Changing perspectives on early hominin diets.

It is axiomatic that knowledge of the diets of extinct hominin species is central to any understanding of their ecology and our evolution. The importance of diet in the paleontological realm has led to the employment of multiple approaches in its elucidation. Some of these have deep historical roots, while others are dependent upon more recent technical and methodological advances. Historically, studies of tooth size, shape, and structure have been the gold standard for reconstructing diet. They focus on species-level adaptations, and as such, they can set theoretical brackets for dietary capabilities within the context of specific evolutionary moments. Other methods (e.g., analyses of dental calculus, biogeochemistry, and dental microwear) have only been developed within the past few decades, but are now beginning to yield evidence of the actual foods consumed by individuals represented by fossil remains. Here we begin by looking at these more "direct" forms of evidence of diet before showing that, when used in conjunction with other techniques, these "multi-proxy" approaches can raise questions about traditional interpretations of early hominin diets and change the nature of paleobiological interpretations.

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus.

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

The evolution and changing ecology of the African hominid oral microbiome.

The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.

Prevalence of rapid calculus formers and its associated factors amongst patients visiting a dental hospital: a preliminary investigation.

BACKGROUND: This study focuses on the determination and classification of patients as rapid or slowcalculusformersbasedontherateofcalculusformationafteroralprophylaxis. It also aims to determine the factors that positively impact the formation and deposition of calculus in patients and identify the factors that accelerate or decelerate the deposition of calculus. METHODS: The study was conducted in the Department of Periodontology, Dr Harvansh Singh Judge Institute of Dental Sciences and Hospital, Panjab University Chandigarh, India. We examined 51 patients after a month of the oral prophylaxis, recorded the amount of calculus present in the oral cavity, and then recorded a detailed history which was briefly divided into Age, Sex, Residence, Oral habits, and maintenance of oral hygiene. RESULTS: An evident and meaningful link was found between age and the rate at which dental calculus forms. The average age of individuals differed significantly between the rapid and slow calculus formers, which could be ascribed to the decline in manual dexterity as age increases, resulting in less effective oral hygiene habits, including toothbrushing. None of the other factors dietary and oral hygiene related could be identified distinctly, probably owing to the small sample of the study. The oral health status exhibited a significant difference between slow and rapid calculus formers. CONCLUSIONS: Within the limitations of the study, the data analyzed, identified age as a significant determinant that impact the rate of formation of calculus in patients and reported a significant difference in the oral health status of rapid and slow calculus formers.

Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus.

Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.

Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species.

Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.

Trends in deamidation across archaeological bones, ceramics and dental calculus.

The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.

Effect of phosphoproteins on intracellular calcification of bacteria.

This study aimed to evaluate the effects of phosphoproteins on bacterial mineralization. Dental calculus formation is attributed to bacterial mineralization in the oral cavity; however, the influence of phosphoproteins (which are abundant in saliva) is not clear. The model bacterium Escherichia coli was suspended in a calcification solution containing casein as a model phosphoprotein. To evaluate mineralization independent of bacterial metabolism, bacteria killed by heat treatment at 70°C were compared with viable bacteria. After incubation at 37°C for 24 h, the mode of calcification was observed using electron microscopy and energy dispersive x-ray spectroscopy. Solutions without casein produced precipitation in solution, which was identical to that in experiments without bacteria. In contrast, calcification solutions with 200 ppm casein only produced calcium phosphate deposition intracellularly. Without heat treatment, intracellular calcification rarely occurred, even when casein was added. Thus, phosphoproteins promoted intracellular calcification of dead bacteria; this is similar to the calcification of insoluble matrices, such as collagen fibrils, promoted by acidic polymers. We concluded that intracellular calcification is caused by the collagen fibril-like behavior of dead bacteria. The promotion of intracellular calcification of dead bacteria by phosphoproteins suggested a basic principle of dental calculus formation.

Association between serum biomarkers and oral health status in children with chronic kidney disease: A cross-sectional study.

