SARS-CoV-2 is the causative agent of the COVID-19 pandemic. It appears to cause only mildto moderate upper respiratory symptoms in children, in addition to gastrointestinalsymptoms resulting from its penetration into intestinal cells. Viral respiratoryinfections are often accompanied by a change in the composition of the gut microbiota(GM). Additionally, intestinal metabolites and integrity appear to be altered. This workaims to study the composition of the GM of Lebanese children, currently (n=14) andpreviously (n=33) infected with SARS-CoV-2 and to compare it to pre-pandemic controls(n=39). Furthermore, the correlation between the composition of the GM and the intestinalhomeostasis are evaluated. Clinical data and stool samples were collected from childrenaged 1 month to 12 years. The bacterial profile is determined by quantitative PCR and 16SrRNA sequencing. Levels of secretory immunoglobulin A (sIgA), fecal calprotectin, betadefensin type 2 (hBD-2), short-chain fatty acids (SCFAs), tryptophan derivatives, andbile acids are also evaluated. Given the well-established relationship between the GM andthe immune system, the results of this study could serve as a potential basis for theimplementation of personalized nutrition and biotic supplementations aimed at restoringthe host-microbiota symbiosis, pointing to the prevention and treatment of COVID-19