Shotgun metagenomic profiling reveals ecological and functional alterations of the oral microbiome in craniosynostosis

Abstract

Objective

To elucidate the microbial drivers underlying of craniosynostosis (CS) , which involves premature suture fusion and secondary dentofacial malformations likely to increase dental disease burden.

Methods

Shotgun metagenomic sequencing of supragingival plaque from 44 participants (22 CS patients and 22 matched healthy controls, aged 6–17 years) were performed, following by bioinformatics evaluation.

Results

Beta diversity demonstrated significant differences between groups ( p < 0.01), whereas alpha diversity trended lower in the CS cohort. Taxonomic profiling revealed a dysbiotic signature in CS with high caries burden, defined by the enrichment of saccharolytic and anaerobic taxa (Scardovia, Actinomyces sp. oral taxon 448, Selenomonas sp. F0473, and Treponema lecithinolyticum)) alongside reduced health-associated genera like Haemophilus and Neisseria. Functional pathway analysis indicated metabolic remodeling, with upregulated fructan biosynthesis and starch degradation III pathways, consistent with caries-active biofilms.

Conclusion

These findings demonstrate that orofacial anomalies in CS favor the assembly of an acidogenic, virulent plaque biofilm. The first shotgun metagenomic profile of the oral microbiome in CS establishes a foundation for future investigations. Furthermore, clinical management of CS should extend beyond structural correction to incorporate microbiological monitoring and preventive strategies, reducing the elevated risk of dental disease in this vulnerable population.