We will outline the factors (e.g., decreased secretory IgA, recurrent infections, antibiotics) that shape gut microbiota composition in patients with CVID, and the potential clinical interventions (e.g., diet, probiotics, prebiotics, drugs and fecal microbiota transplantation) to re-establish and/or to promote a “healthier” microbial community. Here, CD79A is linked to common variable immunodeficiency.