Elucidating a potential role of the infant gut microbiome on L-tyrosine bioavailability in phenylketonuria using whole-body metabolic modelling

Phenylketonuria (PKU) is an inherited metabolic disorder caused by phenylalanine hydroxylase (PAH) deficiency, leading to elevated L-phenylalanine and severe neurological damage if untreated. While phenylalanine-based biomarkers are diagnostic and phenylalanine levels correlate with disease severity, the clinical manifestations of PKU are heterogeneous. To identify additional reliable, potentially novel biomarkers, we used germ-free sex-specific, organ-resolved infant whole-body metabolic models (infant-WBMs) to simulate PAH deficiency and predicted elevated L-phenylalanine and its derivatives, alongside reduced L-tyrosine fluxes, as the product of phenylalanine hydroxylation. To test the reliability of these predicted biomarkers to variations in microbiome composition, we combined the infant-WBMs with gut microbiome models from 48 female and 42 male healthy infants. Upon integrating microbiome data, we found that microbial metabolism significantly increased the predicted L-tyrosine availability, obscuring its utility as a universal biomarker. In ~ 23% of microbiome-PKU models, L-tyrosine fluxes remained low, indicating insufficient microbial compensation. These cases were enriched in Firmicutes and lacked specific Bifidobacterium and Escherichia strains linked to L-tyrosine biosynthesis via the pretyrosine pathway. Shadow price analysis identified microbial species critical for host L-tyrosine metabolism. However, some, such as Bifidobacterium dentium , also contributed to L-phenylalanine synthesis, potentially worsening the PKU phenotype. In contrast, L-phenylalanine, phenylpyruvate, and hydroxyphenylacetic acid remained reliably elevated across all models, validating their diagnostic relevance. Our study demonstrates that microbiome composition can modulate biomarker reliability in PKU, particularly for L-tyrosine. Integrating microbial metabolic models with whole-body physiology enables assessment of biomarker reliability and reveals subpopulations for whom secondary biomarkers or targeted probiotics may be beneficial. This approach offers a powerful framework for refining diagnostics and therapy monitoring in rare metabolic diseases and the development of possible targeted microbiome therapies. Video Abstract