Friday, February 28, 2020

The First Salmonella: Transition from Hunter-Gather to Farmer Brought New Diseases

The oldest bacterial genomes that have been reconstructed to date show that agriculture and animal husbandry brought new diseases with them

On the basis of the genomes of the Salmonella enterica bacterium , which were obtained from skeletons up to 6,500 years old, an international research team was able to find new evidence for a central hypothesis for the development of diseases. Accordingly, the transition from a hunter-gatherer culture to agriculture and animal husbandry favored the emergence of new human pathogens that still exist today.

Dangerous proximity: Research has long suspected a connection between the emergence of agriculture and animal husbandry and the development of pathogens that jump from animals to humans. The analysis of the genetic material of salmonella that is thousands of years old confirms this thesis for the first time.

Credit: © Annette G├╝nzel

The Neolithic Revolution and with it the beginning of agriculture stands for one of the key moments in the history of mankind. It was long believed that this was also the reason for the emergence of many new human diseases.

In a current study, a team led by Felix M. Key, Alexander Herbig and Johannes Krause from the Max Planck Institute for Human History examined human remains from western Eurasia and reconstructed eight ancient genomes from Salmonella enterica . All reconstructed genomes are part of a related group within the much larger variety of today's Salmonella pathogen. The results shed light on what was probably a serious health problem in the past and show how the bacterial pathogen developed over a period of 6,500 years.

Humans, pigs, and the origin of Paratyphi C

The analysis showed that the six salmonella genomes from farmers and ranchers are precursors of the Paratyhpi C bacterial strain - a strain that specifically infects humans, but is now rare. It triggers typhoid-like symptoms that can be fatal if left untreated.

The historical Salmonella, however, were probably not yet adapted to humans and infected animals as well as humans. This suggests that the new cultural habits associated with the introduction of agriculture have facilitated the emergence of these precursors and thus human-specific diseases.

So far, it has been assumed that the Salmonella strain spread to humans via domesticated pigs 4,000 years ago. However, the discovery of the predecessor strain in skeletons more than 5,000 years old suggests that it originated earlier than previously thought and may have spread from humans to pigs. However, the authors of the study advocate the more moderate hypothesis that both human and pig-specific Salmonella developed independently from unspecific precursors within an environment of close contact between humans and animals.

The difficult search for historical pathogens

When examining fossil finds, it is usually difficult to tell whether or not an individual was infected with a pathogen during his lifetime. Because only a few pathogens leave permanent traces on human remains such as bones or teeth. In order to be able to reliably identify previous pathogens and reconstruct their history, research is now using genetic techniques.

In the current work, the team around Key helped a new computer-controlled process called HOPS to overcome these obstacles in the search for historical pathogens in the metagenomic data. "With our newly developed methods, we were able to examine thousands of archaeological samples for traces of Salmonella DNA," explains Alexander Herbig, research group leader at the Max Planck Institute for Human History.

The research team examined a total of 2,739 human remains and was able to use them to construct eight salmonella genomes up to 6,500 years old. These are the oldest reconstructed bacterial genomes to date.

The relationship between the samples examined and the reconstructed genomes illustrates another hurdle in the field of historical pathogen research. Hundreds of samples are often required to decode only one pathogen genome. In the case of the present study, the genetic material of the pathogen could be extracted from the teeth of the human remains. The finding of S. enterica in the teeth suggests that individuals had systemic salmonella infection at the time of their death.

The people examined came from various European regions, from Russia to Switzerland, and were late hunters and gatherers, nomadic ranchers or early farmers. "This broad temporal, geographical and cultural spectrum enabled us, for the first time, to use molecular genetics to link the evolution of pathogens with the advent of a new human lifestyle," explains Herbig.

Contacts and sources: 
Petra Mader, Alexander Herbig, Prof. Dr. Johannes Krause
Max Planck Institute for Human History

Publication: Emergence of human-adapted Salmonella enterica is linked to the neolithization process Felix M. Key et al. Nature Ecology and Evolution (2019)

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