Introduction Several studies have shown an increase in bacterial diversity in HPV-positive cervical cancer patients and the association of specific bacteria with cervical intraepithelial lesions. However, little is known about the cervical microbiome of HIV/HPV coinfected patients. HIV patients have a high prevalence of high-risk HPV and a greater chance of developing persistent HPV infection. The aim of this study is to evaluate the bacterial profiles of the cervical region of HIV/HPV coinfected patients, looking for a putative association of such profiles with cervical intraepithelial lesions.

Methods We analysed 89 HIV⁺ cervical smear samples of women collected from 2010 to 2013. Samples have been categorised according to collection timepoint, CD4⁺ T-cell counts and cervical intraepithelial lesions (CIN). The bacterial 16S rRNA gene was PCR-amplified and processed for next-generation sequencing in an Illumina HiSeq 2500 platform. After sequencing, reads were processed and compared against the 16S database. All bioinformatics analyses were carried out using QIIME.

Results The most abundant bacterial species found was Lactobacillus iners. We found a negative association of the Moryella genus with CIN, independent of the collection timepoint. On the other hand, we observed increased abundance of Gardnerella vaginalis, Shuttleworthia, Veillonellaceae and Aerococcus in CIN, but adjusted p-values were non-significant after false discovery rate and/or Bonferroni corrections.

Conclusion This is first study reporting the Moryella genus in HIV/HPV coinfected women and its potential absence in CIN. The presence of other bacteria in CIN or in normal cervical tissues lacked significance likely due to sample size, and additional investigation is required.