Therapeutic interventions aimed at modulating the gut microbiome in children with HIV have shown limited impact, and their ability to induce long-term microbiome changes remains uncertain. A more functional, longitudinal approach, along with an ecological perspective, is needed to understand the complex interplay between the microbiome and the host. This will help clarify the relevance of microbiota alterations and their potential implications for clinical outcomes, such as inflammation and immune reconstitution in pediatric HIV.