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Scientists track the arms race that’s playing out between bacteria in your gut

Alan Boyle
The mixture of bacteria shown in this photomicrograph contains five different species of the genus Bacteroides. (UW Medicine Photo / Mougous Lab / Kevin Cutler)

The balance of bacteria in your gut can make the difference between sickness and health — and now scientists report that different species of bacteria share immunity genes to protect themselves against each other’s toxins and maintain their balance of power.

In effect, closely related species of bacteria acquire each other’s defense systems to fend off threats from alien invaders.

The findings appear in a paper published today in the journal Nature. The senior authors are Joseph Mougous, a microbiology professor at the University of Washington School of Medicine; and Elhanan Borenstein, a former UW Medicine geneticist who now works at Tel Aviv University.

The researchers focused on a particular species of gut bacteria known as Bacteroides fragilis, which produces toxic proteins to kill off other types of bacteria that get too close. They identified a cluster of genes that gives B. fragilis immunity to its own toxins — but they also found the immunity factors in samples that didn’t contain any B. fragilis bacterla.

“This finding strongly suggests that these anti-B. fragilis immunity elements were encoded by other bacteria in the gut,” the team reported in the Nature paper.

A statistical analysis led the researchers to suspect that the immunity genes were shared by at least four other Bacteroides species: B. ovatus, B. vulgatus, B. helcogenes and B. copracola. Gene sequencing confirmed their suspicion. The acquired shielding effect was observed in lab-dish conditions, as well as in the guts of living lab mice.

As a follow-up experiment, the researchers mixed one type of bacteria that had a specific group of immunity genes with another type that didn’t have those genes. They found that the genes were transferred from the haves to the have-nots, giving them immunity as well.

Such transfers took place in other cases as well — for example, when the target genes helped one species of Bacteroides fend off attacks by non-Bacteroides bacteria.

Gene-swapping thus appears to be a crucial element of a “molecular arms race” by which groups of bacteria maintain their status in the gut microbiome, the researchers said. So if scientists hope to treat diseases by tweaking the microbiome, they might have to account for that strategy in their medical playbook.

Two former UW postdoctoral researchers — Benjamin Ross, who’s now on Dartmouth College’s faculty; and Adrian Verster, a bioinformatician at Health Canada — are the principal authors.of the Nature paper, titled “Human Gut Bacteria Contain Acquired Interbacterial Defence Systems.” In addition to Mougous and Borenstein, the other study authors include Matthew Radey, Danica Schmidtke, Christopher Pope, Lucas Hoffman, Adeline Hajjar and S. Brook Peterson.

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