Baseline Intestinal Microbiota Composition Influences Response to a Real-World Dietary Fiber Intervention

The intestinal microbiota is modulated by dietary-fiber-containing functional ingredients, such as unripe banana flour (UBF), rich in resistant starch (RS). While dietary interventions can modulate the gut microbiome, interindividual variation has been associated with mixed outcomes. Here, we assess the effects of the discontinued intake of RS-rich UBF or the prebiotic inulin on the intestinal microbiota and its interactions with intestinal function. A double-blind, parallel, randomized, placebo-controlled pilot trial was carried out for 6 weeks, with 48 healthy subjects consuming maltodextrin (control group), inulin, or UBF 3 times/week. The intestinal microbial dynamics was accessed by sequencing the bacterial 16S rRNA gene and performing PICRUSt-derived metabolic profiling before and after the intervention. Fecal short-chain fatty acids, blood biochemical, and gastrointestinal functioning parameters were measured pre- and post-intervention. Two baseline microbiome clusters were identified among the participants, characterized by higher levels of genus Prevotella (cluster P) or Bacteroides (cluster B), with differing responses to dietary interventions. A global microbiome change (Permanova, p= 0.007, Weighted Unifrac) was observed in cluster P subjects consuming UBF, unlike the control or inulin groups. Cluster P individuals had a large microbiome metabolic profile change (533 Kegg orthologs, FDR < 0.05), including enriched lipopolysaccharide biosynthesis and transporters pathways, and depleted aminoacyl-tRNA biosynthesis and transcription machinery pathways. Inulin consumption by cluster P subjects induced a much smaller modulation (19 Kegg orthologs, FDR < 0.05). Cluster B showed no global differences with any intervention. Biochemical and gastrointestinal functioning outcomes varied for each intervention. Consumption of RS-rich UBF modulates the gut microbiome of healthy subjects in a composition-dependent manner, inducing changes in gastrointestinal functioning without undesired side effects. Different types of dietary fiber can elicit distinct responses in the gut microbiome. Future dietary fiber interventions would benefit from a priori microbiome cluster profiling to enhance treatment success, with UBF as a potential microbiome modulator.