The researchers found bacteria in samples from a remote tribe of Amerindians contained resistance genes that were activated by exposure to modern antibiotics.
The mountains of southern Venezuela are home to an isolated tribe of Yanomami Amerindians that has lived there since their ancestors first settled in South America over 10,000 years ago.
Before their discovery by Westerners in 2009, the tribespeople had had no contact with the modern world or exposure to modern antibiotics.
In the journal Science Advances, researchers from the US and Venezuela describe how they analyzed bacteria from the skin, mouth and intestines of the Yanomami tribe members and found they contained antibiotic resistance genes.
Inappropriate and overuse of antibiotics in medicine and agriculture is fueling a growing global health problem of drug resistance where once powerful drugs are losing their ability to kill emerging "superbug" strains of disease-causing bacteria.
One explanation for the emergence of antibiotic-resistant bacteria is that random mutations in the microbes coupled with their ability to swap genes is spurring the evolution of resistant strains.
But the new study suggests that resistance genes have been around in the human microbiome (the trillions of bacteria that live in and on the body) for thousands of years - long before antibiotic drugs were invented.
Speculating on the findings, the team says antibiotics are not just a human invention. Bacteria evolved strategies to kill each other long before we were around - they were the first inventors of antibiotics. And to defend against this, they developed resistance mechanisms.
Tribespeople's bacteria had resistance genes that deactivate range of antibiotics
The discovery of the Yanomami village gave the team - including Erica C. Pehrsson of the Washington University School of Medicine, St. Louis, MO - the opportunity to study their bacterial flora and compare it to what we already know from Western human populations.
Pehrsson says the tribespeople's only exposure to antibiotics would have been through ingestion of soil bacteria that make naturally occurring versions of today's modern antibiotics, and notes:
"Yet we were able to identify several genes in bacteria from their fecal and oral samples that deactivate natural, semi-synthetic and synthetic drugs."
The researchers also found that the tribespeople's microbiome was much more diverse than that of the typical Western person.
They do not know if the diversity of specific bacteria they found in the tribe improves or harms human health, but note that the microbiome of the typical Westerner is about 40% less diverse than that of the Yanomami.
Decreased bacterial diversity, modern diet and antibiotics linked to disease
Senior author Maria Dominguez-Bello, associate professor of medicine at New York University Langone Medical Center, says:
"Our results bolster a growing body of data suggesting a link between, on 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.We believe there is something occurring in the environment during the past 30 years that has been driving these diseases, and we think the microbiome could be involved."
Prof. Dominguez-Bello and colleagues exposed bacteria from the tribe to 23 different antibiotics and found the drugs were able to kill all of them.
But when they ran further tests, they found the bacteria contained "silent" resistance genes that were activated by exposure to the antibiotics.
The results showed cultured bacteria from the tribe members contained many resistance genes that can fight off many modern antibiotics.
And when they tested bacteria that are hard to culture, the scientists found even more resistance genes.
Scientists 'alarmed' to find genes resistant to synthetic antibiotics
The team was surprised to find that many of the resistance genes they found in the bacteria from the tribespeople deactivated not only natural antibiotics but also synthetic and semi-synthetic antibiotics, including third- and fourth-generation cephalosporins, which are normally reserved for fighting off the worse infections.
Co-author Gautam Dantas, associate professor of pathology and immunology at Washington University, says:
"It was alarming to find genes from the tribespeople that would deactivate these modern, synthetic drugs."
One explanation for this finding is the idea of cross-resistance, where genes that help bacteria resist natural antibiotics can also help them resist related synthetic drugs, as Prof. Dantas explains:
"We've seen resistance emerge in the clinic to every new class of antibiotics, and this appears to be because resistance mechanisms are a natural feature of most bacteria and are just waiting to be activated or acquired with exposure to antibiotics."
In December 2014, Medical News Today learned how the microbiome may be shaping the human age structure. In the journal mBio, researchers at NYU's Langone Medical Center and Vanderbilt University describe how they created a model of an early hunter-gatherer population to see what role the microbiome might have played. They concluded evolution may have acted on the human microbiome to favor bacteria that help their hosts live longer.