Not just passengers: Phages as agents of genetic exchange in fecal microbiota transplantation

Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection and is increasingly being explored for other microbiota-associated diseases. However, general research has largely focused on bacterial engraftment, overlooking the contribution of the gut virome. In this perspective, we highlight phage-mediated horizontal gene transfer (HGT) as a potentially influential process occurring following FMT. Donor-derived phages may potentially influence community structure, engraft in resident bacteria, and modulate microbial functions or host physiology. In addition, temperate phages are well-equipped to mobilize bacterial genes, such as metabolic functions, stress-response traits, and antibiotic resistance determinants, raising the possibility that gene flow could well contribute to FMT outcomes. We propose a conceptual model in which phages act as bidirectional mediators of adaptation, not only accompanying bacterial communities but also influencing gut ecosystems in subtle, yet potentially consequential, ways. © 2026 The Authors.