Understanding the gut–brain axis with methodological challenges and transitional barriers in neurophysiology

With significant effects on behavior, overall health, and cognition, the gut–brain axis (GBA) serves as a vital communication channel between the gut microbiota and the host neurophysiology. This bidirectional system integrates endocrine, neural, and immune pathways that modulate both the central nervous system and gastrointestinal system operations. Despite the increasing research evidence that the gut microbiome effects neurobehavioral outcomes, there are still substantial gaps in our knowledge on causative pathways, translational obstacles, and methodological inconsistencies. In this narrative review, we thoroughly reassess existing evidence on the impact of microbiota on physiological responses and behavior, highlighting the significant methodological weaknesses, limitations in translating preclinical findings to clinical applications. The mechanisms linking microbiota composition with neurotransmitter signalling, neuroendocrine regulation, and neuroinflammation are examined critically. The special attention is placed on the intricacies of the modulation of neurotransmitters, acknowledging that molecules like serotonin can have both inhibitory and excitatory effects, both of which depend on neural context and receptor subtype. We have discussed the limitations of existing literature, like nonstandardized protocol, small sample group, and possible confounding variables like dietary and environmental changes. Relevant studies were located from Scopus, PubMed, Google Scholar, Web of Science, and Science Direct using predecided keywords related to neurophysiology, GBA, and microbiota; studies were screened for methodological rigor, translational value, and relevance. Finally, we suggest strategies to strengthen scientific understanding, improve clinical translation, and improve reproducibility in subsequent research. This review focused on a more comprehensive understanding of the GBA, while guiding the development of standardized and clinically significant methodologies.