Western diets damage gut microbiota over generations, in ways hard to reverse

It may take more than a tub of yogurt to reverse the effects that a high-fat, low-fibre diet have wrought in the bellies of men and women in the industrialised world, says new research.

Indeed, the depletion of gut microbes that comes with diets deficient in fibre extends well beyond the lives of those whose dietary choices made it happen, a new study finds. Over generations of exposure to diets low in fibre, the research shows that a microbiotic population die-off threatens to drive some of the trillions of species that live in healthy human guts to the brink of extinction.

And just as in the world of larger plants and animals, when the population of a given gut bacterium falls below a certain level, it’s as good as gone, the new research suggests. The reintroduction of more dietary fibre, and the frantic hawking of probiotic powders, may not be enough to bring all the endangered microbiotic taxa back and restore gut health to successive generations.

The new research, published in the journal Nature, was conducted on laboratory mice whose guts were deliberately colonised with a wide array of microbes from humans. Researchers from Stanford, Harvard and Princeton universities fed a generation of lab mice a diet very low in microbiota-accessible carbohydrates — nutrients that are plentiful in the diets of agrarian hunter-gatherers but not in diets that are common in industrialised societies.

The results were stark enough in the mice, whose guts, collectively, were colonised by an increasingly impoverished population of bacteria, viruses and protozoa. They then fed four successive generations of mice a diet that was low in microbiota-accessible carbohydrates. Even when they put parent generations back on a high-fibre diet, the dearth of microbial diversity in the guts of younger generations became ever starker.

Even when the researchers switched subsequent generations back to a high-fibre diet, the shift failed to restore the microbiotic diversity that had originally flourished in the guts of their ancestor generations.

The findings suggest that, when diseases arise from a depleted gut microbiome, it may take more than a course of probiotics or a daily tub of yogurt to manage those diseases.

The findings demonstrate “a diet-induced ratcheting effect” in which species of microbiota “are not effectively transferred to the next generation”, the researchers wrote. Bacteria belonging to the Bacteroidales family were particularly prone to intergenerational die-offs that couldn’t be reversed with intentional reintroduction of a diet high in fibre.

There are no “charismatic megafauna” — the equivalent of tigers and elephants — among the trillions of microbes that colonise the gut. (Suffice it to say, there won’t likely soon be campaigns to “save the Bacteroidales”.) Indeed, the microscopic population of the human gut is so large and diverse, scientists are far from fully characterising what role individual taxa play in health. But there’s clear and growing evidence that species diversity in there is a key factor in digestive, metabolic and even immune health, and when that diversity takes a hit, some aspect of health is sure to suffer.

The authors of the latest study warn that their data hint that “further deterioration of the Western microbiota is possible”, as generational changes drive some taxa closer to the brink. The results of doubling down on diets that pose a threat to the gut’s microbiotic diversity could be downright apocalyptic, they suggest.

“Microbiota can change on a timescale that is much faster than the host,” wrote the team, led by Erica D. Sonnenburg and Justin L. Sonnenburg of the Stanford University School of Medicine. That fact makes it possible that if dramatic forces — including perhaps a wholesale abandonment of diets rich in fibre — wreak abrupt changes in populations of gut microbiota, the resulting changes “cannot be accommodated by our human biology”.

The result might be diseases that defy easy treatment.