WAS HUMAN GUT HEALTHIER IN ANCIENT TIMES?

THE human microbiome — the trillions of microbes that live in our guts — was a stable ecosystem for tens of thousands of years before rapidly changing in industrialized countries, raising possible health concerns for modern people, scientists reported last week.

In a study of Africans and South Americans, researchers identified more than 600 species of bacteria that may once have been common in the gut but are now rare or missing entirely from people in most societies today.

Many of these microbes may have benefited people’s health, said Justin Sonnenburg, a microbiome scientist at Stanford University and an author of the new study, published in Nature.

The changing microbiome, he speculated, may have helped increase some disorders that are common in the industrialized world, from allergies to dementia.

“How bad could this be, the fact that we changed our microbiomes so much?” Sonnenburg said. “This study, I think, points to the fact that it could be pretty bad.”

Our early apelike ancestors had a microbiome adapted to a diet of raw plants and meat. Its composition shifted hundreds of thousands of years ago when early humans started cooking with fire, scientists suspect.

As humans expanded from Africa about 50,000 years ago, they were still living on animals they hunted and wild plants they gathered. It was only about 10,000 years ago that farmers began domesticating crops, precipitating another likely shift in the microbiome.

In recent decades, an even more substantive change took place, as billions of people began eating food rich in sugar and refined grains. And modern medicine also may have had a profound effect: Antibiotics have saved countless lives, but the drugs can also destroy beneficial microbes in the gut.

To chart the history of the human microbiome, Sonnenburg and his colleagues have studied societies around the world at different levels of industrialization. Some of the most striking results have emerged from the Hadza, a small group of hunter-gatherers in Tanzania.

Studying stool samples from Hadza volunteers, Sonnenburg and his colleagues found a wide range of bacteria. “There are around 270 species in the average Californian, and around 730 in the average Hadza,” Sonnenburg said.

Even more striking is the diversity of those species. Many are rare or missing entirely from industrialized countries.

Sonnenburg and his colleagues wondered how similar today’s Hadza microbiome is to the microbes early hunter-gatherers carried.

They decided to compare the Hadza with other people who continue a similar lifestyle. The scientists began collaborating with anthropologists who study a Bolivian group called the Tsimane who live in remote Amazon villages, where they maintain small farms while hunting and foraging. While the Hadza and Tsimane have somewhat similar cultures, they have very different histories.

The Tsimane descend from people who left Africa 50,000 years ago and crossed to the Americas about 15,000 years ago. The Hadza’s ancestry, on the other hand, is restricted entirely to Africa.

Sonnenburg and his colleagues used powerful new methods to detect bacterial DNA in stool samples from both groups and compare them. Researchers found 848 species that were shared by the two groups or absent from industrialized countries. They then identified 636 species that were especially abundant in the samples.

The scientists found each species tended to carry distinct mutations, depending on whether they were found in the Hadza or the Tsimane.

The Hadza continue to carry them today, thanks to their lives as hunter-gatherers. But ancestors of the Tsimane migrated over the Bering land bridge to the Americas 15,000 years ago. That geographic separation made it impossible for microbes to spread from people in the Old World to the Americas.

The findings hint hunter-gatherers shared a distinctive ecosystem of gut microbes for tens of thousands of years. The ancestral bacteria might have been important for training our immune systems or synthesizing compounds our bodies need. And as some microbes vanished in modern societies, new ones took their place.

“You end up with a microbiome that’s very different than what your human genome has come to expect,” perhaps triggering inflammation and other unhealthy changes, Sonnenburg said.