The individuals from El Sidrón - a left-handed adult female and a male who appears to have used his mouth to sharpen the blades of stone tools - have provided the most interesting material to the researchers.
The male individual, dubbed El Sidrón 1, suffered from a dental abscess, visible thanks to a hole in his jaw.
"The plaque showed that he also had an intestinal parasite that causes acute diarrhea, so clearly he was quite sick," said Alan Cooper, director of ACAD.
The researchers found that El Sidrón 1 had been self-medicating the dental abscess.
"This was the only individual whose calculus included sequences corresponding to poplar, which contains the natural pain-killer salicylic acid (the active ingredient in aspirin), and also notably contained sequences of the natural antibiotic producing Penicillium from the moulded herbaceous material," the researchers wrote.
The finding confirms a previous study led by Karen Hardy at the Catalan Institution for Research and Advanced Studies in Barcelona and Stephen Buckley at the University of York, who found evidence for apparent self-medication by chemically analyzing tartar samples from El Sidrón 1.
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Hardy and Buckley found that El Sidrón 1 consumed yarrow, a natural astringent, and camomile, an anti-inflammatory. Both are bitter-tasting plants with no nutritional qualities, and were apparently selected for medical use.
"The new study adds to the evidence for Neanderthal self-medication with plants," Buckley told Seeker. "It's particularly interesting since this was from the same Neanderthal individual self-medicating in our study and indeed the very same tooth."
"The study also shows the usefulness of several of lines of biomolecular evidence, such as DNA, proteomics and lipids, which can help to support and corroborate one another," he added.
The dental plaque collected from El Sidrón 1 turned out to be a treasure trove for the researchers.
It made it possible to retrieve the oldest microbial genome yet sequenced at around 48,000 years old - Methanobrevibacter oralis, a commensal that can be associated with gum disease and periodontitis.
The Neanderthal and modern human strains of M. oralis appear to have diverged between 112,000 and 143,000 years ago, after the two evolutionary lines split.
"The fact that M. oralis was likely swapped in spit between humans and Neanderthals suggests that Neanderthal and human interbreeding interactions were likely much friendlier than anyone every imagined," Weyrich said.
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The researchers compared the Neanderthal oral bacterial population with human samples from Palaeolithic hunter-gatherers, African nomads, the first Neolithic farmers, and present-day man.
They found that the composition of the oral microorganisms correlated closely with the amount of meat in the diet, with the Spanish Neanderthals grouping with chimpanzees and our forager ancestors in Africa.
The bacteria from Belgian Neanderthals were similar to early hunter-gatherers, and quite close to modern humans and early farmers.
Overall, the Neanderthal oral microorganisms had fewer potentially pathogenic bacteria than modern humans typically do.
Nevertheless, the researchers identified several oral pathogens, such as the caries-associated species Streptococcus mutans and a group of bacteria associated with periodontal disease.
"This is an extraordinary window on the past," remarked Keith Dobney of the University of Liverpool. "It provides us with new ways to explore and understand our evolutionary history through the microorganisms that lived in us and with us."
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