The intestinal microbiota harbors an immense diversity of bacteriophages (phages) that shape bacterial communities and influence host physiology. While phages are key players in maintaining microbial balance, the mechanisms that enable their long-term coexistence with bacterial hosts in the gut remain largely unknown. Our research focuses on uncovering the ecological and molecular principles that govern stable phage-bacteria interactions, aiming to shed light on their role in microbiome homeostasis and resilience. This knowledge may support future applications in microbiome modulation and phage therapy.

To better understand how phages interact with their bacterial hosts, we develop and modify the existing computational pipelines to study phage genomes alongside their host genomes. Using a wide range of bioinformatics tools, we analyze newly discovered phage genomes from our experiments and compare them with well-characterized reference genomes. This allows us to identify novel gene functions, explore unique genome architectures, and uncover evolutionary relationships across diverse phage populations. By studying both phage and host genomes together, we gain insight into how phages adapt to their hosts, exchange genetic material, and influence microbial community dynamics. Comparative analyses help reveal patterns of host specificity, genome modularity, and the molecular mechanisms that support long-term coexistence. These findings enhance our understanding of the ecological and evolutionary roles of phages in the gut microbiome and support future strategies for targeted microbiome modulation and phage therapy.