Dynamics of the human gut phageome during the antibiotics therapy

Abstract

Antibiotics are widely used in all sorts of the medical procedures. Without them, modern medical practice is not possible. As much as they are inevitable, they have severe adverse effects in promoting the antibiotic resistance. Each antibiotic therapy has a profound impact on the human gut. Firstly antibiotics select resistant bacteria what results in rapid changes of the taxonomical composition of the human gut. Secondly, the antibiotic pressure prompts the horizontal gene transfer including transduction that is intermediated by the phages, what advances spread of the resistance. Although the taxonomical composition restores after a month from the therapy, the bacteria get enriched with the genes conferring resistance to antibiotics. We have analyzed changes in the microbiome and phageome of the two people throughout the antibiotic therapy and subsequent recovery time. Analysis of the phage genomes is bioinformatically tricky as phages have complex genomic structures and there are no reliable reference databases. Therefore, we developed a novel comprehensive pipeline for the time-series analysis of the metagenomic datasets focusing on the function and changes in the phage sequences. We observed the phages respond to the antibiotic therapy, and are enriched with antibiotic-resistant genes.