A new study has revealed that bacteria in the human body are sharing genes with each other at a much higher rate than expected. Using a new molecular data-mining method, the team discovered that some of the genes are even moving themselves from one part of the body to another without depending on their microbial hosts to carry them.
The mining technique used for the study was initially conceptualized by Kyung Mo Kim, a senior research scientist at the Korea Polar Research Institute, and was developed by Biology Professor Gustavo Caetano-Anollés at the University of Illinois. This new method allowed the experts to pinpoint cases of “horizontal gene transfer,” which is 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,” said Professor Caetano-Anollés. “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,” said Arshan Nasir, a former student of Professor Caetano-Anollés who assisted in developing the technology used for the study.
The scientists used genomic information to build tens of thousands of “family trees” of bacteria that colonize the human body. By comparing these bacterial family trees with trees of microbial genes, the team was able to identify 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,” said Nasir. “This works fairly well for relatively recent gene transfers, but often fails to identify transfer events that occurred millions or billions of years ago.”
“We studied human-associated microorganisms, since they are known to be key players in maintaining human health and metabolism. 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.”
Bacteria samples had been collected from the skin, blood, oral cavity, gut, airway, and the urogenital tract. According to Professor Caetano-Anollés, the researchers 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 percent higher than what you’ll find on the rest of the planet. This implies that our bodies provide a niche that is unique and facilitates innovation at the microbe level.”
The study is published in the journal Scientific Reports.