Fecal Short-Chain Fatty Acid Profiling in Type 2 Diabetes Mellitus Using GC–MS: A Comparative Study in a South African Population

Background: Type 2 diabetes mellitus (T2DM) is associated with altered gut microbiota and reduced short-chain fatty acid production, which may contribute to insulin resistance. However, evidence on fecal Short Chain Fatty Acid (SCFA) profiles in African populations remains limited. This study quantified fecal SCFAs in individuals with and without T2DM using Gas Chromatography–Mass Spectrophotometry (GC-MS) with N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) derivatization. Methods: A cross-sectional study included 140 adults (92 non-diabetic and 48 T2DM). Fecal SCFAs were extracted, derivatized using BSTFA, and analysed by GC–MS. Associations between SCFAs, diabetes status, and HbA1c were evaluated using non-parametric statistics. Results: The GC–MS method demonstrated strong linearity (R2 = 0.9917–0.9978), acceptable recovery, and reproducibility. Acetic, propionic, butyric, pentanoic, hexanoic, and heptanoic acids were detected, with acetic acid being most abundant in both groups. T2DM participants had higher median SCFA levels, although only butyric acid differed significantly (p = 0.027). HbA1c was significantly higher in the T2DM group (p < 0.001). No significant associations were observed between SCFAs and HbA1c in either group. Age differed significantly between groups, with T2DM participants older than non-diabetic controls. Conclusions: Most fecal SCFA profiles were comparable between individuals with T2DM and healthy controls. However, butyric acid was significantly elevated in the T2DM group, indicating that not all SCFAs exhibited similar patterns between the study groups. These findings suggest that fecal SCFAs alone may not serve as reliable biomarkers of T2DM in this population and highlight the influence of complex host–microbiome–environment interactions suggesting that dietary and microbial factors may outweigh disease status in determining SCFA variability in this cohort setting.