Buried Bacterial Treasure
These studies of present-day bacterial diversity are valuable, but to tell the whole story of the human microbiome’s evolution, researchers must turn to fossilized feces, or coprolites, and tartar caked onto ancient teeth.
Among human archaeological remains, coprolites can be a uniquely valuable record of ancient gut microbiomes — but they’re rare to find. In typical, relatively humid and warm environments, stool quickly breaks down. Yet in cool, arid conditions, such as dry caves, excreted feces can preserve bacterial DNA for centuries.
In 2008, Lewis and a team analyzed two coprolites from a Mexican cave. The samples were found in a sandy heap, doubling as a refuse dump and burial site, and had been sealed with adobe mud. The coprolites’ exquisite preservation allowed the scientists to make the first confirmation of an ancestral, distinctly human microbiome, dating back to about A.D. 700. “These bacteria were clearly members of the gut,” Lewis says.
Neanderthals hold the record for the oldest hominin coprolites to date, plopped 50,000 years ago in a fire pit in El Salt, Spain.
In 2012, analyzing two other coprolites from the same site, Lewis and colleagues found that the ancient Native American microbiomes overall corresponded to modern, rural examples from traditional peoples in Africa, but not to industrialized bowel bugs. The team was even able to estimate the age of one of the human hosts from one sample’s recovered bacterial DNA. One coprolite contained high levels of Bifidobacterium breve, often found today in breast-fed infants, and microbes in the genus Prevotella, linked to a carbohydrate-rich diet. Children in rural Africa commonly have these microbes in abundance as well, suggesting that the Mexican coprolite may have been that of a young child.
Deciphering the microbiome of yesteryear can extend to human ancestors, too, even extinct hominins. Neanderthals hold the record for the oldest hominin coprolites to date, plopped 50,000 years ago in a fire pit in El Salt, Spain. The feces contained traces of fats typically produced during digestion by bacteria that are found in microbiomes of omnivores. In other words, it looks like our Neanderthal cousins were probably consuming meat as well as vegetables. Although this particular coprolite sample has not been probed for the identities of its resident bacteria, Warinner says, as only a scientist could about fossilized poop: “I’d love to analyze it.”
A Tale Told in Teeth
Unlike rare, serendipitous coprolites, teeth turn up all the time in archaeological skeletal finds. Tartar, also called calculus, accumulates on teeth throughout our lives, spackling over clinging oral bacteria and bits of food. “Calculus builds up kind of like an onion,” says Warinner. “And what’s extraordinary about it is, it actually fossilizes while you’re still alive.”