The steady increase in life-expectancy of world population, coupled to many genetic and environmental factors (for instance, pre- and post-natal exposures to environmental neurotoxins), predispose to the onset of neurodegenerative diseases, whose prevalence is expected to increase dramatically in the next years. Recent studies have proposed links between the gut microbiota and neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Human body is a complex structure where bacterial and human cells are almost equal in numbers, and most microbes are metabolically active in the gut, where they potentially influence other target organs, including the brain. The role of gut microbiota in the development and pathophysiology of the human brain is an area of growing interest for the scientific community. Several microbial-derived neurochemicals involved in the gut-microbiota-brain crosstalk seem implicated in the biological and physiological basis of neurodevelopment and neurodegeneration. Evidence supporting these connections has come from model systems, but there are still unsolved issues due to several limitations of available research tools. New technologies are recently born to help understanding the causative role of gut microbes in neurodegeneration. This review aims to make an overview of recent advances in the study of the microbiota-gut-brain axis in the field of neurodegenerative disorders by: (a) identifying specific microbial pathological signaling pathways; (b) characterizing new, advanced engineered tools to study the interactions between human cells and gut bacteria.