Analysis of calcified dental plaque (calculus) specimens from Neanderthals shows marked regional differences in diet and microbiota and evidence of self-medication in one individual, and identifies prevalent microorganisms and their divergence between Neanderthals and modern humans. The Neanderthal diet has been much debated, with evidence for a meat-rich diet conflicting with evidence from tooth wear that suggests more varied fare. Laura Weyrich and colleagues sequenced DNA from the dental calculus of five Neanderthal individuals from across Europe to provide a genetic reconstruction of their diet and health. They found that a Neanderthal from Spy in Belgium dined on rhinoceros and mutton, whereas another, from El Sidrón in Spain, ate pine nuts, moss and mushrooms. Their results also suggest that the Spanish Neanderthal had a dental abscess and a stomach bug that they were self-medicating with poplar, a natural painkiller, and the antibiotic-producing Penicillium bacteria. The team also uncovered the oldest microbial genome to date, that of Methanobrevibacter oralis at 48,000 years old. Recent genomic data have revealed multiple interactions between Neanderthals and modern humans1, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering2,3. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess4 and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)—the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus