How Farming Unleashed a Surge of Pathogens around the World

Some religious traditions teach that world history began 6,000 years ago. Science does not support this exact timeline. But a major shift in human life did happen at that point: farming and livestock domestication began spreading across Eurasia.

New research in Nature shows that more than crops and animals multiplied. Zoonotic pathogens—diseases from animals—first appeared about 6,500 years ago. These infections surged around 5,000 years ago. The rise of pastoral life helped them spread more easily.

Scientists studied ancient DNA to trace disease over time and space. They analyzed samples from 1,313 individuals across 37,000 years. The microbes came from 136 different genera—bacteria, viruses, and parasites. Of these, 3,384 matched known human pathogens.

Thousands of these diseases had never been seen in ancient remains. This study reveals how microbes changed with human culture. It marks a turning point in the long story of human health.

How Researchers Used Ancient DNA to Trace Pathogen Spread

Researchers developed a scalable method to detect ancient microbial DNA. They screened 405 billion DNA reads from human remains. Samples came from Western Eurasia, Central and North Asia, and Southeast Asia. Most samples—77%—came from Western Eurasia.

They selected 136 bacterial and protozoan genera and 1,356 viral genera. These groups included many known human pathogens. The study identified 5,486 microbial DNA markers in total. Of these, 3,384 came from 214 known disease-causing species.

Some detected microbes came from the human oral microbiome. Others, like Clostridium and Pseudomonas, came from soil and reflect burial conditions. Researchers used a measure called average nucleotide identity (ANI). ANI compares ancient DNA to modern reference genomes.

High ANI suggests the DNA closely matches modern strains. Low ANI may come from damaged DNA or mixed strains. For example, Mycobacterium leprae, which causes leprosy, showed high ANI. Other species were more distantly related to modern references.

Researchers tested for mixed infections by comparing DNA alleles. Many oral microbes showed high multi-allele rates. This suggests multiple strains existed in the same sample. These mixtures were especially common in oral bacteria.

Some species, like M. leprae, had high read counts. Others, like Borrelia recurrentis—which causes relapsing fever—had very low counts. High read counts meant strong microbial presence in the remains.

Overall, the study showed a complex mix of ancient microbial DNA. It revealed how both pathogenic and environmental microbes coexisted in human remains.

What the Study Revealed About Ancient Pathogens in Eurasia

The new study expands what is known about ancient human pathogens. Researchers identified new species and wider ranges for known infections. Many pathogens had never been reported in ancient DNA before. Others appeared more often or earlier than expected.

Yersinia pestis, the plague bacterium, appeared in 42 ancient individuals. Thirty-five of these plague cases are newly reported. The earliest infections date from 5,700 to 5,300 years ago. These cases came from Russia, Central Asia, and Siberia.

This early spread challenges the idea of isolated plague outbreaks. The findings suggest early local epidemics may have occurred. Some burial sites had several infected individuals. This supports human-to-human or local vector transmission.

Mycobacterium leprae, the cause of leprosy, appeared in seven individuals. All cases came from Scandinavia and post-Iron Age contexts. The earliest case occurred about 1,500 years ago. The results support a link between leprosy and the squirrel fur trade.

Many pathogens appeared in the dataset, but tuberculosis was missing. Tuberculosis bacteria rarely enter the bloodstream unless disease is severe. Latent TB also makes detection more difficult. Tooth and bone samples are not ideal for recovering TB DNA.

The team also found evidence of co-infections. They identified 15 individuals with multiple simultaneous infections. These included bacterial, viral, and parasitic pathogens. One Viking Age individual had both leprosy and smallpox.

Researchers believe co-infections are likely undercounted. Pathogen levels, sample types, and detection limits affect results. Still, ancient DNA offers new insights into past disease burdens. The findings confirm that ancient lives were shaped by widespread illness.

How Ancient Lifestyles Shaped Disease Patterns

Human lifestyles changed with the rise of farming and herding. These changes increased contact with animals and the spread of disease. The new study offers large-scale molecular proof of that shift. Zoonotic pathogens first appeared around 6,500 years ago.

Their spread increased steadily after 6,000 years ago. While zoonoses may have existed earlier, herding raised the overall risk. Pastoralists likely built partial immunity through constant animal contact. As they migrated, they carried infections into new regions.

These disease waves may have reduced local populations. Depopulated areas were later resettled by newcomers. This pattern mirrors the collapse of Indigenous populations after European contact. Infections helped shape who lived, died, and resettled.

The study supports the idea that infection shaped human evolution. Immune system genes began adapting after the Bronze Age. These genetic changes remain present in humans today. Bacterial shifts and poor hygiene likely worsened historical outbreaks.

Crowded living and lice infestations raised infection risks. Together, these forces created long-term disease burdens. Farming and herding deeply changed how humans interacted with disease. The effects of that transition are still seen today.

Conclusion

The study shows how farming and herding reshaped human disease risks. Zoonotic infections rose sharply after 6,000 years ago. These changes still affect human health and immunity today.

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Logan Hamilton is a health and wellness freelance writer for hire. He’s passionate about crafting crystal-clear, captivating, and credible content that elevates brands and establishes trust. When not writing, Logan can be found hiking, sticking his nose in bizarre books, or playing drums in a local rock band. Find him at loganjameshamilton.com.