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Background  Black extrinsic discoloration in primary dentition is a common clinical and aesthetic problem that can co-occur with dental caries, the most common oral diseases in childhood. Although the role of bacteria in the formation of pigment and caries in primary dentition is important, their basic features still remain a further mystery.    Methods  Using targeted sequencing of the V1-V3 hypervariable regions of bacterial 16S ribosomal RNA (rRNA) genes, we obtained a dataset consisting of 831,381 sequences from 111 saliva samples and 110 supragingival plaque samples from 40 patients with pigment (black extrinsic stain), 20 with caries (obvious decay), and 25 with both pigment and caries and from 26 healthy individuals. We applied a Dirichlet multinomial mixture (DMM)-based community typing approach to investigate oral microbial community types.    Results  Our results revealed significant structural segregation of microbial communities, as indicated by the identification of two plaque community types (A and B) and three saliva community types (C-E). We found that the independent occurrence of the two plaque community types, A and B, was potentially associated with our oral diseases of interest. For type A, three co-occurring bacterial genus pairs could separately play a potential role in the formation of pigment ( Leptotrichia  and  Fusobacterium ), caries (unclassified  Gemellales  and  Granulicatella ), and mixed caries and pigment ( Streptococcus  and  Mogibacterium ). For type B, three co-occurring bacterial genera (unclassified  Clostridiaceae, Peptostreptococcus , and  Clostridium ) were related to mixed pigment and caries. Three dominant bacterial genera ( Selenomonas, Gemella,  and  Streptobacillus ) were linked to the presence of caries.    Conclusions  Our study demonstrates that plaque-associated oral microbial communities could majorly contribute to the formation of pigment and caries in primary dentition and suggests potential clinical applications of monitoring oral microbiota as an indicator for disease diagnosis and prognosis.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2891-z) contains supplementary material, which is available to authorized users.

Oral microbial community typing of caries and pigment in primary dentition