The COVID-19 pandemic has demonstrated our global health fragility and exacerbated existing inequalities leaving many vulnerable. To tackle the long-term effects of this infection and prevent other pandemics, it is crucial to understand the virus-microbiota axis. Recent studies suggest the gastrointestinal involvement and a prolonged stay of the virus in the intestinal microbiota, where it can replicate and spread to other organs. It is known that the digestive system is the main site of the immune system, so it is plausible that this organ plays an essential role in the pathogenesis of COVID-19. Thus, in line with the UNs’ Sustainable Development Goals (SDGs), ARCHES is devoting many research efforts to developing an innovative approach for the analysis of the human microbiome with the use of artificial intelligence (AI). This campaign is supporting the achievement of a specific target of the 2030 Agenda, namely Goal 3: Good Health and Well-Being.