In the final decades of the 19th century, scientists showed in rapid succession that many of the worst diseases to afflict humanity were the work of bacteria—germs. Leprosy, gonorrhea, diphtheria, tuberculosis, plague, cholera, dysentery: Barely a year went by without assigning an infamous illness to a newly identified microbe. This concept, where one germ causes one disease, has influenced the way we think about infections ever since, and it implies an obvious solution: Remove the bug, and cure the sickness.
But the links between microbes and poor health can be more complicated. Our bodies are naturally home to tens of trillions of bacteria. Most are benign, or even beneficial. But often, these so-called microbiomes can shift into a negative state. For example, inflamed guts tend to house an unusually large number of bacteria from the Enterobacteriaceae family (pronounced En-ter-oh-back-tee-ree-ay-see-ay, and hereafter just “enteros”). There’s no villain in this scenario, no single antagonist as there would be in the case of tuberculosis or cholera. The enteros are part of a normal gut; it’s the same old community, just altered.
These kinds of shifts are harder to rectify. For a start, it’s often unclear if the enteros cause the inflammation, if the inflammation changes the microbes, or both. Even if the microbes are responsible, how do you fix that? Dietary changes are typically too imprecise. Antibiotics are too crude, killing off beneficial microbes while suppressing the problematic ones.