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Unprecedented Microbial Diversity in Isolated Amazonian Tribe

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Scientists from the Icahn School of Medicine, collaborating with a multicenter team of U.S. and Venezuelan researchers, have discovered the most diverse collection of bacteria yet in humans among an isolated tribe of Yanomami Amerindians in the remote Amazonian jungles of Venezuela. Bacterial diversity in the Yanomami, previously unexposed to antibiotics or industrialized diets, was found to be nearly double that of people living in industrialized countries, and was also significantly higher than in other remote populations moderately exposed to modern practices. The team published its findings in the journal Science Advances.

The results suggest that antibiotic usage or western diet are linked to the reduced bacterial diversity observed in modern societies, and that this loss of diversity happens quickly upon initial exposure to those practices. “There is a gradient of bacterial diversity that appears to be inversely correlated with exposure to modern practices, such as antibiotics, C-section, or processed foods,” said Jose C. Clemente, PhD, Assistant Professor of Genetics and Genomics at the Icahn School of Medicine at Mount Sinai and first author of the study. “Even minimal exposure to these practices greatly decreases diversity and removes potentially beneficial bacteria from our microbiome.”

To date, the vast majority of studies on the human microbiome—the trillions of bacteria harbored in the body that are essential to our well-being—have focused on Western populations. “Characterizing the bacterial communities of non-Western, unexposed populations is essential to understand how the microbiome changes and adapts to westernization,” said Dr. Clemente, “and how those changes might be driving the increased incidence of diseases linked to imbalances in the microbiome.”

The Yanomami villagers of this study, who have subsisted as hunters-and-gatherers for hundreds of generations, are believed to have lived in total seclusion from Western civilization until 2009 when they were first contacted by a medical expedition. Among a rare population of people unexposed to modern antibiotics, the villagers offer a unique window onto the human microbiome.

“We have found unprecedented diversity in fecal, skin, and oral samples collected from the Yanomami villagers,” said Maria Dominguez-Bello, PhD, Associate Professor of Medicine at NYU Langone Medical Center and the senior author of the study. “Our results bolster a growing body of data suggesting a link between, on the one hand, decreased bacterial diversity, industrialized diets, and modern antibiotics, and on the other, immunological and metabolic diseases—such as obesity, asthma, allergies, and diabetes, which have dramatically increased since the 1970s,” said Dr. Dominguez-Bello.

The analysis of gut and oral bacteria also revealed that the Yanomami villagers had bacteria encoding antibiotic resistance genes, despite their lack of previous exposure to antibiotics. Surprisingly, the bacterial genes conferred resistance not only to natural antibiotics, such as those produced by soil microbes, but also to synthetic antibiotics.

“During the 1940s and 1950s, in the heyday of pharmaceutical antibiotic development, most antibiotics were derived from naturally occurring bacteria in the soil,” said co-author Gautam Dantas, PhD, Associate Professor of Pathology, Immunology, and Biomedical Engineering at Washington University School of Medicine. “So, we would expect that natural resistance to antibiotics would emerge over millions of years of evolution,” he said. “We didn’t expect to find resistance to modern synthetic antibiotics.” The presence of resistance genes in microbiota unexposed to antibiotics may help explain the rapid rate at which bacteria develop resistance to new classes of antibiotics, noted Dr. Dantas.   

“The results from this study have given us a much better understanding of our microbial past,” said Dr. Clemente. “Characterizing now the functions encoded in those bacteria that we are missing will provide further insights into the mechanisms behind these immune and metabolic conditions, and potentially guide us in the development of new therapeutics.”