I am excited to share our new paper about the emergence of human-adapted Salmonella enterica linked to the Neolithization process. https://www.nature.com/articles/s41559-020-1106-9
Find below a summary of the main findings in a short thread.

We used HOPS, to screen over 2700 metagenomic datasets available @MPI_SHH and recovered eight Salmonella genomes. The first major application of our recently published tool. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1903-0

We report ancient Salmonella genomes from transitional foragers, pastoralists, and agropastoralists up to 6,500 year old, the oldest bacterial genomes so far and geographically widespread across western Eurasia.

All ancient Salmonella enterica cluster in a previously undetected super-branch, within the much larger genetic diversity of modern S. enterica. Those findings put the spotlight on a type of Salmonella that today most people don’t consider to be a major health concern.

We found all six Salmonella genomes recovered from herders and farmers are progenitors to human-adapted Paratyphi C. This finding provides first aDNA evidence in support of the hypothesis that the Neolithization process facilitated the emergence of human-adapted disease.

Variation in mobile gene content likely led to variation in pathogenicity within the ancient strains, as well as between ancient and modern strains. Importantly, non of the newly reported ancient Salmonella carry SPI-7, which has been linked to enteric fever caused by Paratyphi C

Phylogeny as well as the low level of pseudogenes suggest the prehistoric Salmonella where not yet host adapted, and instead were able to infect humans and also animals. We observe a strong correlation between time and pseudogene accumulation (r2 = 0.48) in the ancient genomes.

Host adapted S. enterica carry high levels of pseudogenes, which we test for signatures of convergent evolution. We find a gene (phoN) lost independently in 4 different host adapted S. enterica, which was previously described to cause strong antibody response in humans and mice.

Lastly, this paper was a huge collaborative effort. I want to thank everybody involved!

Here is a link with no paywall providing access to read the paper https://rdcu.be/b17sP