Effects of Different Types of Pectin Oligosaccharides on the Community Structure and Metabolism of Human Fecal Microbiota

Pectin oligosaccharides have emerged as promising prebiotics whose biological activities are closely tied to their structural features, particularly monosaccharide composition. However, systematic experimental evidence regarding how different monosaccharide compositions collectively influence gut microbiota modulation, SCFA production, and the metabolomic responses of mixed pectin oligosaccharides remains limited. To address this gap, Pool-I (27.92% galacturonic acid, rich in neutral sugars including galactose, glucose, and arabinose) and Pool-II (98.73% galacturonic acid) were evaluated by comparison with inulin, a reference prebiotic, using an in vitro human fecal fermentation model. Microbial community structure, SCFA production, and metabolomic profiles were assessed at 12 h and 24 h via 16S rRNA gene sequencing, gas chromatography, and untargeted metabolomics, respectively. Inulin exhibited superior enrichment of Actinobacteria (predominantly Bifidobacterium) and consistently higher total SCFA production (24.07 ± 0.25 mmol/L acetic acid at 24 h vs. 20.27 ± 0.28 and 20.53 ± 0.76 mmol/L for pectin oligosaccharides), particularly propionic and butyric acids. Although Pool-I and Pool-II yielded lower overall SCFA concentrations, they significantly enriched beneficial SCFA-producing genera (including Coprococcus_3, Butyricicoccus, and Parabacteroides) at 24 h. Metabolomic analysis revealed that Pool-I uniquely upregulated twenty-six differential metabolites (VIP > 1, p < 0.05), including taurine (VIP = 2.40, p < 0.001), L-proline (VIP = 1.72, p = 0.015), and pantothenate (VIP = 1.63, p < 0.001), while reducing uric acid (VIP = 1.05, p < 0.001), whereas only two differential metabolites were identified for Pool-II. We conclude that monosaccharide composition is a key determinant of the prebiotic efficacy of pectin oligosaccharides: Pool-II selectively promotes SCFA-producing taxa, whereas Pool-I elicits broader metabolic regulation. These effects provide a theoretical foundation for developing pectin oligosaccharides as potential prebiotic candidates.