We all know people who act very differently depending on the company they find themselves in. They can be delightful in some circles, and obnoxious in others. The same principles apply to the microbes in our bodies—our microbiome. They have important roles in digestion, immunity, and health, but none of them is inherently good. They can be helpful in one part of the body and harmful in another, beneficial when paired with certain partners and detrimental when teamed up with others.
This means that, as I’ve written before, there’s no such thing as a “healthy microbiome”. Context matters. And contrary to what some companies might tell you, we’re still not very good at looking predicting what any particular community of microbes means for our health. One common approach is to compare microbiomes in people with or without a disease, single out species that distinguish the two groups, and use their presence or absence to make predictions. But those same bugs might have the opposite effect, or none at all, in another setting.
Alyxandria Schubert from the University of Michigan used a less reductionist approach—one that embraces the complexity of the microbiome rather than shoving it aside.
She studied Clostridium difficile: a weedy bacterium, known colloquially as C-diff, which can cause debilitating bouts of diarrhoea. A thriving community of gut microbes can hold C-diff at bay, but when those communities are cleared by antibiotics, the weed can bloom freely. That’s why C-diff is the single biggest cause of hospital-acquired infections in the USA.
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