Farming gave us salmonella, ancient DNA suggests

A new study looking into ancient DNA has revealed that salmonella may have begun effecting humans when the farming took over from the hunter-gatherer lifestyle.

In a paper published in the journal Nature Ecology & Evolution, a team of scientists from the Max Planck Institute for the Science of Human History describes how their investigation of genomes recovered from ancient human skeletons led to the uncovering of evidence to suggest that early farmers in Eurasia facilitated the emergence of the first human-adapted salmonella pathogen.


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Did the farming lifestyle facilitate the emergence of new diseases?

Scientists and anthropologists have long theorized that the transition from the hunter-gatherer way of life to the agricultural lifestyle may be responsible for the emergence of new diseases due to exposure to new kinds of pathogens. However, actual data examining this hypothesis had proved difficult to collect.

The team at the Max Planck Institute set out to innovate a new way to address this problem by utilizing high-throughput technology to uncover how certain pathogens emerged and spread at the dawn of modern human civilization, known as the Neolithic Revolution, or the Agricultural Revolution.

Determining the nature of how pathogens emerged in early human civilizations is vital to providing answers to long-standing questions surrounding microbial evolution which may improve future prevention and treatment techniques.

Using genetics to identify ancient pathogens

Investigating how pathogens impacted earlier civilizations is challenging because they mostly leave no trace on the skeleton. However, scientists innovated a way to get around this problem by using genetic techniques.

The researchers in the current study used HOPS, a bacterial screening pipeline that was recently established to find ancient pathogens in metagenomics data.

In recovering salmonella enterica genomes from ancient human skeletons dating back to as long as 6,500 years ago, scientists were able to trace the evolution of the pathogen.

For the very first-time scientists had gathered ancient DNA evidence to support the theory that the transition from hunter-gatherer to agricultural lifestyles was the event that allowed pathogens to adapt to humans and cause new kinds of disease and illness.

Thousands of archaeological samples were screened using the new technology for traces of salmonella enterica DNA. A total of 2,739 ancient human skeletons were analyzed, resulting in the reconstruction of eight salmonella genomes, the oldest one being 6,500 years old, making it the oldest ever discovered.

The number of samples studied to find eight genomes demonstrates the challenges facing the field of pathogen research. Scientists took evidence from the teeth of just under 3,000 skeletons, the presence of salmonella in which indicated that they were suffering from the systemic disease when they died.

Scientists have hypothesized that when ancient humans turned to agriculture they became in much closer contact with animals in their day to day life. The animals which they turned domestic would sleep in close quarters, and their waste would also be in closer contact than it would have been when living the hunter-gatherer lifestyle.

It is believed that salmonella in the animals and their waste found its way into the human body because of this close contact, where it entered the gut and adapted to humans.

This research gives evidence that Neolithization is likely responsible for exposure to a wider variety of pathogens, and, therefore, the establishment of new human diseases. The findings provide the first molecular evidence of this link.

Pathogen evolution and the Neolithic revolution

The Neolithic revolution represents one of the most significant transitions in human culture. While scientists have long suspected that this shift may be related to the emergence of human-adapted diseases, it has previously been challenging to collect data to support this theory.

The team at the Max Planck Institute has provided this kind of evidence for the first time, allowing scientists to gain a deeper understanding of how pathogens adapted to humans, elucidating how human cultural evolution has affected the rise of human-adapted diseases.


Farming gave us salmonella, ancient DNA suggests. Available at:

Journal references:

Key, F., Posth, C., Esquivel-Gomez, L., Hübler, R., Spyrou, M., Neumann, G., Furtwängler, A., Sabin, S., Burri, M., Wissgott, A., Lankapalli, A., Vågene, Å., Meyer, M., Nagel, S., Tukhbatova, R., Khokhlov, A., Chizhevsky, A., Hansen, S., Belinsky, A., Kalmykov, A., Kantorovich, A., Maslov, V., Stockhammer, P., Vai, S., Zavattaro, M., Riga, A., Caramelli, D., Skeates, R., Beckett, J., Gradoli, M., Steuri, N., Hafner, A., Ramstein, M., Siebke, I., Lösch, S., Erdal, Y., Alikhan, N., Zhou, Z., Achtman, M., Bos, K., Reinhold, S., Haak, W., Kühnert, D., Herbig, A. and Krause, J. (2020). Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nature Ecology & Evolution, 4(3), pp.324-333.

Larsen, C., Knüsel, C., Haddow, S., Pilloud, M., Milella, M., Sadvari, J., Pearson, J., Ruff, C., Garofalo, E., Bocaege, E., Betz, B., Dori, I. and Glencross, B. (2019). Bioarchaeology of Neolithic Çatalhöyük reveals fundamental transitions in health, mobility, and lifestyle in early farmers. Proceedings of the National Academy of Sciences, 116(26), pp.12615-12623.

Sarah Moore

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Sarah Moore

After studying Psychology and then Neuroscience, Sarah quickly found her enjoyment for researching and writing research papers; turning to a passion to connect ideas with people through writing.


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