Mapping the oral microbiome in children with oral diseases using next-generation sequencing: a systematic review

Abstract

Abstract Background The oral microbiome is integral to paediatric oral health and disease. Next-generation DNA sequencing (NGS) technology enables culture-independent profiling of microbial communities, yet findings remain inconsistent due to methodological and population heterogeneity. Objective This review synthesised NGS-based evidence comparing the oral microbiome of children/adolescents with oral diseases and healthy controls. Design The protocol was registered in PROSPERO (CRD42025618407). PubMed, Medline, Embase, Scopus and Web of Science were searched for peer-reviewed studies (2015–2025). Eligible studies used 16S rRNA gene sequencing to compare children/adolescents (0–18 years) with oral diseases and healthy controls. Two reviewers independently screened studies, extracted data and assessed risk of bias using validated tools. Findings were synthesised narratively due to heterogeneity. Results From 4,767 records, 61 studies were included. Most were cross-sectional designs conducted across diverse populations and conditions. Differences in community composition were more consistent than changes in alpha diversity, which varied by disease stage and sampling site. Shifts toward anaerobic, metabolically active communities were observed. Dental caries was consistently linked to acidogenic genera/species, whereas fluorosis, halitosis and gingivitis showed functional shifts involving proteolytic, sulphur-metabolising and anaerobic bacteria. Conclusion Paediatric oral diseases are more strongly associated with condition- and niche-specific compositional alterations than with uniform diversity changes.