“Between animal and human medicine there is no dividing line, nor should there be. The object is different but the experience obtained constitutes the basis of all medicine.” by Rudolf Virchow, 1856; by Klauder, J.V., Interrelations of human and veterinary medicine. N Engl J Med, 258:170-177, 1958 (1).

Shared origins and fates

More than a century and a half ago, Rudolf Virchow, who coined the very term “zoonosis”, recognized that the health of humans and animals is fundamentally intertwined. The words above capture something that remains as relevant today as it was then: that studying disease in one species inevitably teaches us about disease in others. Today, this idea lives on as the One Health concept, which frames infectious disease as a problem that cuts across species boundaries. We are now aware that roughly 60% of known human pathogens are zoonotic, capable of being transmitted between animals and humans (2), and that many of the infectious diseases that have shaped human history, from plague to influenza, jumped from animals to people at some point in the past (3,4). A major question, however, is when and how these zoonotic transitions happened, and whether the shift to farming and animal husbandry during the Neolithic created the conditions for new pathogens to cross into human populations. Ancient DNA has become a powerful tool for investigating these questions in human remains, but the animal side of the equation has remained largely unexplored.

Bones that tell stories

Our AaRC speaker Dr. Anne Kathrine Runge described how she and a large team of collaborators set out to tackle a deceptively simple question: can we systematically recover ancient pathogen DNA from animal bones? And if so, can visible signs of disease on those bones help us pick the right specimens to sample? The challenge was considerable. Unlike human burials, where skeletons are often found articulated and relatively well preserved, animal remains in the archaeological record are mostly found as product of consumption or household waste: fragmented, scattered, exposed to the elements, and sometimes heated or boiled during food preparation. All of this inevitably degrades the DNA contained within. On top of that, most animals under human management died from slaughter rather than disease, and sick individuals may have been sacrificed early upon showing signs of infection, further reducing the chances of finding specimens that still carry traces of any pathology and microorganisms associated. To work around these difficulties, Anne Kathrine and her collaborators assembled a remarkable collection of 346 skeletal elements from at least 328 individual animals, spanning 34 Eurasian sites and roughly six millennia of human history, from the Neolithic to the Medieval period (5). They focused especially on the Bronze Age, a period when human-derived ancient pathogen genomes have been repeatedly recovered in the literature (6). The specimens came mostly from domesticated species (cattle, sheep, pigs, goats, and dogs) but also included wild animals. Critically, about half of the bones were selected because they showed palaeopathological lesions suggestive of infection: periostitis, osteolytic changes, abscesses, or other indicators of potential infectious disease. The rest were teeth or bones without visible lesions, serving as points of comparison.

What the screening revealed

After sequencing, metagenomic screening identified 116 authentic ancient DNA signatures from 29 bacterial species across 55 samples. These included primarily pathogenic species like Salmonella enterica, Erysipelothrix rhusiopathiae, Coxiella burnetii, and Bordetella petrii, alongside a range of opportunistic pathogens from the oral and gastrointestinal microbiome. No viral or eukaryotic parasites were detected. One of the most telling results was that palaeopathological lesions were significantly enriched for pathogen DNA recovery. Among bones with visible lesions, 23.3% produced robust bacterial hits, compared to 8.4% of teeth and none of the 27 bones without lesions. This supports the idea that expert palaeopathological assessment can meaningfully guide specimen selection for ancient pathogen studies in animals, something that had not been systematically tested before. Interestingly, Dr. Runge also observed striking geographic variation: the Bronze Age site of Tilla Bulak in Uzbekistan yielded a disproportionate number of hits, possibly reflecting better overall DNA preservation at that site, or perhaps a genuinely higher pathogenic pressure during that particular period and location.

Placing ancient pathogens on the evolution tree

For two of the recovered species, E. rhusiopathiae and S. lutetiensis, the authors had enough data to attempt phylogenetic placement of the ancient genomes within the known modern diversity. This is far from straightforward with low-coverage shotgun data, so they developed an approach where they first identified variable positions among high-quality modern genomes and then assessed base calls at those positions in the ancient samples. For E. rhusiopathiae, a genome recovered from a Bronze Age cattle tooth excavated at the site of Marinskaya 5 in the North Caucasus (Russia) clustered basally with previously published medieval genomes from Iberian human remains, suggesting that this pathogen was already spreading across multiple hosts in the past. Similarly, three ancient S. lutetiensis genomes from sheep and goat specimens at Tilla Bulak formed a monophyletic group basal to all known modern diversity in the species.

