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.

High conservation of the dental plaque microbiome across populations with differing subsistence strategies and levels of market integration.

Industrialization-including urbanization, participation in the global food chain and consumption of heavily processed foods-is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome is largely speculative. Multiple ecologically distinct surfaces in the mouth, each harbouring a unique microbial community, pose a challenge to assessing changes in the oral microbiome in the context of industrialization, as the results depend on the oral site under study. Here, we investigated whether microbial communities of dental plaque, the dense biofilm on non-shedding tooth surfaces, are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe (n = 38). We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, which may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.

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.

Seasonal and habitat effects on the nutritional properties of savanna vegetation: Potential implications for early hominin dietary ecology.

The African savannas that many early hominins occupied likely experienced stark seasonality and contained mosaic habitats (i.e., combinations of woodlands, wetlands, grasslands, etc.). Most would agree that the bulk of dietary calories obtained by taxa such as Australopithecus and Paranthropus came from the consumption of vegetation growing across these landscapes. It is also likely that many early hominins were selective feeders that consumed particular plants/plant parts (e.g., leaves, fruit, storage organs) depending on the habitat and season within which they were foraging. Thus, improving our understanding of how the nutritional properties of potential hominin plant foods growing in modern African savanna ecosystems respond to season and vary by habitat will improve our ability to model early hominin dietary behavior. Here, we present nutritional analyses (crude protein and acid detergent fiber) of plants growing in eastern and southern African savanna habitats across both wet and dry seasons. We find that many assumptions about savanna vegetation are warranted. For instance, plants growing in our woodland habitats have higher average protein/fiber ratios than those growing in our wetland and grassland transects. However, we find that the effects of season and habitat are complex, an example being the unexpectedly higher protein levels we observe in the grasses and sedges growing in our Amboseli wetlands during the dry season. Also, we find significant differences between the vegetation growing in our eastern and southern African field sites, particularly among plants using the C4 photosynthetic pathway. This may have implications for the differences we see between the stable carbon isotope compositions and dental microwear patterns of eastern and southern African Paranthropus species, despite their shared, highly derived craniodental anatomy.

Dental calculus indicates widespread plant use within the stable Neanderthal dietary niche.

The ecology of Neanderthals is a pressing question in the study of hominin evolution. Diet appears to have played a prominent role in their adaptation to Eurasia. Based on isotope and zooarchaeological studies, Neanderthal diet has been reconstructed as heavily meat-based and generally similar across different environments. This image persists, despite recent studies suggesting more plant use and more variation. However, we have only a fragmentary picture of their dietary ecology, and how it may have varied among habitats, because we lack broad and environmentally representative information about their use of plants and other foods. To address the problem, we examined the plant microremains in Neanderthal dental calculus from five archaeological sites representing a variety of environments from the northern Balkans, and the western, central and eastern Mediterranean. The recovered microremains revealed the consumption of a variety of non-animal foods, including starchy plants. Using a modeling approach, we explored the relationships among microremains and environment, while controlling for chronology. In the process, we compared the effectiveness of various diversity metrics and their shortcomings for studying microbotanical remains, which are often morphologically redundant for identification. We developed Minimum Botanical Units as a new way of estimating how many plant types or parts are present in a microbotanical sample. In contrast to some previous work, we found no evidence that plant use is confined to the southern-most areas of Neanderthal distribution. Although interpreting the ecogeographic variation is limited by the incomplete preservation of dietary microremains, it is clear that plant exploitation was a widespread and deeply rooted Neanderthal subsistence strategy, even if they were predominately game hunters. Given the limited dietary variation across Neanderthal range in time and space in both plant and animal food exploitation, we argue that vegetal consumption was a feature of a generally static dietary niche.

The diet of Australopithecus sediba.

Specimens of Australopithecus sediba from the site of Malapa, South Africa (dating from approximately 2 million years (Myr) ago) present a mix of primitive and derived traits that align the taxon with other Australopithecus species and with early Homo. Although much of the available cranial and postcranial material of Au. sediba has been described, its feeding ecology has not been investigated. Here we present results from the first extraction of plant phytoliths from dental calculus of an early hominin. We also consider stable carbon isotope and dental microwear texture data for Au. sediba in light of new palaeoenvironmental evidence. The two individuals examined consumed an almost exclusive C(3) diet that probably included harder foods, and both dicotyledons (for example, tree leaves, fruits, wood and bark) and monocotyledons (for example, grasses and sedges). Like Ardipithecus ramidus (approximately 4.4 Myr ago) and modern savanna chimpanzees, Au. sediba consumed C(3) foods in preference to widely available C(4) resources. The inferred consumption of C(3) monocotyledons, and wood or bark, increases the known variety of early hominin foods. The overall dietary pattern of these two individuals contrasts with available data for other hominins in the region and elsewhere.

To meat or not to meat? New perspectives on Neanderthal ecology.

