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The (Bacterial) Company You Keep

It's not just what is present in our gut microbiomes that can keep us healthy or make us ill, but what other bacteria they are hanging out with, writes Ed Yong at Not Exactly Rocket Science.

While some microbiome researchers compare the bacteria present in, for instance, the gut microbiome of healthy and sick people to uncover bacteria associated with disease, Yong focuses on the work of the University of Michigan's Alyxandria Schubert, who he says doesn't take such a reductionist approach.

As they report in mBio this week, Schubert and her colleagues have examined how perturbing the gut microbiome of mice by giving them different antibiotics affected their ability to fight off Clostridium difficile infections. Through a random forest model, the researchers attempted to predict C. diff colonization levels after microbiome perturbation. This model, they report, found that the interactions between bacteria is what leads to resistance.

It's not, Yong notes, as simple as one bacterium that's protective and one that's not.

If such predictive models work in people, he adds that they could be used to personalize treatments and tailor probiotics or other therapeutics to a person's particular microbiome.