Saturday, 25 May 2019

How microbes in the human body swap genes


Bacteria in the human body are sharing genes with one another at a higher rate 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.

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. This computationally challenging method allowed 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, 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 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.

The researchers studied human-associated microorganisms, since they are known to be key players in maintaining human health and metabolism and 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 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 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.

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 a higher rate than gene sharing among distantly related bacteria living at the same sites.

The researchers say other scientists can use the tool they developed for this work, HGTree, to more accurately predict which genes were inherited "vertically," through the process of reproduction, and which were picked up from other microbes through horizontal gene transfer. This will lead to an improved understanding of microbial -- and human -- evolution.

See: Hyeonsoo Jeong, Bushra Arif, Gustavo Caetano-Anoll├ęs, Kyung Mo Kim, Arshan Nasir. Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation. Scientific Reports, 2019; 9 (1) DOI: 10.1038/s41598-019-42227-5

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology

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Pharmaceutical Microbiology

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