Scientists have discovered a 'microbial Pompeii' preserved on the teeth of skeletons around 1,000 years old.
The key to the discovery is the dental calculus (plaque) which preserves bacteria and microscopic particles of food on the surfaces of teeth, effectively creating a mineral tomb for microbiomes.
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.
They found 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.
Scientists recovered dietary DNA from ancient dental calculus, allowing the identification of dietary components, such as vegetables, that leave few traces in the archaeological record.
Led by the University of Zurich, the University of Copenhagen, and the University of York, the research 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 environment.
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.
Analysing this wealth of data required overcoming the formidable bioinformatics challenge of sorting and identifying millions of genetic sequences like puzzle pieces in order to reconstruct the complex biology of the ancient oral microbiome.
"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," said Professor Christian von Mering, an author of the study from SIB Swiss Institute of Bioinformatics.
"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 Pompeii," Professor Matthew Collins, of the University of York, said.
The study has wide reaching implications for understanding the evolution of the human oral microbiome and the origins of periodontal disease.
The study was published in the journal Nature Genetics
