Which came first, antibiotics, or antibiotic-resistance? A study of Uncontacted Amerindians.

The geographical location of the Yanomami tribe as a whole. The specific village exists in the highlighted region. (Image courtesy of Viralfast)

Background

The Yanomami people are patches of isolated South American tribes who occupy mountainous regions of southern Venezuela. Recently, a Yanomami tribe of 34 subjects discovered by helicopter, was investigated by a team of researchers who accompanied medical care professionals who were providing care to the villagers. These researchers, Clemente et. al. (2015), then wrote the paper, “The microbiome of uncontacted Amerindians’ to analyze this population which was uniquely untouched by Western Society. An interesting topic that this research paper addresses is antibiotic-resistant bacteria. Antibiotic-resistance are the adaptations of a bacterial species in response to antibiotics. Antibiotics are medications that have been developed in more recent times to destroy bacteria cells but not human cells. They do this by targeting specific differences between the two types of cells, for instance, penicillin inhibits the synthesis of the peptidoglycan layer of bacterial cell walls a feature not present in animal cells. Other bacteria have distinct DNA replication processes and some antibiotics are able to interrupt that function as well. This Yanomami population is intriguing because their microbiomes are likely the most accurate representation of an ancient human microbiome due to their isolation from the Western world. The presence of antibiotic-resistant bacteria in the Yanomami gut provides evidence for the claim that antibiotic-resistant bacteria have been around since before the invention of antibiotics, so stay tuned for a persuasive evidentiary argument further down. Clemente et. al. also state that the Yanomami population that is sampled is the most diverse microbiome ever recorded. It is important to understand what kind of diversity the researchers are talking about. The Yanomami show extremely high beta diversity when compared to Guahibo, Malawi, and U.S. populations but exhibit low alpha diversity amongst individuals in the village population. Beta diversity represents the differences in species composition among samples while alpha diversity is just the diversity of each sample. This means that the Yanomami microbiome sample is extremely unique but microbiomes within that sample are very similar, this is most likely due to the Yanomami leading vastly different lifestyles than Western societies and individuals in the village being in extremely close quarters with each other (eating the same food, drinking from the same water source, no waste removal, etc.).

Central question

In 2009 when a medical mission made first contact with Yanomami tribe of 35 individuals, Clemente et. al. (2015) saw a unique opportunity to analyze an ancient way of life, undisturbed by the Western World. Are primitive hunter-gatherers, who have never encountered western civilization, representative of the ancient overall human microbiome? When antibiotic-resistant bacteria are found in a population that has had conceivably the minimal amount of exposure to Western antibiotics possible, it can be postulated that antibiotic-resistance predates antibiotics!

Evidence

Antibiotic-resistance

Clemente et. al. (2015) have provided evidence that antibiotic-resistant genes are present in this reported uncontaminated Yanomami human genome population. Clemente et. al. tested 131 strains of E. coli from the Yanomami and found 38 strains that yielded antibiotic-resistant genes targeted against eight antibiotics. The team even found a ribosomal protection protein that encodes resistance to tetracycline (a common form of antibiotic) that was not present in several databases which characterize the human microbiome and may be exclusive to this population. In fact, in the paper, “Antibiotic resistance is ancient’ written by D’Costa, V., King, C., Kalan, L., et. al. (2011) and published in the journal Nature, the authors provide evidence that antibiotic resistance predates antibiotics. They do this by analyzing confirmed ancient DNA from megafauna of the time, taken from permafrost cores that have been frozen since the Ice Age. D’Costa et. al. and her team vigorously conduct structure and function studies on a three gene operon vanHAX to show that is it similar in function to a modern antibiotic resistant vancomycin. The combination of D’Costa et. al. and her work with bacteria in permafrost and Clemente et. al. and his work characterizing the Yanomami, a person can say with confidence that antibiotic resistance predates antibiotics.

