique means of tracing population structure, movement and admixture between ancient cultures, as well as the spread of diseases.The increased consumption of domesticated cereals (wheat and barley in the Near East) beginning with the Neolithic was associated with a marked increase in prevalence of dental calculus and oral pathology 20 . These oral diseases include dental caries (tooth decay) 1 and periodontal disease (an infection causing damage to the supporting connective tissues of ...

The processes which shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42kyrs ago and the immigration of Neolithic farmers into Europe ~8kyrs ago appear to have played important roles, but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5,500–1,550 cal BC). We use this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.

The first farmers from Central Europe reveal a genetic affinity to modern-day populations from the Near East and Anatolia, which suggests a significant demographic input from this area during the early Neolithic.

Haplogroup H dominates present-day Western European mitochondrial DNA variability (440%), yet was less common (B19%) among Early Neolithic farmers (B5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this 'real-time' genetic data with cultural changes taking place between the Early Neolithic (B5450 BC) and Bronze Age (B2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (B4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (B2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high‐throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no‐template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long‐term contaminant diversity. We additionally compared the contaminant content within a home‐made silica‐based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human‐associated taxa in comparison to the home‐made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low‐biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high‐throughput metagenomic study.

Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3–V4 region) to compare microbial communities in layers ranging in pH from 4.5–7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies.

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Children’s oral health is in a dire state, with dental decay (caries) being one of the most common chronic diseases. While the role of bacteria in the oral microbiome and dental caries is established, the contribution of fungi is relatively unknown. We assessed the oral mycobiome in childhood (n = 17), to determine if the composition of fungi varies between children with and without caries. Oral mycobiome composition was assessed by using Illumina MiSeq to sequence the ITS2 region, which was amplified from dental plaque. This revealed that the oral mycobiome in the investigated children contained 46 fungal species. Candida albicans was the most abundant species and was ubiquitous in all samples, indicating this species may not be involved in caries development as previously suggested. While the overall diversity of fungi was similar, independent of caries status (p > 0.05), we found caries influenced the abundance of specific fungi. Children without caries had a significantly higher abundance of 17 species compared to children with caries, which had three enriched species (p < 0.001). While the differentially abundant species between health and caries may be specific to an Australian population, our findings indicate the mycobiome plays a role in oral health.