OBJECTIVES: The aim of this study was to investigate the association between serum biomarkers and oral health parameters in children with chronic kidney disease (CKD). MATERIALS AND METHODS: Serum hemoglobin, blood urea nitrogen, serum creatinine, calcium, parathormone, magnesium, and phosphorus levels were measured in 62 children with CKD aged between 4 and 17 years. Intraoral examinations of the patients were performed by two different pediatric dentists. Dental caries was assessed using the decayed-missing-filled-teeth (DMFT/dmft) indexes, and oral hygiene was assessed using the debris (DI), calculus (CI), and simplified oral hygiene (OHI-S) indexes. Spearman's rho coefficient and generalized linear modeling were used to examine the association between serum biomarkers and oral health parameters. RESULTS: The results of the study showed that there were negative and statistically significant correlations between serum hemoglobin and creatinine levels and dmft scores in pediatric patients with CKD (p = 0.021 and p = 0.019, respectively). Furthermore, blood urea nitrogen levels and DI and OHI-S scores (p = 0.047 and p = 0.050, respectively); serum creatinine levels and DI, CI, and OHI-S scores (p = 0.005, p = 0.047, p = 0.043, respectively); and parathormone levels and CI and OHI-S scores (p = 0.001 and p = 0.017, respectively) were found to be positively and statistically significantly related. CONCLUSIONS: There are associations between various serum biomarker levels and dental caries and oral hygiene parameters in pediatric patients with CKD. CLINICAL RELEVANCE: The impact of changes in serum biomarkers on oral and dental health is important for dentists' and medical professionals' approaches to patients' oral and systemic health.

Beyond dirty teeth: Integrating dental calculus studies with osteoarchaeological parameters.

The study of ancient human dental calculus (mineralized dental plaque, also known as tartar) is becoming increasingly important in osteoarchaeology, human palaeoecology and environmental archaeology. Microremains of different origin (e.g. starch granules, pollen, phytoliths, feather barbules) as well as biomolecules and chemical compounds retrieved from its mineral matrix may represent an important link between past humans and their physical, biological and social environment, but they are rarely fully linked to the evidence from skeletal remains. This paper critically reviews the lines of evidence retrieved from dental calculus in relation to osteoarchaeological parameters, employing macroscopic, microscopic and biomolecular approaches, assessing synergy potential and limitations. The scope of this paper is also to contribute to the building of a much needed theoretical framework in this emerging subfield.

Dental calculus as a proxy for animal microbiomes.

The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze all previously available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.

More than what we eat: Investigating an alternative pathway for intact starch granules in dental calculus using Experimental Archaeology.

Starch granules and other plant tissues are commonly found as part of the microdebris assemblage analysed within dental calculus. These are often interpreted as evidence of past diets. However, many of the starch granules extracted from dental calculus are intact, and do not show evidence of alterations as a result of being processed for consumption. This research examines if plant material can accidently enter the mouth while being processed for a meal, with a focus on starch granules. Grinding experiments were performed on three types of cereal grains (wheat, oat and millet). We compare the presence of intact and altered starch granules in mouthwash samples (in place of dental calculus samples) from individuals involved in grinding and also from samples in the environment surrounding the grinding activity. This experiment is a proof of concept aimed to expand experimental research in the field of dental calculus analysis and to encourage the exploration of pathways beyond direct and deliberate consumption.

Dental calculus in the industrial age: Human dental calculus in the Post-Medieval period, a case study from industrial Manchester.

The analysis of dental calculus (mineralised dental plaque) has become an increasingly important facet of bioarchaeological research. Although microscopic analysis of microdebris entrapped within dental calculus has revealed important insights into the diet, health, and environment of multiple prehistoric populations, relatively few studies have examined the contributions of this approach to more recent historical periods. In this study, we analyze dental calculus from an English Post-Medieval, middle-class urban skeletal assemblage from Manchester, England using light microscopy. We characterize all types of microremains, observing heavily damaged starch and plant material, high quantities of fungal and yeast spores, the presence of wood particles, plant (cotton) and animal (wool) fibres, as well as limited quantities of microcharcoal and burnt debris. We observe the presence of non-native, imported plant products, including New World maize and potentially tapioca starch. We compare our results to similar studies from earlier time periods to reveal the impacts of the significant economic, social and environmental changes occurring during the Industrial period in England, including changes in food processing, food access, food storage, and air quality. We conclude by outlining important methodological considerations for the future study of Post-Medieval dental calculus and propose potential areas of future research.

