Isolated Hunter-Gatherers Living in the Amazon Have The Most Diverse Microbiome Ever Documented In Humans

The Yanomami live in the rainforests and mountains of northern Brazil and southern Venezuela / Sam valadi via Flickr CC BY 2.0
Janet Fang 18 Apr 2015, 15:59

The microbiome of an isolated tribe of hunter-gatherers in the Amazon contain the highest levels of bacterial diversity ever documented for humans, according to a study published in Science Advances this week. And despite never having been exposed to commercial antimicrobials, some of their resident microbes carry genes that confer resistance to manmade antibiotics. That means the ability to resist was there long before our drugs came along.

A growing body of evidence links westernization to the loss of bacterial diversity, though no one really knows whether diverse bacterial flora helps or harms health. By studying populations with little or no previous exposure to industrialized lifestyles, researchers hope to understand the makeup of microbiomes similar to that of our early ancestors, and in the process, see if there are benefits to hosting a rich, diverse microbial diversity.

For thousands of years, the Yanomami people lived (and still do live) a semi-nomadic, hunter-gatherer lifestyle in the Amazonian jungle. They were first contacted in the 1960s, and in 2008, an unmapped Yanomami village was spotted by an army helicopter in the High Orinoco state of southern Venezuela. The next year, researchers returned to collect mouth swabs, feces, and forearm skin samples from 34 villagers ages 4 through 50. Now, a large international team led by New York University’s Maria Dominguez-Bello have sequenced and analyzed the microbial DNA contained within. 

Those samples revealed significantly higher bacterial diversity than samples collected from study participants in the U.S., as well as two non-Western groups with limited exposure thus far: Amazonian Guahibo Amerindians in Venezuela and residents of rural Malawian communities in southeast Africa. The microbiome of industrialized peoples are 40 percent less diverse, and even minimal exposure to Western medicines greatly decreased diversity as well. Some of the bacteria found at higher levels are known to be beneficial -- such as preventing kidney stones from forming. 

Furthermore, despite having no exposure to commercial drugs, the fecal samples showed how the Yanomami harbored gut bacteria with functional genes that code for antibiotic resistance. These genes turned on in response to antibiotics, and in tests, they deactivated various natural, semi-synthetic, and synthetic drugs. “The silenced antibiotic-resistant genes show that you don't need exposure to antibiotics to possess antibiotic-resistant genes," Dominquez Bello says in a news release.

These genes may have come from an early exchange between human microbes and soil bacteria, which produce natural antibiotics to kill their competitors. In fact, most antibiotics developed in the 1940s and 1950s were derived from soil bacteria, "so, we would expect that natural resistance to antibiotics would emerge over millions of years of evolution," Washington University’s Gautam Dantas says. However, "it was alarming to find genes from the tribespeople that would deactivate these modern, synthetic drugs,” Dantas adds in a university statement. The work suggests that genes equipped to resist antibiotics may be a natural feature of the human microbiome. 

Images: Sam valadi via Flickr CC BY 2.0 (top), Oscar Noya-Alarcon (middle)

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