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Hunter-Gatherer Lifestyle Boosts Microbial Diversity in Amazon Villagers

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The research team studied the microbial diversity in people from this remote Yanomami village in the High Orinoco region of Amazonas State, Venezuela. | Oscar Noya

Amerindian villagers from the Venezuelan Amazon, who had no previously documented contact with Western peoples, host perhaps the highest levels of bacterial diversity ever reported in a human group, a new study in the 17 April issue of Science Advances reports.

The diverse microbiome of this indigenous population, called the Yanomami, also harbors bacteria with antibiotic resistance genes, including those that confer resistance to synthetic drugs. This is a surprising find since this group has presumably never been exposed to commercial antibiotics. The findings add to evidence suggesting that Westernization is associated with loss of bacterial diversity, and hint that antibiotic-resistant genes may be a natural feature of the human microbiome.

"The world still has a few remote populations of hunter-gatherers that live in a pre-antibiotic era similar to the way our ancestors lived. They are rapidly becoming Westernized," noted co-author Maria Dominguez-Bello in a 15 April press conference. Originally from Venezuela, Dominguez-Bello is currently a professor at New York University School of Medicine and has been collaborating with Venezuelan scientists for the past two decades.

The Yanomami are Amazon peoples who continue to live semi-nomadic, hunter-gatherer lifestyles in the jungle of Venezuela, as they have done for thousands of years. In 2008, an unmapped Yanomami village was sighted by an army helicopter. A year later, a medical mission landed there and collected fecal, skin, and mouth swab samples from 34 individuals between the ages of 4 and 50. Only one of the Venezuelan authors of the study, Oscar Noya of the Amazonic Center for Research and Control of Tropical Diseases, visited the Yanomami village during sample collections in 2009.

In the lab, Dominguez-Bello and her team sequenced and analyzed the microbial DNA in these samples. They found significantly higher bacterial diversity compared to samples from a group of people in the United States, as well as compared to samples from two groups with limited exposure to the West: the Guahibo of Colombia and Southern Venezuela, and the indigenous people of Malawi in Africa.

"The implication of these findings is that even minimal exposure to modern practices, such as in the case of Guahibo and Malawians, can result in a drastic loss of diversity," said Jose Clemente of the New York University School of Medicine at the press teleconference.

 
Maria Gloria Dominguez-Bello describes her work to discover bacteria that have been lost in Westernized people. | Adam Watt and Andrew Neary, NYU Langone Medical Center

Additionally, the Amerindians' fecal samples harbored E. coli that carried functional antibiotic resistance genes against 23 different drugs, including some manmade drugs.

Many of these resistance genes are found in soil bacteria, and the researchers suspect that the Yanomami may have acquired these genes though exchanges between the human microbiota and soil bacteria.

"We're now able to establish clearly that antibiotic resistance is a natural feature of the human microbiota but it's waiting to be activated and amplified after antibiotic use," said Clemente.

Some of the bacteria present at higher levels in the Yanomami have been shown to have beneficial health effects in their hosts, like helping to prevent the formation of kidney stones.

The authors note that studying the microbiomes of traditional hunter-gatherer peoples could potentially lead to ways to help these tribes restore their "lost" microbiome after they are likely to become Westernized in the future. This might reduce their chances of suffering from the same health consequences such as obesity and diabetes that plague Westernized people.

Characterizing the microbiomes of peoples living ancestral lifestyles, before their microbial diversity is lost, could also make it possible to find microbes with therapeutic value for treating immune conditions such as asthma, allergies, and diabetes.