Farmers may cultivate better gut microbes than nearby city dwellers

We rarely give much thought to the bacteria that take up residence in our guts. It’s hard not to forget creatures you can’t see or interact with. Despite their discreteness, researchers have come to understand that as a whole, these microbes do a lot for our health—helping us to digest food, regulate our immune systems, and coordinate how our hormones work. Because of all these bacterial benefits, scientists have recently begun to try to figure out how we get good microbes in our guts in the first place.

To better understand this, researchers compared two unique, yet similar populations: A group of people living in a city in Nigeria and another living far outside the urban area, but within the same geographical region. The researchers found that the gut bacteria of those living in the city was far less diverse in species than those of the rural populations. And that diversity started at a far younger age within the rural group. This study is the first to compare rural and urban populations that live in the same geographical area. Researchers say its results will help us to better understand what a healthy microbiome is, and how to best develop one.

The microbiome still holds many mysteries, but scientists have landed on a few key truths. One is that the gut bacteria of people living in developed, wealthy nations—particularly people eating what’s considered a “western-style diet”—are far less diverse than those living in more rural, less developed areas. Studies indicate that this is not ideal; people seem to be healthier in myriad ways when their guts host a great variety of microbial species. Further, researchers have found that the use of antibiotics, a lack of breastfeeding, and an increased intake of processed foods might contribute to low diversity.

In the past few years, researchers have zeroed in on studying the gut microbiomes of populations far removed from these practices, like the Hadza hunter-gatherer tribe, and comparing them to people living in America. However, comparing those two groups is difficult because the geographical regions, which significantly influence what types of microbes we will have, are far too different.

In the new study, researchers compared the gut microbes of two distinct populations living in the same geographical region: A group of urban Nigerians living in one of four metropolitan cities and the Bassa, an agrarian group of 70 to 80 people living on a hilltop about 500 miles outside the Nigerian city of Abuja. The urban dwellers ate a more processed diet, took antibiotics, and drank and bathed in filtered water. On the other hand, the Bassa people live on tubers, grain, and fruit, among other crops grown on their own farms. They eat fish often, but rarely other meats—aside from during a handful of festival dinners sprinkled throughout the year. Because there is no healthcare center nearby, they rarely take antibiotics.

Overall, the Bassa had far more diverse microbial guts than urban Nigerians. The Bassa also had less gut microbe variation from person-to-person than city folks. In other words, the rural communities’ guts were all individually very diverse, but each person had more or less the same level of diversity.

The researchers also found that diversity started early in life among the Bassa. Whereas the urban dwellers’ microbes didn’t reach their maximum diversity until age three, the Bassa’s became diverse within a few months after birth. In previous studies, researchers found that up until age three, the bacteria inside babies’ guts frequently shift. But at age three, things start to settle down, and the bacterial communities become more stable.

So what does this all mean?

Researchers already know that a more diverse gut microbiome is associated with better gut health. But how we get a diverse gut is still unclear. The fact that two populations living in the same area have such different levels of diversity lends some weight to the idea that diet and lifestyle are the driving forces behind microbiome development.

When the scientists compared the microbial compositions of both the urban dwellers and the Bassa to ones from Western populations, they also noted distinct differences. In particular, Bassa infants completely lacked a bacteria called Bifidobacterium, a bacterium considered highly beneficial in Western populations—so much so that much research has gone into finding ways to replace it in lacking infant guts. But the Bassa babies did just fine without it.

“This strongly supports that the definition of a universal healthy gut microbiome configuration (and trajectory) is only a chimera because it depends on human ecological context,” says study author Silvia Turroni, a microbiologist at the University of Bologna in Italy.

There is no single “healthy” way to get a good bunch of intestinal microbes, she says. Rather, it depends on an individual’s location, as well as their diet and lifestyle. In some ways that makes understanding what a “healthy” microbiome is far more complicated, but in other ways it shows that many different variations can all lead to a healthy life, with less incidence of disease.

The researchers also identified a few unique bacteria present in high quantities in the Bassa, who, like many other groups of similarly rural people, tend to have much lower rates of Western diseases. Studying what these are and what they do might help researchers better understand how gut microbes influence—or even prevent—disease.

Turroni says she wants to confirm these results in a larger population to better pinpoint how significant of an affect the microbiome has on the development of various diseases. For now, though, the study confirmed one of our best understandings of the gut microbiome to date: That a more diverse gut is a better gut. And the best way to get a more diverse gut (at least that we know of now) is to eat a diverse diet, full of a ton of fiber.