Significant bacterial diversity found in the microbiomes of remote Amerindians

A group of Yanomami people in Demini, Brazil  © Fiona Watson/Survival

A group of Yanomami people in Demini, Brazil © Fiona Watson/Survival

The Yanomami Indians are a native people that reside in remote areas of the Amazon jungle in South America, where they live in a society devoid of westernization and modernization.  They were first contacted in the 1960s, and the Venezuelan government has since preserved isolation among these societies by preventing modern development from expanding into their lands.  From an anthropologic perspective, these people therefore represent a glimpse into the past of a hunter-gatherer subsistence living human society.  Capitalizing on this unique characteristic, researchers from several institutions led by AMI Scientific Advisory Board member Maria Gloria Dominguez Bello, set out to investigate the human microbiomes of these remote communities in a twofold manner.  Bacterial diversity of the Yanomami microbiota was characterized, concomitant to exploring bacterial and gene responses to antibiotics commonly utilized in clinics in Western societies. 

Thirty four Yanomami subjects between 4 and 50 years old were selected for analysis.  Forearm skin, oral mucosa, and fecal samples were collected for bacterial analysis and compared to subjects from the U.S., Guahibo Amerindian, and Malawian tribes (the latter two were selected for comparison, as their cultures are in transition to modernization).  E. coli cultures were examined and genomic libraries were created for further analysis of bacterial expression, functional diversity, and resistome (the collection of antibiotic resistant genes) gene expression in response to antibiotic treatment. 

The Yanomami people displayed extraordinary levels of bacterial diversity as compared to the U.S. subjects, Guahibo Amerindians, and Malawians.  Specifically, the Yanomami fecal samples were characterized by high expression of Prevotella and low expression of Bacteroide bacteria.  With respect to functional bacterial diversity, the Yanomami displayed higher fecal and skin functional diversity among the other Amerindian and U.S. subjects.  Furthermore, over-enrichment in bacteria that interact with pathways involved with protein and carbohydrate metabolism was observed in the Yanomami. 

23 antibiotics were tested on 131 E. coli strains isolated from 11 fecal samples, and sensitivity to all antibiotics was observed.  Interestingly, functional libraries created from these E. coli isolates displayed antibiotic resistant genes targeted against 8 of the 23 antibiotics.  This suggests that antibiotic resistance genes have been maintained despite the lack of apparent antibiotic selection pressure that is characteristic among Western societies. 

Results from this study indicate a greater scope of bacterial diversity in a defined group of people than ever reported before.  Furthermore, the investigation illuminated an important characteristic of the bacterial resistome, as the results indicated that resistant genes were present in a population that had not been exposed to any Westernization.  This suggests that some antibiotic resistant genes are archaic, dating back to pre-westernization times and also that westernization affects microbiome diversity.  Ultimately, this study employed a fascinating approach to investigating human microbiome divergence and evolution, in addition to providing more insight to host-species relationships with respect to pharmacologic therapies.  

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