Sonnenburg, his wife Erica, and the graduate student Samuel Smits confirmed this idea in a recent experiment. The researchers started with mice that had been raised in sterile bubbles and then loaded with identical collections of gut microbes. They then fed these mice a high-fiber diet, before randomly switching half of them to low-fiber chow for seven weeks.
Predictably, the fall in fiber caused upheavals in the rodents’ guts. In the low-fiber group, the numbers of 60 percent of the local microbe species fell dramatically, and some remained low even after the mice returned to high-fiber meals. Those seven low-fiber weeks left lingering scars on the animals’ microbiomes.
These scars can cascade through generations. Mice regularly eat each others' poop, and pups often pick up their parents’ microbes in this way. Indeed, when Sonnenburg and Smits bred the mice from their first experiment, they saw that low-fiber parents gave birth to pups with narrower microbiomes, which lacked species present in the progeny of high-fiber parents. And if these bacteria-impoverished pups also ate low-fiber food, they lost even more microbes, especially those from the fiber-busting Bacteroidales group. As four generations ticked by, the rodents’ guts became progressively less diverse, as more and more species blinked out.
It also became increasingly hard to reverse these changes. If the fourth-generation mice switched to high-fiber meals, some of the missing microbes rebounded, but most did not. In other words, these species weren't just lying in wait in small numbers, waiting for the chance to bloom again; they had genuinely vanished. The only way of restoring these missing microbes was through a fecal transplant—loading them with the entire gut microbiomes of rodents that had always eaten a high-fiber diet.
These changes parallel those that have taken place over the course of human history. Many studies have now shown that the gut microbiomes of Western city-dwellers are less diverse than those of rural villagers and hunter-gatherers, who eat more plants and thus more fiber. The Stanford researchers’ experiment hints (but doesn't confirm) that this low diversity could be a lasting legacy of industrialization, in which successive generations of low-fiber meals have led to the loss of old bacterial companions. “The data we present also hint that further deterioration of the Western microbiota is possible,” the team writes.
“Given the infancy of the microbiome field, I think it is difficult to determine what specific impacts the loss of microbiota diversity has on the host,” says Kelly Swanson, a nutritional-science professor at the University of Illinois at Urbana-Champaign. “But I think this paper provides even more evidence for including an adequate amount of dietary fiber in the diet.” For context, dietary guidelines recommend that women and men should respectively eat around 25 and 38 grams of fiber per day, but American adults eat just 15 daily grams on average.