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Chronic neurodegenerative disorders are mostly due to population aging. These invalidating conditions include dementia (as Alzheimer’s disease - AD) and movement disorders (as Parkinson’s disease - PD). In the past decades, we have been accumulating experimental evidence on the molecular triggers of AD/PD and few approved drugs are available, unfortunately with no real disease-modifying action. As AD/PD cases constantly rise in the world, new hypothesis on their pathogenesis are actively under investigation. One of this is based on the microbiota-gut-brain axis, that postulates a direct or indirect influence of the microbial host community of human gut on the nervous system and its functions. This bidirectional interaction may play a role also in neurodegenerative disorders, even though research in this field requires models and tools for growing to a clinical translational perspective. To this respect, innovative in vitro engineered disease models are gaining attention, particularly because they feature desirable characteristics as tridimensional (3D) growing conditions and interstitial fluids movement recapitulation thanks to microfluidics. Here we summarize current data on the impact of gut microbiota on AD/PD models and patients, with a focus on ongoing research projects on the topic that are trying to unravel clinical questions or elaborate technical solutions for research and industry applications in the field.