PhageQuest: Harnessing Gut Phages to Combat Antimicrobial Resistance and Pathogenic Threats in the Gut Microbiota

Abstract

Background: Antimicrobial resistance [AMR] is a growing global health crisis, with the gut microbiome emerging as a critical reservoir for multidrug-resistant [MDR] bacteria. Central to this issue is the gut resistome, the complete set of antimicrobial resistance genes [ARGs] present in both pathogenic and commensal gut bacteria. These genes can be horizontally transferred, facilitating the spread of resistance across species and environments. Conventional antibiotics are increasingly ineffective, especially in the gut where biofilms and complex resistance mechanisms prevail. In this context, bacteriophages offer a promising alternative, capable of targeting bacteria with high specificity and minimal impact on beneficial microbiota. Environmental sources like sewage and fecal filtrates may provide phages already adapted to the gut ecosystem.

Methods: This study used a combination of culturomics, 16S rRNA gene sequencing via Oxford Nanopore Technology, and phage activity screening to evaluate the potential of phages sourced from sewage and fecal filtrates. Stool samples from healthy donors were processed to isolate bacterial strains under anaerobic conditions. Sequencing was performed to assess microbial diversity, and phage activity was screened by monitoring bacterial growth inhibition in the presence of filtrates using a 96-well microplate reader.

Results: Of the 247 bacterial isolates screened, 83 [33.6%] exhibited a significant decrease in optical density, indicating potential bacteriophage-induced lysis. This included 23 isolates responsive to both filtrates, 36 to sewage only, and 24 to fecal filtrate only. Sequencing revealed that nearly 60% of microbial sequences were unclassified, highlighting the presence of unexplored taxa. Culturomics enabled the growth of both common and hard-to-culture organisms, including opportunistic pathogens relevant for phage targeting.

Conclusion: The study demonstrates that sewage and fecal filtrates contain bacteriophages capable of lysing MDR gut bacteria under anaerobic conditions. These findings support the potential of phage therapy as a targeted, microbiome-sparing approach to combat AMR. The integration of culturomics and sequencing proved essential for both bacterial host identification and phage discovery. Future research should focus on isolating individual phages, confirming their lytic activity, and evaluating their efficacy in clinical or in vivo settings.