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Microbes in the human body swap genes, even across tissue boundaries, study indicates



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IMAGE: University of Illinois alumnus Arshan Nasir and his colleagues at Illinois and in Korea studied genetic exchange among human-associated microorganisms. Nasir is now a postdoctoral fellow at the Los Alamos …
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Credit: Photo courtesy of Carlos Trujillo at Los Alamos National Laboratory

CHAMPAIGN, Ill. ̵

1; Bacteria in the human body are sharing genes with one another at higher rates than is typically seen in nature, and some of those genes appear to be traveling – independent of their microbial hosts – from one part of the body to another, researchers report in the journal Scientific Reports.

The findings are the result of a molecular data mining method initially conceptualized by Kyung Mo Kim, a senior research scientist at the Korea Polar Research Institute. University of Illinois crop sciences and Carl R. Woese Institute for Genomic Biology Professor Gustavo Caetano-Anollés developed the approach with his former student Arshan Nasir, or COMSATS University Islamabad, Pakistan, who is currently a Distinguished Fellow at the Los Alamos National Laboratory Mexico.

This computationally challenging method allows them 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, "Caetano-Anollés said. "These exchanges allow microorganisms to adapt and thrive, but they are probably also important for human health. There are some bacteria that cannot live outside our bodies and without which we cannot live."

"A better understanding of this phenomenon. will have significant public health value, since the emergence of multidrug-resistant pathogens as a result of the horizontal spread of antiobiotic-resistant genes has become a global concern, "Nasir said.

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 Allowing the team to release which genes had been inherited and which were the result of horizontal gene transfer [MostcurrentmethodsfordetermininghorizontalgenetransfercompareDNAfeaturesorstatisticalsimilaritybetweengenomestoidentifyforeigngenes"Nasirsaid"Thisworksfairlywellforrelativelyrecentgenetransfersbutoftenfailstoidentifytransfereventsthatoccurredmillionsorbillionsofyearsago"

The more labor-intensive approach enabled the team to surmount this barrier, he said.

"We studied human-associated microorganisms, since they are known to be key players in maintaining human health and metabolism," Nasir said. "We calculated genes-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 bacteria had been sampled from six human body sites: the gut, skin, oral cavity, blood, urogenital tract and airways.

The researchers found evidence to support earlier findings that human-associated bacteria are quite prominent with their genes, said Caetano-Anollés.

"The horizontal exchange between microbes in our bodies are about 30 percent higher than what you'll find on the rest of the planet, "he said. "This means that our bodies provide a niche that is unique and facilitates innovation at the microbe level." About 40 percent of gene swapping occurred among bacteria living in the same body sites. The other 60 percent 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 higher rates than gene sharing among distant 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 said. "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. to test this tantalizing possibility. "

The researchers say other scientists can use the tool they developed for this work, HGTree, to more accurately predicted which genes were inherently" vertically, "through the process of reproduction, and which were picked up. from other microbes through horizontal gene transfer.

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Forms graduate students Hyeonsoo Jeong and Bushra Arif contributed to this research.

The National Science Foundation supported the international collaboration that made this work possible.

Editor's notes:

To reach Gustavo Caetano-Anollés, call 217-333-8172; email gca@illinois.edu.

To reach Arshan Nasir, call 505-606-0138; email arshan.nasir@gmail.com.
To reach Kyung Mo Kim, call + 82-32-760-5379; email: kmkim@kopri.re.kr.

The paper "Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation" is available to members of the media from the U. or I. News Bureau

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