Neanderthals have been commonly depicted as top predators who met their nutritional needs by focusing entirely on meat. This information mostly derives from faunal assemblage analyses and stable isotope studies: methods that tend to underestimate plant consumption and overestimate the intake of animal proteins. Several studies in fact demonstrate that there is a physiological limit to the amount of animal proteins that can be consumed: exceeding these values causes protein toxicity that can be particularly dangerous to pregnant women and newborns. Consequently, to avoid food poisoning from meat-based diets, Neanderthals must have incorporated alternative food sources in their daily diets, including plant materials as well.

Plant foods and the dietary ecology of Neanderthals and early modern humans.

One of the most important challenges in anthropology is understanding the disappearance of Neanderthals. Previous research suggests that Neanderthals had a narrower diet than early modern humans, in part because they lacked various social and technological advances that lead to greater dietary variety, such as a sexual division of labor and the use of complex projectile weapons. The wider diet of early modern humans would have provided more calories and nutrients, increasing fertility, decreasing mortality and supporting large population sizes, allowing them to out-compete Neanderthals. However, this model for Neanderthal dietary behavior is based on analysis of animal remains, stable isotopes, and other methods that provide evidence only of animal food in the diet. This model does not take into account the potential role of plant food. Here we present results from the first broad comparison of plant foods in the diets of Neanderthals and early modern humans from several populations in Europe, the Near East, and Africa. Our data comes from the analysis of plant microremains (starch grains and phytoliths) in dental calculus and on stone tools. Our results suggest that both species consumed a similarly wide array of plant foods, including foods that are often considered low-ranked, like underground storage organs and grass seeds. Plants were consumed across the entire range of individuals and sites we examined, and none of the expected predictors of variation (species, geographic region, or associated stone tool technology) had a strong influence on the number of plant species consumed. Our data suggest that Neanderthal dietary ecology was more complex than previously thought. This implies that the relationship between Neanderthal technology, social behavior, and food acquisition strategies must be better explored.

Microfossils in calculus demonstrate consumption of plants and cooked foods in Neanderthal diets (Shanidar III, Iraq; Spy I and II, Belgium).

The nature and causes of the disappearance of Neanderthals and their apparent replacement by modern humans are subjects of considerable debate. Many researchers have proposed biologically or technologically mediated dietary differences between the two groups as one of the fundamental causes of Neanderthal disappearance. Some scenarios have focused on the apparent lack of plant foods in Neanderthal diets. Here we report direct evidence for Neanderthal consumption of a variety of plant foods, in the form of phytoliths and starch grains recovered from dental calculus of Neanderthal skeletons from Shanidar Cave, Iraq, and Spy Cave, Belgium. Some of the plants are typical of recent modern human diets, including date palms (Phoenix spp.), legumes, and grass seeds (Triticeae), whereas others are known to be edible but are not heavily used today. Many of the grass seed starches showed damage that is a distinctive marker of cooking. Our results indicate that in both warm eastern Mediterranean and cold northwestern European climates, and across their latitudinal range, Neanderthals made use of the diverse plant foods available in their local environment and transformed them into more easily digestible foodstuffs in part through cooking them, suggesting an overall sophistication in Neanderthal dietary regimes.

Reconstructing dietary practices at Tell Kamid el-Loz (Lebanon) during the Bronze and Iron Age III / Persian to Hellenistic periods using plant micro-remains from dental calculus and stable isotope analysis of bone collagen.

Tell Kamid el-Loz (Lebanon) was an important Bronze Age urban center that dominated one of the central crossroads of the Ancient Near East, connecting Egypt and the Levant with northern Mesopotamia, Anatolia, and Syria, as well as the interior with the Mediterranean coast. However, by the early Iron Age, the site had shrunk to a small rural settlement. Later, in the Iron Age III / Persian-Hellenistic, only enigmatic pits and a large cemetery remained. In this paper, we analyzed plant micro-remains from the dental calculus of 15 individuals (3 from the Middle Bronze Age II and 12 from the Iron Age III / Persian-Hellenistic) and δ 13C and δ 15N stable isotope data from tbulk bone collagen of 74 individuals (10 from the Middle Bronze Age II and 64 from the Iron Age III / Persian-Hellenistic) and 13 Late Bronze Age animal bones (7 Ovis/Capra and 6 Bos). Our results indicate general stability of human diet throughout the Middle Bronze Age II and the Iron III / Persian-Hellenistic periods, with a reliance on C3 plant crops and terrestrial animals also consuming C3 plants. In the later period, the plant micro-remains indicate the consumption of C4 plants and sedges, and the stable isotope analysis indicates differences in diet between males and females. Supplementary Information: The online version contains supplementary material available at 10.1007/s12520-024-02000-w.

Synchrotron radiation-based phase-contrast microtomography of human dental calculus allows nondestructive analysis of inclusions: implications for archeological samples.

