The oral microbiome in human immunodeficiency virus (HIV)-positive individuals.

Human immunodeficiency virus (HIV) infection is associated with a range of oral conditions, and increased numbers of disease-associated microbial species have previously been found in HIV-positive subjects. The aim of this study was to use next-generation sequencing to compare the composition of the oral microbiome in HIV-positive and -negative individuals. Plaque and saliva were collected from 37 HIV-positive individuals and 37 HIV-negative individuals, and their bacterial composition determined by pyrosequencing of partial 16S rRNA genes. A total of 855,222 sequences were analysed. The number of species-level operational taxonomic units (OTUs) detected was significantly lower in the saliva of HIV-positive individuals (mean = 303.3) than in that of HIV-negative individuals (mean = 365.5) (P < 0.0003). Principal coordinates analysis (PCoA) based on community membership (Jaccard index) and structure (Yue and Clayton measure of dissimilarity) showed significant separation of plaque and saliva samples [analysis of molecular variance (AMOVA), P < 0.001]. PCoA plots did not show any clear separation based on HIV status. However, AMOVA indicated that there was a significant difference in the community membership of saliva between HIV-positive and -negative groups (P = 0.001). Linear discriminant analysis effect size revealed an OTU identified as Haemophilus parainfluenzae to be significantly associated with HIV-positive individuals, whilst Streptococcus mitis/HOT473 was most significantly associated with HIV-negative individuals. In conclusion, this study has confirmed that the microbial composition of saliva and plaque is different. The oral microbiomes of HIV-positive and -negative individuals were found to be similar overall, although there were minor but significant differences in the composition of the salivary microbiota of the two groups.