Diet Quality Modulates Gut Microbiota Structure in Blastocystis-Colonised Individuals from Two Distinct Cohorts with Contrasting Sociodemographic Profiles

Diet and gut microbiota are significant determinants of host health, but how dietary quality modulates gut microbiota in Blastocystis-colonised individuals remains underexplored. We studied two contrasting cohorts: university students (FACSA, n = 46) and institutionalised children with their caregivers (PAVILA, n = 37), representing distinct dietary and sociodemographic contexts. Eight participants from each cohort tested positive for Blastocystis; however, two PAVILA samples could not be sequenced, resulting in a final microbiota subcohort of 14 individuals (FACSA n = 8, PAVILA n = 6). Dietary quality was assessed using the Healthy Eating Index-2020 (HEI-2020), and faecal microbiota was characterised through 16S rRNA sequencing. Alpha and beta diversity were analysed, and genus-level transformed data were further evaluated using permutational multivariate analysis of variance (PERMANOVA), principal coordinates analysis (PCoA), and distance-based redundancy analysis (db-RDA). The FACSA cohort exhibited higher microbial richness and diversity (Shannon and Simpson indexes, p < 0.01) compared to PAVILA, with marked differences in microbial composition (PERMANOVA R² = 0.39, p = 0.002). Total diet quality correlated with microbial structure (R² = 0.26, p = 0.016), with protein (R² = 0.23, p = 0.017) and vegetable components (R² = 0.17, p = 0.044) as primary contributors. Multivariate analysis showed that higher protein and vegetable intakes were associated with genera such as Sellimonas, Murimonas, Alistipes, and Desulfovibrio (FACSA group). In contrast, Hydrogenoanaerobacterium, V9D2013_group, and Haemophilus were linked to lower-quality diets (PAVILA group). Our results indicate that diet quality significantly influences gut microbiota composition in individuals colonised by Blastocystis, underscoring its potential as a target for nutritional interventions in vulnerable populations.