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Background  Microbial flora in several organs of HIV-infected individuals have been characterized; however, the palatine tonsil bacteriome and mycobiome and their relationship with each other remain unclear. Determining the palatine tonsil microbiome may provide a better understanding of the pathogenesis of oral and systemic complications in HIV-infected individuals. We conducted a cross-sectional study to characterize the palatine tonsil microbiome in HIV-infected individuals.    Results  Palatine tonsillar swabs were collected from 46 HIV-infected and 20 HIV-uninfected individuals. The bacteriome and mycobiome were analyzed by amplicon sequencing using Illumina MiSeq. The palatine tonsil bacteriome of the HIV-infected individuals differed from that of HIV-uninfected individuals in terms of the decreased relative abundances of the commensal genera  Neisseria  and  Haemophilus . At the species level, the relative abundances and presence of  Capnocytophaga ochracea ,  Neisseria cinerea , and  Selenomonas noxia  were higher in the HIV-infected group than those in the HIV-uninfected group. In contrast, fungal diversity and composition did not differ significantly between the two groups. Microbial intercorrelation analysis revealed that  Candida  and  Neisseria  were negatively correlated with each other in the HIV-infected group. HIV immune status did not influence the palatine tonsil microbiome in the HIV-infected individuals.    Conclusions  HIV-infected individuals exhibit dysbiotic changes in their palatine tonsil bacteriome, independent of immunological status.    Electronic supplementary material  The online version of this article (10.1186/s12866-018-1274-9) contains supplementary material, which is available to authorized users.

The palatine tonsil bacteriome, but not the mycobiome, is altered in HIV infection