Widespread microbial exchange of genes in our human body

Evolutionary genomics provides strong support to the notion that the microbes of the human 'microbiome' are swapping genes between them at an extraordinary pace. This widespread genomic exchange carries also memory of its deep history. The findings are the result of a molecular data-mining method that allows to identify instances of 'horizontal gene transfer' (HGT), the direct transfer of genes between organisms outside of sexual or asexual reproduction. Results show that HGT is a major force of exchange of genetic information on Earth and that exchange is massive inside our human bodies.

The method uses genomic information to build tens of thousands of “family trees” of microbiome bacteria . Reconciling those with trees of microbial genes allowed o tease out which genes had been vertically inherited and which were the result of HGT processes. Besides finding evidence to support earlier findings that human-associated bacteria are quite promiscuous with their genes, the new study revealed that 40% of swapping occurred between microbes living in the same body sites. The other 60% involved gene sharing among bacteria in different tissues, for example between organisms in the gut and in blood. In all cases, gene transfer was most common among closely related organisms, regardless of whether they occupied the same or different bodily tissues. In fact, gene sharing among organisms in different body sites occurred at a higher rate than gene sharing among distantly related bacteria living at the same sites. This interplay between genetic relatedness and physical location of microbes in our body will lead to improve understanding of microbial evolution and the role that microbes play in human makeup.

Jeong H et al. (2019) Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation. Scientific Reports 9(1):12173