In Japan's Edo period, women blackened their teeth in a tradition called ohaguro—a status symbol and sign of marriage. Now, researchers peering into those darkened teeth have uncovered something unexpected: a window into four centuries of human microbiome history.
Scientists at Toho University, the University of Tokyo, and Kyushu University analyzed DNA trapped in dental calculus—the mineralized plaque that builds up on teeth—from hundreds of skeletal remains excavated across Japan, from Tokyo and Saitama to Fukushu and Okinawa. By comparing the oral microbes preserved in these ancient teeth with those of modern samples, they've revealed how Japanese people's mouth bacteria shifted dramatically over time and varied significantly by region.
The discovery matters because our oral microbiome—the community of microorganisms living in our mouths—is shaped by what we eat, how we live, and where we live. It's also linked to everything from cavities to periodontal disease. Yet until now, researchers had limited tools to understand how these microbial communities changed across Japanese history. Dental calculus, it turns out, is a time capsule. "Microbial DNA preserved in dental calculus can provide new evidence for examining past diet, regional variation, cultural practices, and the history of relationships between humans and microorganisms," the researchers note in their study, published in Scientific Reports.
The team collected samples from archaeological and burial sites spanning centuries—including Jomon-period remains alongside Edo-period skeletons—and meticulously filtered out soil contamination using oral microbiome databases to ensure they were looking at microbes that actually lived in ancient mouths. The differences they found were striking. Edo-period dental calculus contained oral microbes markedly different from modern samples. In particular, they frequently detected Methanobrevibacter oralis, an archaeon associated with periodontal disease, in the ancient samples—something rarely seen in contemporary mouths.
Geography mattered too. Researchers observed clear differences in microbial composition between samples from Honshu and Kyushu compared to Okinawa, pointing to the influence of regional diets and living conditions on oral bacteria. The findings suggest that what people ate—and how they lived—left a measurable biological signature in their mouths that persisted for centuries.
Perhaps most intriguingly, when the researchers conducted a phylogenetic analysis of Methanobrevibacter oralis from the blackened teeth of Edo-period women, they discovered that all the archaea from those teeth belonged to the same genetic clade. This suggests a shared microbial ancestry among women who practiced ohaguro, adding another layer of evidence to how cultural practices left traces in the human body.
This research opens an unexpected avenue for historians and anthropologists. Rather than relying solely on written records or archaeological artifacts, scientists can now read the bacterial DNA embedded in ancient teeth to infer details about diet, lifestyle, and health in past populations. It's a reminder that the tiniest organisms in our bodies tell vast stories about who we were, what we ate, and how we lived—stories we're only now learning to read.