Researchers have discovered an underworld of genetic exchange among bacteria, one more vast than previously imagined.

A comparison of thousands of bacterial genomes from around the world found genes flowing easily between species separated by hundreds, even thousands of miles. Whether the bacteria were related or not didn’t matter — a fascinating phenomenon on its own, but disturbing when the genes involved could turn pathogens into drug-resistant superbugs.

“We should have done this study and asked these questions five years ago,” said microbiologist Eric Alm of MIT, leader of a study published online Oct. 30 in Nature. “The significance was off the charts.”

Bacteria readily exchange DNA between closely related species, and much less frequently across unrelated lineages. This so-called horizontal gene transfer fuels adaptation, allowing for rapid adjustments to local pressures. Its full extent, however — especially in bacteria associated with humans, including those in our bodies, where bugs outnumber cells by 10 to 1 — are unknown.

To get a global picture of horizontal gene transfer, Alm, two graduate students and other collaborators compared 2,235 different bacterial genomes. “I was hoping to find five to 10 examples of recent gene transfers,” he said. “My students came back in a week with 10,000 different genes that had been transferred.”

The researchers compared transfers in several ways: first by the microbes’ genetic similarities, and then by geographic distance separating the locations of their collection. Neither followed a predictable pattern, but patterns did emerge when the researchers analyzed ecological niches.

Instead of swapping genes with microbes genetically related to them, or near them, bacteria seem to be swapping with microbes fulfilling similar roles. Alm’s team also found that genes especially important to humans — those found in our stomach flora, for example, or genes conveying antibiotic resistance — are particularly good at long-distance swaps.

In the future, Alm hopes to look more closely at gene transfer in virulent microbes, such as those that cause meningitis. Tracking genes that are especially likely to flow could help identify new disease-battle targets. Alm also wants to find out exactly how business is conducted in what he called a genetic “black market.” DNA can travel on dead cell fragments, viruses, and other sub-cellular vehicles, and the exact routes remain unknown.

“It could be almost anything,” he said. “We have no idea. I would love to know.”

Image: Transfer of genes occurs more frequently and intensely in bacteria that share ecological niches, such as a human gut or a patch of soil. Hotspots in the top right triangle, which compares all gene transfer events, shows microbes that live in the same niche more readily exchange genetic material. Looking at antibiotic resistance genes (bottom left triangle), however, paints a more complex and nuanced portrait of genetic transfer. (Nature)

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