Diet-Associated Gut Microbiome Signatures in Pediatric Phenylketonuria: A Shotgun Metagenomic Study from Ecuador

Background Phenylketonuria (PKU) requires lifelong phenylalanine (Phe) restriction to prevent neurotoxicity. Dietary management may remodel the gut microbiome, with potential clinical implications. We characterized taxonomic and functional features of the gut microbiome in pediatric PKU patients managed with Phe-restricted versus non-restricted diets in Ecuador. Methods We performed a cross-sectional exploratory shotgun metagenomic analysis of 15 PKU patients (non-restricted diet, n  = 9; Phe-restricted diet, n  = 6). Taxonomic profiles were resolved to the species level, and functional potential was assessed using KEGG orthologs and CAZy enzyme families. Community structure was evaluated using Bray–Curtis-based ordination analyses. Results Both groups were dominated by Firmicutes and Bacteroidetes, with lower representation of Actinobacteria, Proteobacteria, and Verrucomicrobia. At the genus and species levels, non-restricted samples (G1) were characterized by multiple short-chain fatty acid–associated Firmicutes, including Ruminococcus , Oscillibacter , Clostridium spp., Faecalibacterium sp. CAG74, and Subdoligranulum . In contrast, Phe-restricted samples (G2) showed recurrent enrichment of Bacteroides uniformis , Bacteroides vulgatus , Eggerthella lenta , and Bilophila wadsworthia . Ordination analyses demonstrated diet-associated stratification, with tighter clustering in G1 and greater dispersion in G2. Functionally, G2 exhibited higher relative abundance of carbohydrate-active enzymes—particularly glycoside hydrolases and glycosyltransferases—and increased KEGG orthologs related to membrane transport and signal transduction. Conclusions In this Ecuadorian pediatric cohort, dietary management in PKU is associated with distinct taxonomic and functional gut microbiome profiles. These hypothesis-generating findings support integrating microbiome analyses into PKU care and motivate larger longitudinal studies in under-represented Latin American settings.