Challenges ahead

As Anne Kathrine described, this study represents an important first step toward expanding palaeomicrobiology into the zooarchaeological record. Her results show that pathogen DNA can indeed be recovered from animal remains despite the many challenges involved, and that palaeopathological analysis, which remains rare in animal contexts, can make a real difference in guiding sampling strategies. At the same time, the study highlights several open questions: Lesions are non-specific and cannot point to a particular pathogen, which limits how sampling strategies can be tailored to specific infections. The more porous remodeled bone within lesions may actually work against long-term DNA preservation. And the low coverage obtained from shotgun screening alone is not sufficient for in-depth genomic analyses, meaning that future work using targeted enrichment may be needed to reconstruct more complete pathogen genomes from animal remains. More broadly, this work brings the One Health perspective into the deep past. Recently, this retrospective approach has been formalized under the concept of One Paleopathology (7), which advocates for integrating archaeological evidence and deep-time perspectives on health across humans, animals, and the environment. By combining palaeopathological analysis, zooarchaeology, and ancient genomics, the work lead by Dr. Runge and her collaborators provides a concrete example of how this framework can be put into practice, opening a path to tracing zoonotic disease reservoirs, spillover events, and pathogen adaptation across millennia.

References

1. Klauder, J.V. Interrelations of human and veterinary medicine. N Engl J Med, 258:170-177 (1958).
2. Woolhouse, M.E.J. & Gowtage-Sequeria, S. Host range and emerging and reemerging pathogens. Emerg Infect Dis 11: 1842-1847 (2005).
3. Gage, K. L. & Kosoy, M. Y. Natural history of plague: perspectives from more than a century of research. Annu Rev Entomol 50, 505–528 (2005).
4. Taubenberger, J. K. The Origin and Virulence of the 1918 “Spanish” Influenza Virus. Proc Am Philos Soc 150, 86 (2006).
5. Runge, A.K.W. et al. Probing the zooarchaeological record across time and space for ancient pathogen DNA. Nat Commun 17, 3469 (2026).
6. Sikora, M. et al. The spatiotemporal distribution of human pathogens in ancient Eurasia. Nature 643, 1011–1019 (2025).
7. Buikstra, J.E., Uhl, E.W. & Robbins Schug, G. One Paleopathology and lessons from the past. BioScience, biaf115 (2025).

Below, Anne Kathrine shared with us further details about her profile, career, prospects and future projects:

1. Briefly introduce yourself. What is your origin story for how you got into science?
I grew up in the Danish countryside with nature just outside my door. One of my grandfathers was a farmer who loved animals and plants, and the other was so enthused by beetles that he was one of the leading entomologists in the country, and I loved following them around learning about all the different species that surround us. For this reason, no one was really surprised that I wanted to study biology. At uni I fell in love with genetics then genomics, and especially ancient genomics, and I was lucky that I got the opportunity to pursue this interest.

2. How and/or why did you start working on this project?
That was a bit of a happy accident, I think. Originally the project was quite different, but despite having everything in place and verbally agreed on, in the end we did not get the sampling permit. So we had to pivot, and fortunately our amazing collaborators stepped in with samples from sites they had already worked on. Together we made it work, and I’m really grateful for everyone who contributed to that.

3. Were there any major challenges in this project? How did you overcome them?
I think the biggest challenge in the project was that we could not know beforehand which pathogen we would find if we managed to get DNA at all. There are a lot of really interesting questions that can be asked about zoonotic diseases, early spillover events, reservoir populations, host adaptation, and evolution, but they hinge on being able to obtain specific pathogen DNA from non-specific lesions that are less than optimal for DNA preservation. We overcame this by processing a lot of samples, but even then, we only had a handful of samples that produced something really interesting, and for these, we still only had the screening data and could not do anything in depth.

4. What do you think are the main take-home messages of this project?
Genuinely, I think the take-home message is that this was really difficult, but also that there are ways to make studying ancient pathogens from animal remains easier. It does require collaboration with an expert in palaeopathology, and these people, especially those that focus on animal pathology, are rare. I also think that there are some really interesting implications for future studies and I hope it will help future researchers design some super cool studies.

5. What do you think is missing in the field that you would like to work on?
The biggest thing? That’s definitely the ability to look at a lesion and know which pathogen caused it. Unfortunately, that is unlikely to become any easier and looking for specific pathogens in animal remains is likely going to continue to be really difficult. What can be worked on, however, is sampling strategies. For example, where on the bone is the best place to sample, as well as optimizing DNA extraction methods for pathogen DNA.

6. Where do you see yourself in the near future?
I see myself back in Denmark and hopefully in an industry job. I have not quite figured out what I want, but I know it is not academia.

7. Free space to tell something you would like to remark.
I’m really looking forward to seeing where this field will go in the future.