In recent years, the crucial role of microbiota in human health has become increasingly evident. The human body hosts billions of microbial species, predominantly in mucosal layers such as the gut, lungs, and cervico-vaginal tract. Recent research highlights the interconnection between microbiota from different districts through circulating metabolites. For instance, alterations in gut microbiota have been linked to conditions like cystic fibrosis in the lungs and endometriosis in the reproductive tract, underscoring the need for predictive in vitro models to study these interactions and develop new therapeutic strategies in the fields of probiotics, prebiotics, and antibiotics. Various methods, including animal models, 2D cultures, bioreactors, and microfluidic systems, have been employed to study microbiota.