Scientists Reconstructed Eight Ancient Salmonella Pathogens

The Neolithic revolution, as well as the associated transition to agricultural and pastoralist lifestyles, portrays one of the most drastic shifts in human history, and it has been theorized for some time now that this might have offered the chance for the rise of human-adapted diseases.

A new paper published in the journal Nature Ecology & Evolution led by three scientists from the Max Planck Institute for the Science of Human History, namely, Felix M. Key, Alexander Herbig, and Johannes Krause, details the analyses of human remains unearthed from Western Eurasia.

The study authors reconstructed eight ancient Salmonella enterica genomes, all of them belonging to a related group of the modern S. enterica. These findings showcase what was probably a major health concern in the past and unveil the way this bacterial pathogen developed throughout 6,500 years.

Eight Ancient Pathogens Reconstructed

A major part of pathogens does not generate any lasting effects on the skeleton, which can make detecting impacted archaeological remains challenging for experts. But to identify ancient diseases and reconstruct their development, scientists have utilized genetic methods.

Using a recently created bacterial screening pipeline known as HOPS, the team of researchers was able to subdue numerous difficulties of finding ancient viruses in metagenomics data.

“With our newly developed methodologies, we were able to screen thousands of archaeological samples for traces of Salmonella DNA,” says Herbig.

The team screened 2.739 ancient human remains and managed to reconstruct eight Salmonella genomes about 6,500 years old, which are the oldest reconstructed bacterial genomes until now.

The remains that were examined came from sites located in Switzerland and Russia, portraying various cultural groups, from hunters to nomadic herders to early farmers.

“This broad spectrum in time, geography, and culture allowed us, for the first time, to apply molecular genetics to link the evolution of a pathogen to the development of a new human lifestyle,” explained Herbig.

The ‘neolithization process’ allowed the pathogen to evolve.

“Ancient metagenomics provides an unprecedented window into the past of human diseases,” says lead author Felix M. Key. “We now have molecular data to understand the emergence and spread of pathogens thousands of years ago, and it is exciting how we can utilize high-throughput technology to address long-standing questions about microbial evolution.”

The Origins are Way Older Than Previously Thought

The team of scientists could determine that six of the Salmonella genomes restored from herders and farmers are ancestors to a strain that particularly contaminated humans, known as Paratyphi C, but which is rather rare today.

Those old Salmonella, though, were most likely not yet configured to humans, and rather, infected both humans and animals. Researchers have previously suggested that this strain of Salmonella extended from domesticated pigs to humans about 4,000 years ago, but the finding of more ancient strains in humans over 5,000 years ago, implies that the pathogen might have spread from humans to pigs.

Even so, the authors plead for a more moderate theory, where both human and pig-particular Salmonella developed independently from uncertain precursors as the environment permitted close contact between humans and animals.

“The fascinating possibilities of ancient DNA allow us to examine infectious microbes in the past, which sometimes puts the spotlight on diseases that today most people don’t consider to be a major health concern,” says Johannes Krause, director at the Max Planck Institute for the Science of Human History.

The study enables researchers to a glimpse of the changes in these illnesses as time passed and in various human cultural environments.

“We’re beginning to understand the genetics of host adaptation in Salmonella,” says Key, “and we can translate that knowledge into mechanistic understanding about the emergence of human and animal adapted diseases.”

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