Skip to main content
Premium Trial:

Request an Annual Quote

Ancient Microbes Found in Neanderthal Plaque DNA

NEW YORK (GenomeWeb) – By sequencing ancient DNA captured in Neanderthal plaque samples, researchers have put together some of the oldest microbial draft genomes so far.

An international team led by investigators in Australia used a combination of targeted and metagenomic sequencing to profile microbial, plant, and animal DNA in plaque samples from five Neanderthals found at cave sites in present-day Belgium, Spain, and Italy. As reported online today in Nature, the sequence data offered a peek at the archaic hominin's preferred cuisine at these sites — for example, it pointed to a meaty diet for Neanderthals in Belgium, but more plant- and fungus-based fare for Neanderthals from a Spanish cave.

By focusing in on microbial DNA in a few of the plaque samples, the researchers were also able to put together a close-to-complete draft genome for a 48,000-year-old archaeal species nestled in dental calculus from a Spanish Neanderthal at El Sidrón cave. They also sequenced seven more microbial genomes to lower depths using a sample from the same Neanderthal.

"Within the El Sidrón 1 specimen that was deeply sequenced, we were able to recover draft genomes … for the eight most prevalent microbial species," senior author Alan Cooper, a researcher with the University of Adelaide's Australian Centre for Ancient DNA, and his co-authors wrote. "Of particular note was a dominant archaeal species in El Sidrón that was present in lower proportions in other Neanderthals."

The researchers used 16S ribosomal RNA and/or metagenomic sequencing to profile the organisms present in plaque samples from two El Sidrón Neanderthals, two Neanderthals from Spy cave in Belgium, and one Italian Neanderthal from Breuil Grotta. But they also did more in-depth sequencing on plaque samples from the Spanish Neanderthal El Sidrón 1, whose remains were relatively well preserved and showed symptoms of dental disease.

Of the eight draft genomes the team assembled from prominent microbial reads present in El Sidrón 1's plaque, the archaeal species Methanobrevibacter oralis was represented most completely, making it possible to define a Neanderthal-associated strain known as M. oralis sub-species neandertalensis.

The researchers estimated that this sub-species split off from a M. oralis strain found in modern humans roughly 112,000 to 143,000 years ago, though they noted that the microbe may have moved between mixing populations of modern and archaic humans at some point.

As for El Sidrón 1's dental troubles, the team noted that his plaque contained DNA from Penicillium mold and from poplar, a plant that contains the painkiller salicylic acid (found in modified form in aspirin). Such findings hint that the Neanderthal may have been seeking medical comfort for the dental abscess or for a bellyache caused by Enterocytozoon bieneusi, a gastrointestinal pathogen that El Sidrón 1 may have carried, based on other reads in the plaque sample.

The study's authors noted that "[p]reserved dental calculus represents a notable source of information about behavior, diet, and health of ancient hominin specimens, as well as a unique, long-term system that can be used to study how hundreds of different microbial species have evolved and spread among hominins."