Analyzing Horizontal Gene Transfer in the Human Body

Bacteria in the human body share genes with one another at a higher rate than is typically seen in nature. The findings, published today in Scientific Reports, resulted from a molecular data-mining method that allowed scientists to identify instances of horizontal gene transfer—the direct transfer of genes between organisms outside of sexual or asexual reproduction.

“Horizontal gene transfer is a major force of exchange of genetic information on Earth,” says coauthor Gustavo Caetano-Anollés of the University of Illinois. “These exchanges allow microorganisms to adapt and thrive, but they are likely also important for human health. There are some bacteria that cannot live outside our bodies and some without which we cannot live.”

For their analysis, the scientists used genomic information to build tens of thousands of “family trees” of the bacteria that colonize the human body. Reconciling those with trees of microbial genes allowed the team to tease out which genes had been inherited and which had resulted from horizontal gene transfer.

“Most current methods for determining horizontal gene transfer compare DNA features or statistical similarity between genomes to identify foreign genes. This works fairly well for relatively recent gene transfers, but often fails to identify transfer events that occurred millions or billions of years ago,” says senior author Arshan Nasir of COMSATS University Islamabad.

Looking at human-associated microorganisms, the researchers calculated rates of gene-transfer and found that only about 40% of gene swapping occurred among bacteria 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 blood. In all cases, gene transfer was most common among closely related organisms, regardless of whether they occupied the same or different bodily tissues.

“Some of these could be very old gene transfer events that happened before the microbes colonized the human body,” Nasir says. “It also could be that some bacteria colonize different human body sites at different time points in an individual’s lifespan. The others could be the result of the transfer of bacterial DNA from one site to another, perhaps through the blood. We need further experimental evidence to test this tantalizing possibility.”

Other scientists can use the tool the researchers developed—HGTree—in order to more accurately predict which genes were inherited vertically versus horizontally.