Isolated Hunter-Gatherers Have Most Diverse Microbiome

Lara C. Pullen, PhD

April 17, 2015

Investigators report on the first characterization of the microbiome and resistome of uncontacted Amerindians in an article published online April 17 in Science Advances. The data show the population has the highest level of bacterial diversity yet found in a human population and suggest that potentially beneficial microbes may be harbored in the bodies of such populations.

In their analysis, Jose C. Clemente, PhD, from the Icahn School of Medicine at Mount Sinai in New York City, and colleagues characterized an isolated group of Yanomami hunter-gatherers that has been minimally exposed to modern practices. The Yanomami have remained relatively isolated in the 11,000 years since their ancestors arrived in the Americas.

"[B]acteria play important roles in physiology, including immune responses, metabolism, and even behavior. Yet, we don't know the extent to which our westernized microbiome has changed in relation to the microbiome of our ancestors. We have many antimicrobial practices such as C-section birthing, antibiotics, soaps, and cleansers," explained senior author M. Gloria Dominguez-Bello, PhD, from New York University School of Medicine in New York City, in a press conference.

She explained that there are only a few remote populations of hunter-gatherers remaining in the world. The current article describes a village that has had no previous reports of contact with Western society. The village was spotted from the air in 2008, and the villagers claim to have never before seen non-Yanomami people.

The researchers collected fecal, oral, and skin microbiome samples from 34 of the 54 inhabitants of the village. Overall they found that the Yanomami had significantly greater diversity in fecal and skin microbiomes relative to a comparative Western population. However, their level of oral diversity was similar to that seen in the Western population.

A closer analysis showed that the Yanomami microbiome was high in Prevotella and low in Bacteroides, which is the opposite of what is seen in the US population. In addition, their skin microbiota contained more environmental bacteria taxa, which are consistent with higher environmental exposure relative to westernized people, who spend time indoors and wear clothes.

Moreover, the microbiome of the Yanomami contained antibiotic-resistance genes despite the lack of known exposure to pharmacologic-dose antibiotics. Many of the antibiotic-resistance genes appear to be encoded by commensal taxa.

"Our work emphasizes the value of deep characterization of microbiomes of people living ancestral life-styles, particularly if practices in industrialized societies might eradicate potentially beneficial microbes and their encoded functions. Characterization of the commensal resistome of diverse people will also inform the design and prudent deployment of antibiotics to minimize enrichment for preexisting resistance. Causation and functional consequences of microbiome changes need to be understood before functional restoration of the microbiome is possible to attempt to reverse the current global trends in metabolic and inflammatory diseases," the authors conclude.

Another microbiome study, performed by Ines Martinez of the University of Alberta, Edmonton, Canada, and colleagues, and published online April 16 in Cell Reports, added to the discussion by concluding that modern lifestyle factors limit bacterial dispersal, thereby affecting human health.

The authors have disclosed no relevant financial relationships.

Sci Adv. Published online April 17, 2015. Full text

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