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The progression of early childhood caries (ECC) is caused by microbial colonized in dental plaque. However, the association framework both from 16s genus down to high resolution metagenomic strain level and from composition to genome function analysis on caries lacks. 16S rRNA sequence revealed the composition of 3–6 years dental caries (ECC,  n  = 29), and severe dental caries (SECC,  n  = 36) children are significantly different from caries-free controls (CF,  n  = 31). Especially, genus  Neisseria  is enriched in caries ( P  < 0.05). Metagenomics sequence of 3 ECCs, 3 SECCs, and 3 CFs reveals  Neisseria bacilliformis  ATCC BAA-1200 in genus  Neisseria  is also significantly enriched in caries ( P  < 0.05). Then, we recovered high-quality metagenomic assembly genomes (MAG), named bin 86, which have 99% identity with  Neisseria bacilliformis  ATCC BAA-1200 genome. Function analysis of  Neisseria bacilliformis  ATCC BAA-1200 genome shows its metabolism power of sugar and adhesion, colonization, acid production, and acid tolerance ability, which suggested  Neisseria bacilliformis  ATCC BAA-1200 may serve as a biomarker for childhood caries.

Metagenomic Analysis Reveals Neisseria bacilliformis Variation in the Early Childhood Caries Plaque Microbiome