Genetic analysis of plaque on 1000-year-old teeth gives clues to
ancient diet and disease
24 February 2014
An large international team of researchers has painstakingly pieced
together genetic fragments preserved in the dental plaque of
skeletons around 1,000 years old, indicating the bacteria present
and food eaten by the person.
The research team discovered that the ancient human oral cavity
carries numerous opportunistic pathogens and that periodontal
disease is caused by the same bacteria today as in the past, despite
major changes in human diet and hygiene.
Led by the University of Zürich, the University of Copenhagen,
and the University of York, this pioneering analysis of ancient oral
microbiome ecology and function involved the contributions of 32
scientists at twelve institutions in seven countries.
The researchers discovered that the ancient human oral microbiome
already contained the basic genetic machinery for antibiotic
resistance more than eight centuries before the invention of the
first therapeutic antibiotics in the 1940s. As well as health
information, the scientists recovered dietary DNA from ancient
dental calculus, allowing the identification of dietary components,
such as vegetables, that leave few traces in the archaeological
The research, published in Nature Genetics, reveals that
unlike bone which rapidly loses much of its molecular information
when buried, calculus grows slowly in the mouth and enters the soil
in a much more stable state helping it to preserve biomolecules.
This enabled the researchers, led by Dr Christina Warinner, to
analyse ancient DNA that was not compromised by the burial
They applied shotgun DNA sequencing to dental calculus for the
first time. They reconstructed the genome of a major periodontal
pathogen and produced possibly the first genetic evidence of dietary
biomolecules to be recovered from ancient dental calculus.
Analyzing this wealth of data required overcoming a formidable
computing challenge of sorting and identifying millions of genetic
sequences like puzzle pieces in order to reconstruct the complex
biology of the ancient oral microbiome.
Fossilized dental plaque (calculus) on the
teeth of a middle-aged man from the Medieval site of Dalheim,
Germany, ca. AD 1100. Photo credit: Christina Warinner.
“Dental calculus is a window into the past and may well turn out
to be one of the best-preserved records of human-associated
microbes," says Professor Christian von Mering, an author of the
study and Group Director at the SIB Swiss Institute of
Bioinformatics, which performed the bioinformatics analysis
Professor Matthew Collins, of the University of York, said: “We
knew that calculus preserved microscopic particles of food and other
debris but the level of preservation of biomolecules is remarkable.
A microbiome entombed and preserved in a mineral matrix, a microbial
Dr Warinner, of the University of Zurich and the University of
Oklahoma, added: “Dental calculus acts both as a long-term reservoir
of the oral microbiome and as a trap for dietary and environmental
debris. This allows us to investigate health and disease, as well as
reconstruct aspects of an individual’s life history and activities.
Never before have we been able to retrieve so much information from
one small sample.”
The study has wide reaching implications for understanding the
evolution of the human oral microbiome and the origins of
periodontal disease. Periodontal disease causes distinctive
proteomic changes in the dentition and is characterized by chronic
inflammation resulting in tooth and bone loss. Dr Enrico Cappellini
of the University of Copenhagen, a senior author of the study,
describes the dental calculus analyzed in this study as a kind of
“battlefield archaeological site, just at the molecular scale.”
“As we learn more about the evolution of this microbiome in
response to migration and changes in diet, health and medicine, I
can imagine a future in which most archaeologists regard calculus as
more interesting than the teeth themselves,” says Professor Collins.
“The study of ancient microbiomes helps us understand the
evolutionary history of human health and disease," says Professor
Frank Rühli, a senior author of the study and Head of the Centre for
Evolutionary Medicine at the University of Zürich. “It informs
Today, moderate to severe periodontal disease affects more than
10% of the world’s population and is linked to diverse systemic
diseases, including cardiovascular disease, stroke, pulmonary
disease, and type II diabetes. Although common in humans, domestic
pets, and zoo animals, periodontal disease does not typically
develop in wild animals, leading to speculation that it is an oral
microbiome disease resulting from modern human lifestyles.
Pathogens and host immunity in the ancient human oral
cavity. Nature Genetics.