Recent Developments and Applicability of In Vitro Gut Microbiota Models in Biomedical Research and Digestive Diseases—A Systematic Review

Background and Objectives: Current research approaches focusing on the human gut microbiota require complex in vitro systems that could provide sufficient viability and similarity with the conditions provided by the human intestine. As critical physiological functions, such as metabolic and inflammatory modulation, are associated with gut microbiota activity, complex host–microbiota interactions represent a pivotal new direction for therapeutic and nutritional interventions. However, there are several limitations to the current development of advanced in vitro models. Materials and Methods: A systematic review was performed according to the PRISMA guidelines for data collection and interpretation. Results: This manuscript summarizes the most advanced in vitro approaches for studying the gut microbiota, including batch fermentation models, dynamic fermentation models, and state-of-the-art technologies, such as organoids and gut-on-a-chip platforms. Each model offers beneficial study backgrounds, advantages, limitations, and the capacity to replicate the physiological complexity of the intestinal environment. However, due to the increased heterogeneity of the reported models, there is an urgent need for standardization. In this way, coherent regulatory frameworks are needed to guide the development and application of in vitro models. Conclusions: By consolidating knowledge and critically addressing current challenges, this study contributes to gut microbiota research by providing a direction for ethical, precise, and high-impact scientific studies.