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
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Background
Dental caries is increasingly understood as an ecological biofilm disorder rather than solely 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: 44 with rampant caries and 44 who were caries-free (BioProject PRJNA1141721). Single-end DADA2 processing yielded 25,669 amplicon sequence variants (ASVs), including one ASV identified as S. mutans by exact matching within the sequenced region to eHOMD RefSeq v15.23. 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-R 2 =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 reference-supported S. mutans ASV was detected in 8/44 rampant-caries and 42/44 caries-free samples and had lower relative abundance in rampant caries. Among 758 prevalence-filtered non- S. mutans ASVs, 239 non-structural-zero ASVs were FDR-significant, 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-R 2 =0.0149, P=0.085) in the presence of strong collinearity.
Conclusions
Rampant caries was associated with a modest plaque-community compositional difference after exclusion of a reference-supported S. mutans ASV; the result was robust to rarefaction and was not accompanied by a corresponding difference in Shannon diversity. These findings support a community-level ecological interpretation but do not establish statistical independence from S. mutans or a causal role for individual taxa.
