Prophages and their interactions with lytic phages in the human gut microbiota and their impact on microbial diversity, gut health, and disease.

Bacteriophages (phages), the dominant prokaryotic viruses that specifically target bacteria in the human gut microbiome, play a crucial role in maintaining intestinal balance, regulating bacterial populations, and preserving microbial diversity within the gut microbiota. While prophages can enhance bacterial virulence and antibiotic resistance, potentially posing health risks, they also provide beneficial functions, including enhancing host fitness, promoting immune modulation, and contributing to ecosystem resilience, which supports intestinal homeostasis. Human gut microbiota is essential for various physiological functions, including digestion, vitamin synthesis, immune modulation, and protection against pathogens. Dysbiosis, or microbial imbalance, is associated with various disorders such as inflammatory bowel disease, obesity, diabetes, and mental health disorders. Consequently, prophages are important considerations for developing therapies to prevent intestinal diseases. Recently, there has been significant interest in prophage induction in the gut due to its functional impacts on microbial dynamics, gut health, and disease modulation. Prophage induction can be regulated by diet, antibiotics, metabolites, gut health, lifestyle, and intestinal environments. However, compared with lytic phages, prophages remain underexplored, leaving gaps in our understanding of their functions within the gut. Therefore, further research is needed to fully elucidate the complex interactions between phages, prophages, and the gut microbiota, and their effects on health and disease. This knowledge could inform the development of phage-based therapies and improve therapeutic strategies for gut health.