COVID-19 has reminded us just how devastating infectious diseases can be. Animals are a major source of these diseases, with around 60% of emerging infectious diseases being zoonotic, meaning they jump from animals to humans. And we might share some of the blame for zoonoses – humans have created the ideal circumstances for zoonotic diseases to spread. Around 10 000 years ago in southwest Asia humans started to domesticate livestock animals, an important environmental change for animals, humans, and the pathogens affecting both. By bringing different animals together to have access to steady supplies of meat and milk, humans also created a favourable environment for pathogens to jump between species, specialising to new hosts.
But which infectious diseases were early livestock and herders facing? Were the first farmers dealing with the same zoonoses we see today? Did domestication influence pathogen evolution?
Today, the most prevalent bacterial zoonosis is brucellosis, an infection causing illness such as waves of “undulating” fever and joint pain in animals and humans. Furthermore, infection can induce abortions in both pregnant animals and women, causing great emotional and economic harm around the world. Given Brucella’s impact on modern humans and livestock, we wanted to explore if early herders and their animals were already infected by this bacterium and how different these ancient pathogens were from today’s strains.
Despite the high prevalence nowadays, only two ancient Brucella genomes from humans have been recovered so far – both from the Middle Ages. However, it’s believed that brucellosis is much more ancient. Skeletal and archaeological evidence suggests the disease was present in Neolithic settlements in Southwest Asia, where animal farming was first practised, but no DNA evidence has been found yet. Most ancient pathogen DNA studies focus on human remains, but animal remains can also be a source of pathogen DNA. So, instead of targeting humans, we decided to investigate their domesticated ruminants—cattle, sheep, and goats—which can also be infected by Brucella.
To uncover ancient infections, we extracted DNA from ruminant bones and teeth dating back to the era of animal domestication in Southwest Asia. DNA degrades over time, but it’s still possible to find ancient DNA in archaeological remains. However, only a tiny fraction of the extracted DNA is actually ancient; the rest is modern environmental contamination. To avoid contaminating the ancient samples with human or human microbiome DNA, we wear full-body lab coats designed to minimise contamination.
Ancient DNA lab work means we have to wear full-body lab coats to protect the samples from contamination – us. Image copyright: Kevin G. Daly.
Using various metagenomics approaches – searching the ancient DNA molecules for some which might match a particular microbe – we discovered one specimen carrying ancient Brucella DNA. This DNA came from the petrous part of the temporal bone (which surrounds the inner ear), known for its density and excellent preservation of DNA in ancient samples. The infected specimen was an ~8000-year-old female sheep from Menteşe Höyük – an ancient farming settlement in Northwest Türkiye. We called the sample Mentese6.
The petrous part of the temporal bone in which we found ancient Brucella DNA.
Pathogenic Brucella bacteria are so closely related that telling one species from another can be quite a challenge. When we examined the ancient Brucella DNA from Mentese6, we focused on genetic changes (variants) that define different Brucella species. This showed that the Menteşe Höyük Brucella had nearly all (99%) of the genetic variants shared by both Brucella melitensis (infecting mostly sheep and goat) and Brucella abortus (infecting mostly cattle). This made us confident we had detected one of these two bacterial species. Mentese6 also carried 28% of the sites specific to Brucella melitensis and none (0%) of those specific to Brucella abortus (see figure below).
This suggests that the Menteşe Höyük Brucella is an ancestral Brucella melitensis – the species which today infects sheep and goat, and is the most common cause of brucellosis in humans. But as Mentese6 only had 28% of genetic variants specific to Brucella melitensis , we reasoned the genome was from shortly after Brucella melitensis and Brucella abortus split into separate species.
Figurative representation of the genetic sites species detection method used on the ancient Brucella DNA. The proportion of sites that our genome is matching is outputted in front of each species name. The typical animal hosts of each Brucella species are shown in silhouette.
Ancient pathogen genomes are a goldmine of information. They are molecular fossils and can be used to calibrate the timing of speciation between pathogen species.
Using the ancient Brucella melitensis genome, we estimated that Brucella melitensis (which infects sheep and goats) and Brucella abortus (which infects cattle) evolved from their common ancestor around 9,800 years ago. This period coincided when the Neolithic early farmer began keeping different animals together, notably sheep, goats, cattle, and pigs. Often, these species were living closely together for the first time. Early herders might have also kept these mixed herds packed together into enclosures or even in houses. This new proximity between the livestock animals likely facilitated the spread of pathogens and host specialisation during the Neolithic – maybe from a more generalist Brucella ancestor.
Potential scenario of Brucella melitensis and Brucella abortus evolution linked with animal domestication. Brucella abortus is represented in green and Brucella melitensis in red.
Our work presents the oldest reported livestock pathogen and zoonotic genome to date. It reveals that Brucella melitensis, a common modern zoonosis, was already infecting animals during the Neolithic period and dates the origin of this zoonosis to around 9,800 years ago. This finding suggests that the process of domestication significantly impacted the evolution of this modern disease. Hopefully, we will learn more about how domestication affected the risk of disease and zoonoses – animal bones may be hiding the story of their evolution.