RNA sequencing points to active Lactobacillus in severe childhood tooth decay

A University of Washington study used paired DNA and RNA sequencing to separate which bacteria were present from which were metabolically active in severe early childhood caries. The findings, published online in the International Journal of Oral Science, suggest active Lactobacillus species may be driving lesion progression more than traditionally blamed microbes like Streptococcus mutans.

Why it matters: - Severe early childhood caries affects millions of children worldwide and can rapidly destroy baby teeth. - The study suggests that finding bacteria in a lesion is not the same as finding the microbes driving damage. - Better distinction between presence and activity could improve diagnostics, risk prediction, and treatment targets for children with advanced tooth decay.

What happened: - Researchers at the University of Washington analyzed microbial communities in deep dentin lesions from children with severe early childhood caries. - The team, led by Dr. Allison A. Naumann, combined DNA sequencing with RNA sequencing to measure both bacterial presence and metabolic activity. - The study was made available online in the International Journal of Oral Science on February 24, 2026. - The paper is titled "DNA and RNA-based amplicon sequencing of paired supragingival and dentin lesion plaque in children with severe early childhood caries." - The DOI is 10.1038/s41368-025-00421-4.

The details: - The cross-sectional study included 13 children ages 1 to 5 diagnosed with severe early childhood caries. - Researchers collected matched supragingival plaque and deep dentin plaque from the same teeth. - Deep dentin samples were obtained immediately after tooth extraction. - DNA-based 16S rRNA gene sequencing identified bacteria present in the samples. - RNA-based 16S rRNA transcript sequencing identified bacteria that were metabolically active. - Sequencing results were analyzed with established bioinformatics pipelines and the expanded Human Oral Microbiome Database. - Deep dentin plaque had lower bacterial diversity than supragingival plaque. - Deep dentin plaque was enriched for caries-associated taxa. - Lactobacillus casei, Oribacterium sp. HMT-078, Atopobium parvulum, and Prevotella denticola were consistently enriched in deep dentin lesions. - RNA-to-DNA ratios showed Lactobacillus species, especially L. casei, had the highest metabolic activity. - Streptococcus mutans was abundant, but its metabolic activity was lower than Lactobacillus species in the lesions.

Between the lines: - The results point to a shift in oral microbiome research from "who is there" to "who is active." - That matters because metabolically active bacteria are more likely to be causing ongoing demineralization and tissue destruction. - The findings also suggest some well-known cariogenic bacteria may be overemphasized if researchers rely on DNA alone. - The study supports a broader view of severe early childhood caries as a disease driven by a subset of acid-tolerant organisms in the low-oxygen dentin environment.

What's next: - The approach could help researchers identify lesions more likely to progress. - Future studies may use RNA-based methods to find new therapeutic targets in severe childhood tooth decay. - The work may also guide more precise microbiome studies and better oral health diagnostics. - The University of Washington website is here.

The bottom line: - In severe early childhood caries, the most dangerous bacteria may be the ones still metabolically active inside the tooth, not just the ones easiest to detect.