Eat like a hunter-gatherer and you’ll be healthier—so goes the thinking behind so-called paleo diets. But a new study suggests that humans who live in industrialized societies don’t have the guts to stomach a real hunter-gatherer diet. Compared with hunter-gatherers, industrialized peoples’ intestines have fewer kinds of microbes—and are missing at least one major group of ancient bacteria. Yet even with all of these extra microbes, hunter-gatherers have fewer gut ailments, such as Crohn’s disease, colitis, and colon cancer.

Our bodies are home to trillions of bacteria—collectively known as the microbiome—but it’s unclear how our diet impacts the composition of these tiny organisms. Some studies have detected differences in the types of gut bacteria in obese and thin people, for example, while others have shown that hunter-gatherers harbor more diverse gut bacteria than do people in the industrialized world—a difference that may protect preagricultural communities from Crohn’s disease and colon cancer.

In a new study published online today in Nature Communications, an international team of researchers offers the first comprehensive look at the full-scale diversity of gut microbes in one group of hunter-gatherers and how the bacteria unique to them might function in their guts and affect their health. Anthropologist Cecil Lewis of the University of Oklahoma in Norman and his colleagues set out to detect differences in the core gut bacteria in hunter-gatherers and farmers in Peru, and compared them with residents of Norman. The researchers traveled by canoe upriver into the Amazon to study the diet and health of the Matses community, who are among the last hunter-gatherers in the world; they still hunt monkey, sloth, alligator, and other game, as well as gather wild tubers in the forest and fish in the rivers.

Getting “informed consent” from the Matses to gather their fecal samples, which are the best source of bacteria from the gastrointestinal (GI) tract, was a challenge, Lewis says, so the anthropologists gave the Matses a crash course in bacterial biology by showing them gut microbes under microscope. Once they explained that the gut bacteria lived inside them and could affect their health, one Matses man asked if the gut bacteria were the reason he couldn’t drink milk anymore, even though he could as a child. (The answer is yes, in part, because gut bacteria influence how much gas is produced by people who are lactose intolerant.) The researcher collected samples from 25 Matses and also from 31 Tunapuco, a traditional community of potato farmers from the Andean highlands who also eat guinea pig, pork, lamb, and some cheese from cows. They also collected feces from 23 people living in Norman, mostly academics who eat processed foods, including canned fruits and vegetables and prepackaged meals, as well as meat and dairy products such as milk and cheese.

Back in the lab in Norman, Lewis and his colleagues used state-of-the-art gene sequencing methods that allowed them to get long segments of the gene that is used as the standard for classification and identification of microbes, because it differs in various bacteria. They found that the hunter-gatherers’ and farmers’ gut bacteria were far more diverse than those in the people from Norman. The traditional groups have the most diversity in their microbiomes, including new types of bacteria that have yet to be named and several different strains of Treponema, spirochete bacteria that are usually absent in Western industrialized populations. There are strains of Treponema that cause disease, such as syphilis, but the strains found in the traditional people are more closely related to nonpathogenic strains in other mammals, such as pigs.

The detection of several strains of Treponema in the Matses suggests this type of bacteria has been present in human guts for a long time, because it was also found in the GI tracts of the Hadza hunter-gatherers in Tanzania and in nonhuman primates. “Suddenly a picture is emerging that Treponema was part of core ancestral biome,” says co-author Christina Warinner, an anthropologist at the University of Oklahoma. “What’s really striking is it is absolutely absent, not detectable in industrialized human populations.”

The team’s study also analyzed the function of the gut bacteria and found that the Treponema species in the Matses are most like those in the guts of pigs. There, the microbes play a role in digesting carbohydrates, or sugars. This suggests that the existence of Treponema “is likely a good indicator of a general high level of microbial diversity in the human gut,” says evolutionary anthropologist Stephanie Schnorr of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “Now it seems clear that their function is related to helping metabolize carbohydrates, and this can have a number of benefits and implications for host health.”

The key question now is does the absence of Treponema leave industrialized humans without a valuable player in the metabolism of their food—and the prevention of autoimmune disorders, such as Crohn’s and colitis, for example? “What’s starting to come into focus is that having a diverse gut microbiome is critical to maintaining versatility and resiliency in the gut,” Warinner says. “Once you start to lose the diversity, it may be a risk factor of inflammation and other problems.” And trying to eat like our ancestors may not be enough to get the benefits of a true paleo diet and lifestyle. “So even if you could mimic a true paleo diet, you are still missing ancestral gut bacteria that were involved in food digestion in the paleo gut,” Lewis says.