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Neandertal Life Reconstructed One Bacterium at a Time

The complete jaw of Spy II, with small and thin dental calculus deposits that pr

The complete jaw of Spy II, with small and thin dental calculus deposits that provided usable DNA sequences. Credit: Royal Belgian Institute of Nature Sciences

By Laura Weyrich

Fossilised dental calculus is revealing that Neandertals weren’t the oafish brutes we’ve long considered them to be.

Our vision of Neandertals often includes a grunting, club-touting, beastly individual who may or may not be covered in fleas. The Neandertal is likely wearing furs from the animals it killed and is probably looking a bit confused.

But is that how Neandertals really were? New evidence from bacteria preserved on their teeth suggests otherwise.

Why Are Neandertals Portrayed as Oafs?

Decades of research have worked to unhinge this perception, but in many cases only reinforced it. Researchers assumed that the Neandertal diet would be a healthy mixture of meat and gathered food items, but when they used isotopes to examine the major food groups for Neandertals, the results suggested they were as carnivorous as polar bears! When researchers looked at artifacts to learn more about their daily lives, they found tools used for hunting large game, further suggesting that Neandertals were running around with spears, clubs and fur cloaks. Other research also suggested that they may have been cannibals, which painted a picture of a mean, oafish lifestyle.

Despite these decades of research, this is the equivalent of saying that we know all humans today because we know they ate meat, carried cell phones and wore blue jeans. This shows almost nothing about how humans live their daily lives, and says absolutely nothing about their culture, beliefs or behaviours.

DNA from Oral Bacteria Paint a New Picture

We now have a new tool to learn more about ancient hominids and how they once lived – by looking at the bacterial gunk that sticks to their teeth. The slimy, gross feeling that seems to grow on your teeth after you consume a sugary drink is actually millions of bacteria growing in response to the sucrose that you just ingested.

If you don’t brush your teeth – as many of our ancestors and cousins did – the bacteria in your mouth become locked in a calcified matrix when you sleep. This matrix, otherwise known as dental calculus, can preserve microorganisms, diseases and other dietary and environmental microparticles in the mouth for thousands of years. In fact, dental calculus preserves as well as bone in most cases. So wherever there’s an ancient skeleton, there’s a good chance that there will also be an accompanying fossil record of the bacteria and food that was once present in the mouth of an ancient person.

We can sequence the DNA preserved from these micro­organisms and microparticles in dental calculus to understand more about ancient humans. Perhaps the most telling evidence preserved in dental calculus is the oral bacteria. These incredibly diverse oral bacterial communities (referred to as microbiota) are extremely adaptable and can rapidly respond to changes in their microenvironment, such as changes in a human’s diet, environment, hygiene, health, or even medicine. By sequencing bacterial DNA, researchers can now use ancient oral microbiota to understand more about past human lifestyles, diet and health.

In a recent study published in Nature (http://tinyurl.com/ya5us67p), we applied this new technique to Neandertal dental calculus to learn more about Neandertal’s diet, lifestyle and behaviour. Two Neandertals from Spy Cave in Belgium, two Neandertals from El Sidron Cave in Spain, and one Neandertal from Brueil Grotta in Italy were chosen for this project. Not all Neandertals have dental calculus, and some Neandertals used hygienic practices of tooth-picking to help remove calculus from their teeth. We also selected a wide range of ancient humans and historic apes for comparison.

Neandertals Shared Bacteria with Ancient Humans and Chimpanzees

The DNA revealed that Neandertals contained a unique set of oral microbiota that is not shared today with modern humans. Neandertal oral microbiota was shared with chimpanzees and ancient human hunter-gatherers from both Europe and Africa. This finding suggests that Neandertals, humans and chimpanzees once shared a similar set of oral microbiota, and that the microorganisms that once lived in the human mouth co-evolved with humans over millions of years.

Two distinct types of microbiota could be observed within the Neandertals and hunter-gatherers. The type of microbiota found in El Sidron Neandertals was shared with ancient gatherers and chimpanzees, while the type found in Spy Neandertals was shared with individuals who largely based their diet around hunting. In fact, it was the Spy Neandertals that were as carnivorous as polar bears.

This split in the microbiota suggests that Neandertals may have been living very different lifestyles, and that these may have corresponded to differences in diet.

Could Neandertals Have Been Vegetarians?

The difference between meat-eating or simply gathering plant-based foods appeared to separate two groups of Neandertals. To explore the diet and its contributions to oral bacterial diversity further, we looked at DNA from the microparticles that were also preserved in Neandertal dental calculus. These microparticles often correspond to dietary sources, although they can also be non-dietary fragments, such as rope that was cut using the teeth.

In the Spy Neandertals, we found evidence of meat-eating that corresponded with previous isotope findings. We found DNA corresponding to woolly rhinoceros (which went extinct in Europe about 38,000 years ago), wild sheep (perhaps like the mouflon sheep that are still present in Europe today) and mushrooms.