They also tested antibiotic resistance in cultured samples from the Yanomami Amerindians to provide evidence that antibiotic resistance predates antibiotics. In contrast to the first part, the researchers examined all the DNA (metagenome) from the samples from the Yanomami, then compared the new datasets from their samples to existing databases and discovered they shared antibiotic resistant genes despite the Yanomami never coming into contact with Western medicines. Which is not surprising due to the previously mentioned paper written by D’Costa, V., King, C., Kalan, L., et. al. (2011) which provides evidence that antibiotic resistance is present in permafrost that has been untouched since the Ice Age. Clemente et. al. even discovered a ribosomal protection protein that did not align to any database they compared it to and may be unique to this population.

Yanomami Diversity

To show the diversity of the Yanomami population Clemente et. al. (2015) use specific DNA (from the 16S rRNA gene) sequence data to describe the microbial communities from fecal, oral, and skin samples of uncontacted Amerindians and compared them to data from previous studies of various population groups. Researchers claimed that the Yanomami had the highest reported diversity of any other previously reported sample group. They provided strong evidence in support of this idea using rarefaction curves of Yanomami, Guahibo, Malawi, and U.S. populations for all three of the sample sites (fecal, oral, and skin). A rarefaction curve is a plot of the number of species, on the y axis, compared to the number of samples, on the x axis. The rarefaction curve will grow quickly at first as more and more species are discovered, but the rate of discovery will soon decline and the curve will plateau at the approximate diversity of the population. While the Yanomami had higher diversity among all three sites compared to United States sample groups, it was not significantly higher in the oral samples. The lower diversity in oral samples is hypothesized to be because of tobacco use in the Yanomami village. Tobacco polyphenols have been shown to be antioxidants and antimicrobial agents. In the paper, “Identification of polyphenols in tobacco leaf and their antioxidant and antimicrobial activities‘ written by Wang, H., Zhao, M., et. al. (2008) and published in the journal Food Chemistry, a Kirby-Bauer antibiotic test showed that when polyphenols from tobacco leaves were compared against gentamycin, which is a common chemical with known antimicrobial potential, there was no significant difference between the diameters of the tested inhibition zones. They also showed that although the Yanomami sampling group have the highest diversity comparative to other groups, within their own group they have very close similarity. This is most likely due to the Yanomami group that was sampled being a small village of around 40 people who most likely ate the same food, drank the same water, and were in close proximity to each other. They used accumulation curves of fecal OTUs and phylogenetic species richness to show this.

What’s Next?

The researchers of this paper tagged along with a medical team that were sent by the government to ensure that the people of this village were healthy and to possibly give them treatment to prevent the spread of disease. It would be fascinating to follow up and analyze how this group’s microbiome changed over time in response to new antibiotic-resistance stimulus. I hypothesize that as the Yanomami are further exposed to medical care providers, etc. their relative diversity to other populations will decrease

We know that diet is important to the gut microbiome. I wish I could conduct an interview of the population and try to discern what their diet consists of, or how much exercise they are getting so that we could have more background on what might be causing this high level of diversity. I would also like to see an analysis of the data where age is accounted for and where we might see the diversity rise or fall depending on how old you are. This is important because there are less factors in such an isolated population and it could let researchers point to age (or time exposed to your environment) as a factor in microbiome composition.

References

Clemente, C. Jose, et. al. “The microbiome of uncontacted Amerindians.’ Science Advances, vol. 1, no. 3, (April 17, 2015), doi: 10.1126/sciadv.1500183
D’Costa, V., King, C., Kalan, L., et. al. “Antibiotic resistance is ancient.’ Nature, vol. 477, pp. 457—461, (September 22, 2011), doi: 10.1038/nature10388
Wang, H., Zhao, M., Yang, B., Jiang, Y., and Rao, G. “Identification of polyphenols in tobacco leaf and their antioxidant and antimicrobial activities.’ Food Chemistry, vol. 107, (2008), pp. 1399-1406, doi: 10.1016/j.foodchem.2007.09.068