Gut harbors antibiotic resistance

The millions of microbes that crowd the human intestinal tract are teeming with new antibiotic resistance genes that could jump to disease-causing pathogens, according to researchers from Harvard University.An artist's conception of microbialecology in the gut. Pathogenic bacteria(green coats) receiving Penicillinresistance genes from beneficialgut bacteria (blue rounded chains)Image courtesy of A. Canossa, M.Sommer and G. Dantas They found more than 90 undiscovered bacterial genes capable of c

Written byBob Grant

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An artist's conception of microbial
ecology in the gut. Pathogenic bacteria
(green coats) receiving Penicillin
resistance genes from beneficial
gut bacteria (blue rounded chains)
Image courtesy of A. Canossa, M.
Sommer and G. Dantas

They found more than 90 undiscovered bacterial genes capable of conferring antibiotic resistance hiding in microbes harvested from two healthy adults. They report their linkurl:findings;https://www.sciencemag.org/ in __Science__ today (August 27). "I thought this was an incredibly cool story," linkurl:Gerry Wright,;https://www.science.mcmaster.ca/biochem/faculty/wright/ McMaster University chemical biologist, told __The Scientist__. "It tells you just how ignorant we are of microbial ecology." Wright, director of McMaster's Michael G. DeGroote Institute for Infectious Disease Research, said that the findings raise several key questions. "If there's so much resistance out there, how come [antibiotics] work at all?" asked Wright, who was not involved with the study. "It either means that we really don't understand how antibiotics work or we really don't understand how microbes work." This lack of understanding is underscored by the fact that humans have exposed their bodies to a potentially dangerous flood of antibiotics -- directly in medicines and indirectly through agriculture and cleaning products -- for decades. This exposure has likely selected for the newly discovered antibiotic resistance genes in our internal microbiome, according to lead author linkurl:Morten Sommer,;https://connects.catalyst.harvard.edu/PROFILES/ProfileDetails.aspx?Person=MOS2 a postdoc in Harvard geneticist linkurl:George Church's;https://arep.med.harvard.edu/gmc/ lab. "And that could be a problem when the microbiome interacts with disease-causing microbes," he told __The Scientist__. Sommer and his colleagues analyzed saliva and fecal samples from two healthy volunteers who had not been treated with antibiotics for at least one year, and the researchers isolated more than 500 bacterial strains. They cloned genes from those strains, inserted them into __E. coli__ hosts, and then exposed the __E. coli__ to 13 different antibiotics to determine which genes conferred resistance. linkurl:Stuart Levy,;https://www.tufts.edu/med/microbiology/faculty/levy/ Tufts University microbiologist and geneticist, agreed that the study highlights the dangers of irresponsible antibiotic use. He told __The Scientist__ that pathogenic bacteria could easily add antibiotic resistance genes to their genomes via horizontal gene transfer. "There's every chance that [antibiotic resistance genes] could come out of [the microbiome] genome and become a force for resistance in bacteria that we face," said Levy, who is also president of the Alliance for the Prudent Use of Antibiotics. "The majority of antibiotic resistance genes reside in bacteria that are harmless. These are reservoirs of antibiotic resistance." Indeed, Sommer and his colleagues are now searching for chemical signatures of horizontal gene transfer in known resistance genes. But just because a cache of antibiotic resistance genes exists in our own guts doesn't mean that bacteria are readily swapping them. "If there was horizontal gene transfer, you would expect that [antibiotics] would be useless by now," said Wright. While some multi-drug resistant strains of pathogenic bacteria have emerged recently, many antibiotics are still effective if administered properly. In addition to finding scores of new antibiotic resistance genes, Sommer and his colleagues showed that almost half of the already identified resistance genes they isolated from the gut were identical to antibiotic resistance genes now found in clinically pathogenic microbes, such as pathogenic strains of __E. coli__ and __Salmonella enterica__. While this does not conclusively prove that horizontal gene transfer has occurred between beneficial bacteria in the human gut and disease-causing bacteria, said Sommer, "It does say that there's a close evolutionary history between strains in the human microbiome and pathogens."
**__Related stories:__***linkurl:The Microbial Health Factor;https://www.the-scientist.com/article/display/55864/
[August 2009]*linkurl:The number two-ome;https://www.the-scientist.com/article/display/55786/
[July 2009]*linkurl:Mysterious resistance;https://www.the-scientist.com/article/display/54963/
[September 2008]

Meet the Author

Bob Grant

From 2017 to 2022, Bob Grant was Editor in Chief of The Scientist, where he started in 2007 as a Staff Writer. Before joining the team, he worked as a reporter at Audubon and earned a master’s degree in science journalism from New York University. In his previous life, he pursued a career in science, getting a bachelor’s degree in wildlife biology from Montana State University and a master’s degree in marine biology from the College of Charleston in South Carolina. Bob edited Reading Frames and other sections of the magazine.

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