Early human gut bacteria may have cycled with the season

You may be what you eat, but trillions of other lives depend on your diet: the microbes that live in your digestive tract. Scientists have long known that the foods we eat influence our intestinal microbiomes, but a new study finds that the gut residents of one of the world’s few remaining hunter-gatherer groups change seasonally, with different bacterial profiles in the dry and wet seasons. The findings—the first to show such a cyclical change in humans—may help researchers understand what our ancestors’ microbiomes were like before most of them switched to agriculture.

Nearly 200 of the 1000 Hadza who live near Lake Eyasi in Tanzania’s Rift Valley practice a traditional hunter-gatherer lifestyle, eschewing agriculture in favor of hunting and foraging. In 2014, anthropologist Stephanie Schnorr and colleagues at the University of Oklahoma in Norman found that many of them harbored considerably more species of gut bacteria than people living in modern Western nations (a finding that dovetails with evidence that the Hadza don’t suffer from colon cancer, colitis, or Crohn’s disease). The Hadza’s gut bacteria also appeared to specialize in breaking down their fiber-rich diet.

Unlike most people in industrialized nations, the Hadza eat seasonally: During the wet season, they forage for berries and eat honey, and during the dry season they hunt and eat game like warthogs, antelopes, and giraffes. They eat starchy tubers and baobob fruits year-round.

To find out whether the Hadza microbiome also varies with the seasons, Jeff Leach, director of the Terlingua, Texas–based Human Food Project, and microbiologist Justin Sonnenburg of Stanford University in Palo Alto, California, and their colleagues got 188 Hadza people to collect their own stool samples in 2013 and 2014. “They simply went off into the bush, pooped, and dipped the swab immediately in the stool,” Leach wrote in an email to Science . To demonstrate how to do this without contaminating the samples, the researchers rolled wet clay which “made for hours of endless humor for the Hadza.”

Back in his lab, Sonnenburg and colleagues analyzed the samples’ RNA and put together a list of which bacteria they contained. A stark pattern emerged: The Hadza people’s guts hosted a more diverse bacterial population during the dry season than the wet season. Bacteria from the Bacteroides genus were particularly abundant throughout the dry season; their numbers dropped off during the wet season, but returned to prominence with the next dry season. It’s the first evidence of seasonal cycling in the human microbiome, the researchers report today in Science .

Looking more closely at the enzymes in the bacteria, Sonnenburg found that plant carbohydrate–digesting enzymes were more common during the dry season. That’s a bit of a mystery because the Hadza eat more meat and fewer plants that time of year, notes Alyssa Crittenden, an anthropologist at the University of Nevada in Las Vegas, who has studied the Hadza for 13 years. Crittenden and Schnorr note that the researchers don’t include detailed logs of what the Hadza participants were eating when they donated their stool samples. “Without dietary and behavior data to contextualize these data, this paper poses more questions than it answers,” Crittenden says. “I’m hungry for more data.”

She agrees that the study sheds light on how the seasonal availability of plants and animals might have influenced the gut microbes of our ancient human ancestors, who would have hunted and gathered in a similar fashion to the Hadza. Knowing this could help researchers understand where ancestral humans lived and foraged, as well as which nutrients were available to them. It also suggests the human gut evolved a “biorhythm” in sync with natural food cycles, Schnorr adds, and that industrialized people’s microbiomes could be out of sync with that cycle. There are not yet enough data to determine how that affects our gut health, though, she says. But she stresses that the Hadza themselves don’t possess an “ancestral microbiome.” Evolutionarily speaking, they’re as modern as anyone else.

Unfortunately, the window of opportunity to learn from the Hadza is closing, Crittenden says. Every year, more and more are leaving their small camps to work in nearby villages, and aid agencies active in the area are distributing nonnative foods like wheat flour and corn. “We’re running out of time … while this interview is happening, they are undergoing nutritional transition,” Crittenden says. “More data on their health, their biology, and their nutrition status will hopefully help change the types of [aid] programs put into place.”