Oral microbiome signatures of molar-incisor hypomineralisation: insights from a pilot study

Molar-incisor hypomineralisation (MIH) is a developmental condition that may increase plaque retention and caries risk, yet its microbial signature remains unclear. We compared plaque microbiome diversity and community composition in children with MIH and healthy controls, including tooth-level MIH severities.

In this cross-sectional pilot study, supragingival plaque was collected from 30 children aged 7-16 years (15 MIH, 15 controls), yielding 63 samples. Controls contributed one pooled molar sample per child (n = 15), whereas MIH participants provided 48 pooled molar samples stratified by lesion severity. The V3-V4 region of the 16S rRNA gene was sequenced (via the Illumina NovaSeq platform), and reads were processed in R. Diversity and differential abundance were analysed in R using mixed-effects models, PERMANOVA, and ANCOM-BC2.

Children with MIH had significantly higher plaque scores (p = 0.009). Community structure remained similar between groups and across severities (PERMANOVA R² <0.06), with variation driven more by individual differences. The core microbiome was largely shared; however, controls retained nine additional genera (≥ 90% prevalence) not consistently present in MIH. Bacterial evenness was significantly lower in MIH (Shannon β = 0.404; 95% CI 0.10-0.71; FDR-adjusted p = 0.042), whilst community richness and phylogenetic diversity were comparable. Effect sizes suggested higher Neisseria and Abiotrophia, and lower TM7x in MIH although not statistically significant (all q ≥ 0.161).

MIH was associated with higher plaque accumulation and reduced microbial evenness, without a clear alteration of overall community structure. Directional trends and reduced consistency of highly prevalent core genera warrant confirmation in larger studies.