Plaque microbial community differences in rampant dental caries after exclusion of a reference-supported Streptococcus mutans ASV: an analysis of public 16S rRNA sequencing data

Abstract

Background: Dental caries is increasingly understood as an ecological biofilm disorder rather than the consequence of a single organism. Although Streptococcus mutans is strongly implicated in cariogenesis, it remains unclear whether caries-associated plaque-community differences persist beyond this organism. Methods: We reanalysed publicly available supragingival-plaque 16S rRNA sequencing data from 88 preschool children with rampant caries (n=44) or who were caries-free (n=44; BioProject PRJNA1141721). Single-end DADA2 processing yielded 25,669 amplicon sequence variants (ASVs), including one ASV confirmed as S. mutans by an eHOMD reference-window procedure. The pre-specified primary analysis compared Bray-Curtis community composition after exclusion of this ASV. Results: Non-S. mutans community composition differed between groups (PERMANOVA pseudo-R2=0.0462, pseudo-F=4.16, P<0.001), without evidence of unequal multivariate dispersion (P=0.796); rarefaction produced a nearly identical result. Shannon diversity did not differ (P=0.486). The confirmed S. mutans ASV was detected in 8/44 rampant-caries and 42/44 caries-free samples and was lower in abundance in rampant caries. Among 758 prevalence-filtered non-S. mutans ASVs, 239 showed conventional FDR-significant differential abundance, with more showing lower than higher bias-corrected abundance in rampant caries (176 versus 63); 239 additional ASVs were classified as structural zeros. Individual ASV findings were sensitive to prevalence filtering. Adjustment for S. mutans abundance attenuated the global caries-group association (marginal pseudo-R2=0.0149, P=0.085) in the presence of strong collinearity. Conclusions: Rampant caries was associated with modest but reproducible plaque-community restructuring after exclusion of a confirmed S. mutans ASV, without a corresponding Shannon-diversity difference. These findings support a community-level ecological interpretation but do not establish statistical independence from S. mutans or a causal role for individual taxa.