CHAMPAIGN, Ill. – Bacteria in the human body share genes with each other at a higher rate than observed in nature, and some of these genes seem to travel – regardless of their microbial hosts – from one part of the body to another, the researchers report in the journal Scientific Reports.
The findings are the result of a molecular data mining method originally designed by Kyung Mo Kim, a senior scientist at the Korean Polar Research Institute. Gustavo Caetano-Anollés, professor at the Institute of Genomic Biology of the University of Illinois, has developed the approach with his former student, Arshan Nasir, of COMSATS University. from Islamabad, Pakistan, who is currently a distinguished member of the Los Alamos National Laboratory in New Mexico.
This complicated computer method allowed them to identify examples of "horizontal gene transfer", the direct transfer of genes between organisms outside of sexual or asexual reproduction.
"Horizontal gene transfer is a major force in the exchange of genetic information on Earth," said Caetano-Anollés. "These exchanges allow microorganisms to adapt and grow, but they are also probably important for human health.Some bacteria can not live outside of our body and others without which we can not live. "
"A better understanding of this phenomenon will also have significant value for public health, as the emergence of multidrug-resistant pathogens resulting from horizontal spread of antibiotic-resistant genes has become a global concern," Nasir said. .
For the new analysis, scientists have used genomic information to create tens of thousands of "family trees" of bacteria that colonize the human body. Reconciling those with microbial gene trees allowed the team to determine which genes had been inherited and which ones resulted from horizontal gene transfer.
"Most current methods for determining horizontal gene transfer compare DNA characteristics or statistical similarity between genomes to identify foreign genes," Nasir said. "It works pretty well for relatively recent gene transfers, but often fails to identify transfer events that occurred millions or billions of years ago."
The more laborious approach allowed the team to overcome this barrier, he said.
"We have studied the microorganisms associated with humans because they are known to be key players in the maintenance of human health and metabolism," said Nasir. "We calculated the gene transfer rates and the direction – who transferred what to whom – for more than 1,000 reference bacterial genomes sampled by the National Institutes of Health's human microbiome project."
The bacterium had been sampled from six sites of the human body: the intestine, the skin, the oral cavity, the blood, the urogenital tract and the respiratory tract.
Researchers have found evidence to support earlier findings that genes associated with human-associated bacteria are quite promising, said Caetano-Anollés.
"Horizontal exchanges between microbes in our bodies are about 30% higher than what you find on the rest of the planet," he said. "This implies that our bodies provide a unique niche that facilitates microbial innovation."
About 40% of gene exchange occurred in bacteria living in the same body sites. The remaining 60% involved gene sharing between bacteria of different tissues, for example between intestinal and blood organisms.
In all cases, gene transfer was the most common among closely related organisms, whether they occupied identical or different body tissues. In fact, the researchers reported that gene sharing between organisms in different body sites was more common than sharing between distant bacteria living at the same sites.
"Some of these events could be very old gene transfer events that occurred before microbes colonized the human body," said Nasir. "It's also possible that some bacteria colonize different sites of the human body at different times in life, and others may result from the transfer of bacterial DNA from one site to another, perhaps through the blood. We need additional experimental evidence to test this tempting possibility. "
The researchers say that other scientists can use the tool that they developed for this work, HGTree, to more accurately predict which genes were inherited "vertically" during the reproductive process, and which were taken from other microbes by horizontal gene transfer. This will lead to a better understanding of microbial and human evolution, the researchers said.
Former graduate students Hyeonsoo Jeong and Bushra Arif contributed to this research.
The National Science Foundation has supported the international collaboration that has made this work possible.
To join Gustavo Caetano-Anollés, dial 217-333-8172; email [email protected]
To reach Arshan Nasir, call 505-606-0138; email [email protected]
To join Kyung Mo Kim, call + 82-32-760-5379; email: [email protected]
The document "Horizontal Gene Transfer in Human-Associated Microorganisms Induced by Phylogenetic Reconstruction and Reconciliation" is available to members of the media at the U. Of I. News Bureau
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