Dietary changes affect gut microbes within a day

One day is all it takes for the mix of microbes in the human gut to fluctuate when diets change.

People who radically altered their eating habits from an omnivorous diet to one composed of plants or to one containing only meat, eggs and cheeses changed the relative amounts and activities of their gut microbes, researchers report December 11 in Nature.

“A few decades ago people said, ‘You are what you eat,’ ” says microbiologist Martin Blaser of New York University. The new study, he says, shows that “what you eat definitely affects your bugs.”

While both diets affected the abundance of certain gut microbes, switching to animal-based diets had the bigger effect. Some groups of bacteria increased in abundance while others declined in response to the high-fat, high-protein diet. Most of those changes happened within a day of starting the regimen. Once people stopped the meaty diet, their microbes settled back into an omnivorous profile within a day or two, computational biologist Lawrence David of Duke University Medical Center and his colleagues discovered after tracking 10 people’s microbes.

Previous research had indicated that stability is the norm for the human microbiome — the collection of bacteria, viruses, fungi, archaea and other microorganisms that live in and on the body. The new findings aren’t a contradiction, says David Relman, a microbiologist at Stanford University.

That’s because other studies have taken single microbiome snapshots or a series of microbial profiles spaced months apart, says Relman, who was not involved in the new study. “As soon as you start to measure on shorter timescales, you see increasing variability around a somewhat stable baseline.”

When volunteers switched to the animal-based diet, bacteria including Bilophila wadsworthia, Alistipes putredinis and species in the genus Bacteroides quickly rose to prominence. Those bacteria can withstand bile, which the body releases after a person eats fat. On the meat diet, Alistipes and Bacteroides bacteria also began pumping out short-chain fatty acids. Some of the fatty acids have been associated with inflammation in animal studies, although this study did not measure long-term health effects.

Many of the microbes that came into the gut through food, such as bacteria from cheese, stayed only as long as people ate those foods, David says. Bacteria were not the only component of the microbiome that changed. Rubus chlorotic mottle virus, which can infect spinach, a major component of the plant-based diet, popped up in the poop of people who ate that diet but was absent from the feces of people on the animal-based diet.  

The transience of the microbial changes probably means that people hoping to change their microbiomes need to make radical dietary shifts, rather than just adding new foods to their menus, Relman says.

“You wouldn’t see this if they’d simply had an extra serving of spinach or a chunk of steak at dinner.”