Repeatability of dental plaque quantitation by light induced fluorescence technology in current, former, and never smokers.

BACKGROUND: The effects of smoking on the accumulation of dental plaque have not been studied in depth. We compared dental plaque quantitation obtained with a novel light induced fluorescence technology among current, former, and never smokers and verified measurements' repeatability. METHODS: Dental plaque quantitation was objectively assessed by quantitative light induced fluorescence (QLF) technology on three separate study visits in current, former, and never smokers: baseline (day 0), day 7, day 30. Increase in the fluorescence intensity of at least 30% (ΔR30) and 120% (ΔR120) together with the simple oral hygiene (SOH) scoring were considered for analysis. RESULTS: The QLF parameters were highly repeatable in each study group (p < 0.0001, by regression analyses). All QLF parameters showed a significant difference between never smokers and current smokers (p = 0.041 for ΔR30; p = 0.027 for ΔR120; p = 0.04 for SOH). No significant differences were observed between never and former smokers and between current and former smokers except for ΔR120 (p = 0.033). CONCLUSION: Dental plaque measurements by QLF technology were highly reproducible and showed greater plaque formation among current smokers compared to non-smokers. Objective and reproducible quantitation of dental plaque can be a valuable clinical and regulatory science endpoint to investigate the effect of smoking cessation medications, combustion-free tobacco products, and consumer care products on oral health. CLINICAL RELEVANCE: There is a need to objectively evaluate the relationship between smoking and plaque build-up as well as maturation. Current smokers demonstrated greater and more mature plaque buildup when compared to never and former smokers. Differences in plaque build-up and maturation between current, former and non-smokers may be utilized as an effective tool for patient motivation, identifying therapeutic end-points, translational research as well as prognostication. TRIAL REGISTRATION: The study is a pilot study parts of a larger project with registration ID: NCT04649645. As preliminary study, the pilot study referred into this paper started before the larger study registered in ClinicalTrials.gov.

Prevalence and description of dental disorders in skulls of free-living wild primates from Paraná State, Brazil.

BACKGROUND: Non-human primates can present oral diseases. However, differences among the dentition of the various species make it difficult to understand their dental features and associated diseases. This research hypothesizes that the prevalence of dental disorders varies in the species studied according to distinct types of diet. METHODS: Forty-five syncraniums of the species Alouatta caraya, Alouatta guariba clamitans, Sapajus nigritus, Callithrix jacchus, and Callithrix penicillata were evaluated by visual inspection, magnifying glasses, and on cone-beam computed tomography. RESULTS: Disorders identified consisted of missing teeth before death, agenesis, dental calculus, dental wear, dental staining, dental fracture, exposure of pulp chamber, alveolar bone resorption, tooth discoloration, and persistence of deciduous teeth. Alouatta guariba clamitans presented the most disorders. CONCLUSIONS: The results suggest that neotropical primates have a high prevalence of dental changes, even in free-living conditions, and that the differences observed among them may be associated with different diet patterns.

The Hidden Secrets of the Dental Calculus: Calibration of a Mass Spectrometry Protocol for Dental Calculus Protein Analysis.

Dental calculus is a solid deposit that forms and accumulates on the tooth surface, entrapping oral microorganisms, biomolecules, and other micro-debris found in the oral cavity. A mass spectrometry analysis of its protein content opens a vista into the subject's diet, oral flora, and even some aspects of health, thus providing new insight and expanding our knowledge of archaic cultures. Multiple experimental protocols have been proposed for the optimal extraction of proteins from dental calculus. Herein, we compared various experimental conditions in order to calibrate and validate a protocol for protein extraction. Our results show that a high concentration of acetic acid followed by mechanical crushing and sonication provided the highest protein yield, while acetone precipitation enabled the identification of more distinct proteins. We validated this protocol using archeological samples, identifying human and microbial proteins in specimens from the eighth and seventeenth centuries (approximately 250-1300 years ago). These findings demonstrate that the developed protocol is useful for studying excavated archaeological samples and that it might be utilized to explore the biohistory, dietary habits, and microbiome of archaic populations.

Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics.

