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The interplay between vaginal microbiome and human papillomavirus (HPV) remains unclear, partly due to heterogeneity of the microbiota. We used data from 546 women enrolled in a cross-sectional study conducted in five Brazilian regions. We genotyped vaginal samples for HPV and sequenced V3-V4 region of 16S rRNA gene for vaginal microbiome analysis. We used stepwise logistic regression to construct two linear scores to predict high-risk HPV (hrHPV) positivity one based exclusively on presence of individual bacterial taxa (microbiome-base