While promiscuity has historically been frowned upon in many societies, in the microbial world, it is essential for survival. The idea that bacteria swap genetic material between themselves was first described in the late 1920s and was dubbed horizontal gene transfer (HGT). Though an abundance of research has elucidated the molecular mechanisms for this transfer of genetic information, only recently have researchers discovered that bacteria in the human body are sharing genes with one another at a higher rate than is typically seen in nature. More interestingly, these genes appear to be traveling—independent of their microbial hosts—from one part of the body to another.
These new findings are part of a novel molecular data-mining method employed by investigators at the University of Illinois and the University of Islamabad. This computationally challenging method allowed the researchers to identify instances of horizontal gene transfer, the direct transfer of genes between organisms outside of sexual or asexual reproduction. Findings from the new study were published today in Scientific Reports through an article titled “Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation.”
“Horizontal gene transfer is a major force of exchange of genetic information on Earth,” explains study author Gustavo Caetano-Anollés, PhD, a professor at 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.”
“A better understanding of this phenomenon also will have significant public health value, since the emergence of multidrug-resistant pathogens as a result of the horizontal spread of antibiotic-resistant genes has become a global concern,” states senior study investigator Arshan Nasir, PhD, of COMSATS University Islamabad, and who is currently a distinguished fellow at the Los Alamos National Laboratory in New Mexico.
For the new analysis, the scientists used genomic information to build tens of thousands of “family trees” of 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 were the result of horizontal gene transfer.
“Most current methods for determining horizontal gene transfer compare DNA features or statistical similarity between genomes to identify foreign genes,” Nasir says. “This works fairly well for relatively recent gene transfers, but often fails to identify transfer events that occurred millions or billions of years ago.”
While more labor-intensive, the new approach enabled the team to overcome this barrier.
“We studied human-associated microorganisms since they are known to be key players in maintaining human health and metabolism,” Nasir says. “We calculated gene-transfer rates and direction—who transferred what to whom—for more than 1,000 reference bacterial genomes sampled by the National Institutes of Health Human Microbiome Project.”
The researchers sampled bacteria from six human body sites: the gut, skin, oral cavity, blood, urogenital tract, and airways. Amazingly, the research team found evidence to support earlier findings that human-associated bacteria are quite promiscuous with their genes.
“The horizontal exchange between microbes in our bodies is about 30% higher than what you’ll find on the rest of the planet,” he says. “This implies that our bodies provide a niche that is unique and facilitates innovation at the microbe level.”
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 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, the researchers report, 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.
“Some of these could be very old gene transfer events that happened before the microbes colonized the human body,” Nasir concludes. “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.”