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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.

etween 1994 and 1996, during the excavation of a 7-m 2 test pit, a sample of Ϸ100 hominin fossil remains was found in the so-called Aurora Stratum of the stratigraphic unit TD6 of the Gran Dolina site in Sierra de Atapuerca, Burgos, northern Spain (1). The hominin remains were associated with 268 lithic artifacts made of flint, quartzite, sandstone, limestone, and quartz. This sample is characterized by the presence of small artifacts, and includes flakes, denticulates, notches, and side-scrapers and can be characterized as Mode 1 technology (2). The excavation of the Aurora Stratum also yielded a rich small mammal assemblage (26 species, including the water vole Mimomys savini) as well as Ϸ1,000 large mammal fossil remains. The study of the arvicolids suggests that the TD6 level can be referred to the Biharian biochron (3). The macromammal assemblage is biochronologically consistent with the end of the Early Pleistocene or early Cromerian (4, 5). Paleomagnetic dating places TD6 in the Matuyama reversed Chron, hence, before 780 thousand years ago (6, 7). These paleomagnetic data combined with electron spin resonance and uranium series results give an age range of between 780 and 857 thousand years for TD6 (8). Pollen analysis suggests that the Aurora Stratum was deposited under wet, temperate conditions (9); thus, the Aurora Stratum possibly correlates to oxygen isotope stages 21 or 19.In 1997, the TD6 hominins were attributed to Homo antecessor, a new European Lower Pleistocene species (10). On the basis of cranial and dental features, it was suggested that this species could be the common ancestor of modern humans (Homo sapiens) and Neandertals (Homo neanderthalensis). The new taxon was defined in part by using facial and mandibular traits observed in immature individuals. Although the TD6 remains were compared with those of individuals of the same dental age (e.g., KNM-WT 15000), it was clear that the credibility of the species would improve if new specimens corresponding to adult individuals were found. In 2003, we obtained in the Aurora Stratum an excellently preserved mandible, whose description and comparative analysis is the subject of the present study. Mandible ATD6-96Preservation and Age at Death. The specimen catalogued as ATD6-96 was recovered in a planar section of Ͻ1 m 2 , near the area excavated during the 1994-1997 field seasons (1). ATD6-96 is a left half of a gracile mandible of an adult individual (Hominid 7) with the premolars and molars in place (Fig. 1). The specimen is broken at the level of the lateral incisor-canine septum, and the left genial apophysis is preserved. Some postmortem fractures are observed at the region between the corpus and ramus and near the neck of the condyle, but there is no noticeable distortion. Molar (M)3 is fully erupted and exhibits a minimal wear facet at the mesial marginal ridge. During restoration, the corpus and ramus were separated, and the roots of the M3 were observed directly. These roots are at stage Rc of tooth formation (11). Thus, according to mo...

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