As the only effective therapy against diagnosed celiac disease (CD), the gluten-free diet (GFD) has inevitable repercussion on the gut microbiome composition and functionality. Being the cause or the consequence of the disease, an altered homeostasis of the gut microbiome usually affects CD patients at diagnosis. After describing the main features of this altered physiological condition, this review defines the main nutritional aspects of the GFD and elucidates how this diet regimen does not fully restore the optimal gut microbiome composition and functionality. Unbalanced ratios between beneficial and potentially harmful bacteria are frequently present in fecal materials, biopsy specimens and saliva, used as ecological model systems to observe CD. Metabolome analyses also show how an altered microbiome synthesize different metabolite with respect to healthy conditions. The review concludes illustrating the current supplementations (biotics family), which fortify the GFD with the aim of restoring the homeostasis of the gut microbiome