Over the past two decades, proteomic analysis has greatly developed in application to the field of biomolecular archaeology, coinciding with advancements in LC-MS/MS instrumentation sensitivity and improvements in sample preparation methods. Recently, human dental calculus has received much attention for its well-preserved proteomes locked in mineralized dental plaque which stores information on human diets and the oral microbiome otherwise invisible to other biomolecular approaches. Maximizing proteome recovery in ancient dental calculus, available only in minute quantities and irreplaceable after destructive analysis, is of paramount importance. Here, we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach in order to test the influence of demineralization acid on recovered proteome complexity obtained from specimens as well as the sequence coverages matched for significant proteins. We found that a protocol utilizing EDTA combined with paramagnetic beads increased proteome complexity, in some cases doubling the number of unique peptides and number of proteins matched, compared to protocols involving the use of HCl and either acetone precipitation or ultrafiltration. Although the increase in the number of proteins was almost exclusively of bacterial origin, a development that has implications for the study of diseases within these ancient populations, an increase in the peptide number for the dairy proteins ß-lactoglobulin and casein was also observed reflecting an increase in sequence coverage for these dietary proteins of interest. We also consider structural explanations for the discrepancies observed between these two key dietary proteins preserved in archaeological dental calculus.

Paleomicrobiology of the human digestive tract: A review.

The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.

Dietary evidence from Central Asian Neanderthals: A combined isotope and plant microremains approach at Chagyrskaya Cave (Altai, Russia).

Neanderthals are known primarily from their habitation of Western Eurasia, but they also populated large expanses of Northern Asia for thousands of years. Owing to a sparse archaeological record, relatively little is known about these eastern Neanderthal populations. Unlike in their western range, there are limited zooarchaeological and paleobotanical studies that inform us about the nature of their subsistence. Here, we perform a combined analysis of carbon and nitrogen stable isotopes on bone collagen and microbotanical remains in dental calculus to reconstruct the diet of eastern Neanderthals at Chagyrskaya Cave in the Altai Mountains of Southern Siberia, Russia. Stable isotopes identify one individual as possessing a high trophic level due to the hunting of large- and medium-sized ungulates, while the analysis of dental calculus also indicates the presence of plants in the diet of this individual and others from the site. These findings indicate eastern Neanderthals may have had broadly similar subsistence patterns to those elsewhere in their range.

Exploring late Paleolithic and Mesolithic diet in the Eastern Alpine region of Italy through multiple proxies.

OBJECTIVES: The analysis of prehistoric human dietary habits is key for understanding the effects of paleoenvironmental changes on the evolution of cultural and social human behaviors. In this study, we compare results from zooarchaeological, stable isotope and dental calculus analyses as well as lower second molar macrowear patterns to gain a broader understanding of the diet of three individuals who lived between the end of the Late Pleistocene and the Early Holocene (ca., 17-8 ky cal BP) in the Eastern Alpine region of Italy. MATERIALS AND METHODS: We analyze individuals buried at the sites of Riparo Tagliente (Verona), Riparo Villabruna, and Mondeval de Sora (Belluno). The three burials provide a unique dataset for diachronically exploring the influence of climatic changes on human subsistence strategies. RESULTS: Isotopic results indicate that all individuals likely relied on both terrestrial and freshwater animal proteins. Even though dental calculus analysis was, in part, hindered by the amount of mineral deposit available on the teeth, tooth macrowear study suggests that the dietary habits of the individuals included plant foods. Moreover, differences in macrowear patterns of lower second molars have been documented between Neanderthals and modern humans in the present sample, due to a prevalence of Buccal wear among the former as opposed to higher values of Lingual wear in modern human teeth. DISCUSSION: Isotopic analyses have emphasized the contribution of animal proteins in the diet of the three foragers from the Eastern Alpine region. The possible intake of carbohydrate-rich plant foods, suggested by the retrieval of plant remains in dental calculus, is supported by the signal of macrowear analysis. Moreover, the latter method indicates that the distribution of macrowear in lower second molars (M2 s) allows us to discriminate between Neanderthals and modern humans within the present reference sample. Overall, our results show these three prehistoric hunter-gatherers were well adapted to the environment in which they lived exploiting many natural resources.