A microbiome analysis of equine peripheral dental caries using next generation sequencing

Background: Although, peripheral caries (PC) affects almost half of UK horses, no comprehensive microbiological study has been performed on this disorder. As a high proportion of oral bacteria cannot be conventionally cultured, molecular microbiological techniques such as Next Generation Sequencing are required to examine the complex oral bacteria community. Objectives: To identify the microbiota involved in equine PC, including comparing microbiota at the more commonly and severely affected three caudal cheek teeth with the less commonly affected three rostral cheek teeth. Study design and Methods: Equine dental plaque samples were collected from the palatal aspects of cheek teeth of 63 horses. DNA was isolated and amplified using PCR, targeting the V4 region of the 16S rRNA gene and Next Generation Sequencing of these gene amplicons was performed. The acquired data were processed and analysed using Mothur and R. Results: Streptococcus species was the genus most commonly associated with equine PC, whereas Gemella species was the genus most associated with the control group. In a further analysis where the rostral and caudal cheek teeth were compared with each other and with the control group. Veillonella species was the most commonly associated genus with PC of the rostral cheek teeth, Streptococcus species was the most associated genus with the caudal cheek teeth, and Corynebacterium with the control group. Main limitations: Some bacteria can have multiple heterogeneous copies of the 16S rRNA gene, which can affect the estimation of their relative abundance. Conclusions: Similar to caries studies in other species, acidogenic and aciduric microorganisms including Streptococcus species were found to be associated with equine peripheral caries.