This study presents an integrated metabolite-centered framework for the comparative evaluation of plant-based substrates through the simultaneous profiling of fermentation-associated short-chain fatty acids (SCFAs) and neuroactive compounds within a single in vitro experimental platform. Unlike conventional studies focusing on individual metabolite classes, the present approach combines in vitro gastrointestinal digestion with simplified bacterial fermentation to characterize substrate-dependent metabolic responses under controlled experimental conditions. Concurrent evaluation of SCFA production and neuroactive compound formation enabled multidimensional assessment of fermentation-associated metabolite profiles and their potential biochemical interrelationships. Significant differences (p < 0.05) were observed among substrates in both SCFA production and neuroactive compound formation. Hemp seed flour exhibited the highest acetate concentration (4.67 mg/100 g) and γ-aminobutyric acid (GABA) level (114.00 µg/g), whereas lentil and corn flour showed elevated propionate levels. Chickpea and bulgur produced the highest butyrate concentrations. Among neuroactive compounds, bulgur exhibited the highest dopamine and serotonin levels, while lentil demonstrated a more balanced metabolite profile. Correlation analysis suggested exploratory associations between SCFA production and neuroactive compound formation. A strong positive correlation between acetate and GABA (r = 0.89) indicated potential co-variation between carbohydrate fermentation and neuroactive metabolite formation, whereas divergent dopamine and serotonin patterns suggested substrate-dependent metabolic differences. Functional mapping further classified substrates into SCFA-oriented, neuroactive compound-dominant, and mixed metabolic profile groups. Collectively, these findings support a metabolite-centered framework for comparative assessment of plant-based substrates based on fermentation-associated metabolite profiles obtained under controlled in vitro conditions. Although the simplified two-strain fermentation model does not reproduce the complexity of the human colonic microbiota, the observed substrate-dependent metabolic differences may provide preliminary insights into biochemical outputs potentially relevant to gut-brain axis-associated pathways. Further studies employing complex microbial communities and in vivo validation are required to confirm the physiological relevance of these findings.