Purpose: Dental calculus forms on teeth during the life of an individual and its investigation can yield information about diet, health status, and environmental pollution. Currently, the analytical techniques used to visualize the internal structure of human dental calculus and entrapped inclusions are limited and require destructive sampling, which cannot always be justified. Approach: We used propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SR- µ CT ) to non-destructively examine the internal organization of dental calculus, including its microstructure and entrapped inclusions, on both modern and archeological samples. Results: The virtual histological exploration of the samples shows that PPC-SR- µ CT is a powerful approach to visualize the internal organization of dental calculus. We identified several important features, including previously undetected negative imprints of enamel and dentine growth markers (perikymata and periradicular bands, respectively), the non-contiguous structure of calculus layers with multiple voids, and entrapped plant remains. Conclusions: PPC-SR- µ CT is an effective technique to explore dental calculus structural organization, and is especially powerful for enabling the identification of inclusions. The non-destructive nature of synchrotron tomography helps protect samples for future research. However, the irregular layers and frequent voids reveal a high heterogeneity and variability within calculus, with implications for research focusing on inclusions.

Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation.

The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.

Phytoliths can cause tooth wear.

Comparative laboratory sliding wear tests on extracted human molar teeth in artificial saliva with third-body particulates demonstrate that phytoliths can be as effective as silica grit in the abrasion of enamel. A pin-on-disc wear testing configuration is employed, with an extracted molar cusp as a pin on a hard disc antagonist, under loading conditions representative of normal chewing forces. Concentrations and sizes of phytoliths in the wear test media match those of silica particles. Cusp geometries and ensuing abrasion volumes are measured by digital profilometry. The wear data are considered in relation to a debate by evolutionary biologists concerning the relative capacities of intrinsic mineral bodies within plant tissue and exogenous grit in the atmosphere to act as agents of tooth wear in various animal species.

Dental calculus evidence of Taï Forest Chimpanzee plant consumption and life history transitions.

Dental calculus (calcified dental plaque) is a source of multiple types of data on life history. Recent research has targeted the plant microremains preserved in this mineralised deposit as a source of dietary and health information for recent and past populations. However, it is unclear to what extent we can interpret behaviour from microremains. Few studies to date have directly compared the microremain record from dental calculus to dietary records, and none with long-term observation dietary records, thus limiting how we can interpret diet, food acquisition and behaviour. Here we present a high-resolution analysis of calculus microremains from wild chimpanzees (Pan troglodytes verus) of Taï National Park, Côte d'Ivoire. We test microremain assemblages against more than two decades of field behavioural observations to establish the ability of calculus to capture the composition of diet. Our results show that some microremain classes accumulate as long-lived dietary markers. Phytolith abundance in calculus can reflect the proportions of plants in the diet, yet this pattern is not true for starches. We also report microremains can record information about other dietary behaviours, such as the age of weaning and learned food processing techniques like nut-cracking.

Earliest evidence of dental caries manipulation in the Late Upper Palaeolithic.

Prehistoric dental treatments were extremely rare, and the few documented cases are known from the Neolithic, when the adoption of early farming culture caused an increase of carious lesions. Here we report the earliest evidence of dental caries intervention on a Late Upper Palaeolithic modern human specimen (Villabruna) from a burial in Northern Italy. Using Scanning Electron Microscopy we show the presence of striations deriving from the manipulation of a large occlusal carious cavity of the lower right third molar. The striations have a "V"-shaped transverse section and several parallel micro-scratches at their base, as typically displayed by cutmarks on teeth. Based on in vitro experimental replication and a complete functional reconstruction of the Villabruna dental arches, we confirm that the identified striations and the associated extensive enamel chipping on the mesial wall of the cavity were produced ante-mortem by pointed flint tools during scratching and levering activities. The Villabruna specimen is therefore the oldest known evidence of dental caries intervention, suggesting at least some knowledge of disease treatment well before the Neolithic. This study suggests that primitive forms of carious treatment in human evolution entail an adaptation of the well-known toothpicking for levering and scratching rather than drilling practices.

Mechanisms and causes of wear in tooth enamel: implications for hominin diets.

The wear of teeth is a major factor limiting mammalian lifespans in the wild. One method of describing worn surfaces, dental microwear texture analysis, has proved powerful for reconstructing the diets of extinct vertebrates, but has yielded unexpected results in early hominins. In particular, although australopiths exhibit derived craniodental features interpreted as adaptations for eating hard foods, most do not exhibit microwear signals indicative of this diet. However, no experiments have yet demonstrated the fundamental mechanisms and causes of this wear. Here, we report nanowear experiments where individual dust particles, phytoliths and enamel chips were slid across a flat enamel surface. Microwear features produced were influenced strongly by interacting mechanical properties and particle geometry. Quartz dust was a rigid abrasive, capable of fracturing and removing enamel pieces. By contrast, phytoliths and enamel chips deformed during sliding, forming U-shaped grooves or flat troughs in enamel, without tissue loss. Other plant tissues seem too soft to mark enamel, acting as particle transporters. We conclude that dust has overwhelming importance as a wear agent and that dietary signals preserved in dental microwear are indirect. Nanowear studies should resolve controversies over adaptive trends in mammals like enamel thickening or hypsodonty that delay functional dental loss.