In contrast, there was little evidence for meat-eating in the El Sidron Neandertals; DNA corresponding to pine nuts, mushrooms and even moss were identified, suggesting that their diet at the time may have been much more vegetarian than their Spy cousins.

Regardless of these differences, the evidence suggests that Neandertals were very much in tune with their environments and knew where to collect certain foods. The results also suggest that even though previous research suggested they were only eating meat, Neandertals were eating plant-based foods such as mushrooms. Knowledge of which types of foods to gather, such as edible mushrooms rather than poisonous ones, would have been passed down from generation to generation.

Neandertals would have needed a way to interact and share this knowledge with their young ones. This also means that they did not spend all of their days touting clubs and chasing after large game; they likely spent some days holding a basket and gathering mushrooms and nuts from a forest floor.

While the idea that we can identify specific food sources from Neandertals is incredibly exciting, it is also still early days for this new methodology. Further research needs to be done to verify and authenticate these findings.

For example, we know that Neandertal bones were once coated with varnish when they were taken out of the ground – a practice that often helped preserved the bones to later showcase them in museums. Hundreds of years ago, when these bones were being dug up by archaeologists, much of this varnish was made from animal’s hooves, typically goat hooves. As a result we cannot be sure that the sheep DNA identified in Spy Neandertal dental calculus did not correspond to the DNA present in the varnish, but we can be sure that the woolly rhinoceros was not used to make varnish because the animal became extinct more than 38,000 years ago in Europe.

We also know that DNA from bacteria and larger mammals, such as humans, can also be shared, so identifying dietary DNA that corresponds to mammals can be difficult. Dental calculus samples are more than 95% bacterial, which leaves very few DNA sequences that correspond to food. Microbial DNA sequences can also integrate into sources of food DNA, further complicating matters.

Sequencing DNA from other bones in the cave and from any known dietary sources may provide more clarity, but for now, inferring dietary or non-bacterial information from the DNA in calculus is tough business.

Neandertals and Humans Swapped Bacteria

The bacteria in Neandertal mouths can also tell more nuanced stories about a Neandertal’s life beyond their diet, health, traditions and daily behaviours. By looking at the genetic mutations in individual bacteria in Neandertals, we can track their evolutionary history and give evidence to support the origins of specific bacteria in the human body.

Several studies have used genomic mutations in micro­organism to identify when ancient outbreaks occurred, or to identify the ancient causes of plagues. In this study, one of the El Sidron Neandertals had large amounts of a unique oral micro­organism, Methanobrevibacter oralis, present in his mouth. We compared the mutations in the M. oralis genome from Neandertals with those in modern humans, and found that Neandertals obtained this oral microorganism about 120,000 years ago. Neandertals and humans likely diverged about 700,000 years ago, so Neandertals must have obtained this microorganism much later in their evolutionary history; this strain of M. oralis may not have been present in Neandertals since their origins.

While highly speculative, this suggests that Neandertals may have obtained M. oralis from either humans or shared environmental sources. We know that modern humans can transfer oral bacteria by sharing food, caring for others or even kissing.

While it’s easy to let the imagination run wild and assume Neandertals and humans must have been kissing, it’s just as easy to assume they may have drank from the same water source.

It is interesting to note that the origin of this oral micro­organism in Neandertals is also about the same time as the earliest cases of interbreeding between Neandertals and humans. Whether or not Neandertals and humans were kissing during interbreeding remains to be seen, but it’s certainly enough evidence to start examining these interactions closer. Analysing more microbial genomes from Neandertals and ancient humans may provide the clues we need to understand how intimate Neandertals and humans were with one another.

What Does Knowing More About Neandertals Mean for Me?

If Neandertals and ancient human hunter-gatherers once shared a microbiome, what happened to that microbiota in humans today? The study also verified an early finding that modern human oral microbiota was drastically impacted during the onset of agriculture about 7500 years ago in Europe, when readily available carbohydrates became the major food source and lifestyles became more sedentary.

We also identified another change in the microbiota from ancient humans to today. The evidence also suggested that more recent events, most likely since the Industrial Revolution, have also impacted our microbiota. While researchers are unsure what has caused these recent changes, processed food, pollution, and antibiotics are all likely candidates.

One thing is for sure, Neandertals had much healthier mouths than modern humans. They contained fewer disease-causing micro­organisms and had pearly whites analogous to the gods. Their superb oral health is likely because of their healthy diet, which lacked most of the sugar and refined carbohydrates that we now eat on a regular basis today. Even if they were grunting and hunting meat on some days, they certainly knew how to interact with their environment, pass on knowledge to their offspring, and even potentially how to interact with humans in a positive way.

Despite the clubs and fur cloaks, we can imagine that they were healthier than us. Would you live like a Neandertal today, if it meant you wouldn’t have to go to the dentist?


Laura Weyrich is an ARC Discovery Early Career Research Fellow at the Australian Centre for Ancient DNA, The University of Adelaide.