A European study unveils the diversity of antibiotic resistance genes present in bacteria in the gut bacteria. Teams from Beaujon and Bichat Claude-Bernard AP-HP hospitals, INRA (MetaGenoPolis), Institut Pasteur, Inserm, Paris Diderot, and Paris-Saclay universities have developed a new bioinformatics method for predicting gene function based on the three-dimensional structure of the proteins they code.
The researchers, in collaboration with other European teams, then applied it to a catalog of several million genes in the intestinal microbiota. Through this method, they have identified more than 6000 antibiotic resistance genes that are very different from known genes. This work, published in the journal Nature Microbiology, illustrates the diversity of bacterial resistance genes in our intestinal microbiota.
To establish the identity of antibiotic resistance genes in the gut bacteria, it was not possible to rely solely on DNA sequence similarity. So, the DNA of intestinal microbiota is very different from that of known bacteria, which is not without difficulties for tools for predicting gene function based on similarity with known DNA sequences.
Over 6000 Antibiotic Resistance Genes Discovered In The Gut Bacteria
This highly original prediction method has identified more than 6000 genes that could confer antibiotic resistance to gut bacteria, with an average of more than 1000 resistance genes per individual. These so-called “in silico” predictions have been verified in the laboratory on certain classes of antibiotics such as beta-lactam antibiotics. In addition to that, the composition of resistance genes was strictly related to the structure of bacterial species, and researchers were able to identify six groups of individuals based on their resistance genes.
However, the majority of these resistance genes in gut bacteria have never been found either on mobile genetic elements or in pathogenic bacteria, claiming that their transfer to the latter is a rare event. The researchers also observed that exposure to antibiotics influenced the content of resistance genes – short and high exposure altered the composition of the intestinal microbiota and paradoxically decreased the abundance of resistance genes.
These results open new perspectives on the role of gut bacteria antibiotic resistance genes, most of which appear to be at low risk of being transferred to pathogenic bacteria, and which could be beneficial in protecting their hosts from the impact of antibiotics in the intestinal microbiota since non-pathogenic bacteria would thus be protected.