The impact of bacteriophages on gut microbial communities

Antibiotics have been used as first-class treatment for bacterial infections for decades . However, their widespread use has led to two major health issues: the rise of antibiotic-resistant pathogens, making infections harder to treat, and the disruption of gut microbiota equilibrium, resulting in dysbiosis and associated health problems. For these reasons, discovering novel therapeutic approaches to fight bacterial infections is a research priority. Bacteriophages, the viruses that infect bacteria, are a promising alternative to antibiotics for fighting bacterial infections. Yet, fundamental knowledge of bacteriophages remains limited to a few traditional model systems, leaving significant gaps in our understanding of bacteriophage behavior in bacterial communities, and their interaction with the host. For instance, while phage therapy is believed to have minimal impact on the gut flora, supporting data is scarce. In this study, I tested the impact of 80 representative Escherichia coli phages (BASEL collection ) on a synthetic bacterial community comprising 25 anaerobic gut microbes and one E. coli strain (BW25113). These microbes were selected to represent the most common genera of the human gut microbiota. Following treatment of this community with each BASEL bacteriophage, I determined whether E. coli was properly eliminated after the phage treatment and identified changes in the community composition by 16S rRNA sequencing. The collected data will enhance our understanding on phage infections in a controlled community and increase our knowledge on the impact of phage therapy on the gut microbiome composition.