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Prehistoric dental plaque

DNA preserved in dental plaque for thousands of years harbours a wealth of new information about the biodiversity and functioning of ancient microbes.

Harvesting prehistoric DNA

Researchers in the new discipline of palaeobiotechnology want to use the DNA found in prehistoric bacteria to develop antibiotics that are effective against resistant pathogens. The following photo essay shows how archaeologist Christina Warinner and chemist and biotechnologist Pierre Stallforth are working towards this goal.

1. The search

Christina Warinner (left) and her team are working with a stock of thousands of archaeological finds from sites located all over the world; some of the finds are up to 100 000 years old. — Christina Warinner (left) and her team are working with a stock of thousands of archaeological finds from sites located all over the world; some of the finds are up to 100 000 years old. Many have already undergone genetic testing, and now the next step is for the team to select the specimens in the database that are most likely to lead to natural products having antibiotic properties—and that are thus promising candidates for developing new antibiotic drugs.

2. The dental plaque

A 3000-year-old mandible. — The teeth preserved in a 3 000-year-old mandible are prized objects for Christina Warinner and her team: nowhere else have researchers found more or betterpreserved ancient DNA than in dental plaque, where food scraps and bacteria have been naturally conserved. The archaeologist scrapes away the plaque in a cleanroom, where the air is largely particle-free to avoid contamination. She also wears protective gear to prevent her own DNA from mixing with the prehistoric samples.

3. The puzzle

The latest genetic-sequencing technology makes it possible to determine the structure of prehistoric DNA in dental plaque and then identify the genetic sequences responsible for producing natural products. — The latest genetic-sequencing technology makes it possible to determine the structure of prehistoric DNA in dental plaque and then identify the genetic sequences responsible for producing natural products. The researchers apply bioinformatics methods to piece together the scraps of DNA and close gaps in the sequence.

4. The reactivation

Once the DNA sequences responsible for producing antibiotic natural products have been identified, biotechnologist Pierre Stallforth (centre) and his team can introduce them to modern bacteria in cultures. — Once the DNA sequences responsible for producing antibiotic natural products have been identified, biotechnologist Pierre Stallforth (centre) and his team can introduce them to modern bacteria in cultures. Despite recent technological advances, the researchers must first develop some of the instruments needed for the project.

5. The harvest

Steel tanks in the lab of the researchers. — The bacteria with additional DNA are grown in steel tanks. During the so-called fermentation process, the bacteria multiply and produce natural products—including ancient natural products, which was the aim of changing the genetic structure of the bacteria. Over the course of the multistep procedure, the researchers extract the natural products from the bacteria cultures. Afterwards, the pure natural product is separated out in special flasks.

6. The moment of truth

The researchers then examine the natural products in culture dishes and can quickly determine whether they are effective against the most common kinds of multiresistant bacteria. — The researchers then examine the natural products in culture dishes and can quickly determine whether they are effective against the most common kinds of multiresistant bacteria. By 2029, Pierre Stallforth and his team aim to have developed new kinds of agents from the ancient DNA that are interesting to the pharmaceutical industry—as potential antibiotics or cancer drugs.

Text: Adrian Ritter
Photos: Felix Wey

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A 3000-year-old mandible.

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Prehistoric dental plaque

September 2019 – The problem: antibiotic resistance

Lab bacteria and the ancient natural products they produce are stored at minus 80 degrees centigrade.

September 2019 – Portrait of project leader Pierre Stallforth

Archaeologist Christina Warinner

September 2019 – Portrait of archaeologist Christina Warinner