| Summary: | Bacterial vaginosis (BV) is characterized by a reduction in <i>Lactobacillus (L.)</i> spp. abundance and increased abundance of facultative anaerobes, such as <i>Gardnerella</i> spp. BV aetiology is not fully understood; however, bacteriophages could play a pivotal role in the perturbation of the vaginal bacterial community. We investigated the vaginal viral community, including bacteriophages and the association to the bacterial community and BV-status. Vaginal samples from 48 patients undergoing IVF treatment for non-female factor infertility were subjected to metagenomic sequencing of purified virus-like particles. The vaginal viral community was characterized and correlated with the BV-status by Nugent score, bacterial community, structure, and the presence of key vaginal bacterial species. The majority of identified vaginal viruses belonged to the class of double-stranded DNA bacteriophages, with eukaryotic viruses constituting 4% of the total reads. Clear links between the viral community composition and BV (<i>q</i> = 0.006, <i>R</i> = 0.26) as well as the presence of <i>L. crispatus</i> (<i>q</i> = 0.001, <i>R</i> = 0.43), <i>L. iners</i>, <i>Gardnerella</i> spp., and <i>Atopobium vaginae</i> were found (<i>q</i> < 0.002, <i>R</i> > 0.15). The eukaryotic viral community also correlated with BV-status (<i>q</i> = 0.018, <i>R</i> = 0.20). In conclusion, the vaginal virome was clearly linked with bacterial community structure and BV-status.
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