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Although local excisional treatment can clear hrHPV infection and restore the cervicovaginal microbiota, it is unclear which cervicovaginal microbiota represents recovery. Our objective was to describe the cervicovaginal microbiota before and after treatments and to assess the association between the microbiota and HPV persistence.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A cohort of 91 participants was classified into four groups (healthy control women and HPV16\u2010infected women with CIN I, CIN II\/III, and squamous cell carcinoma [SCC]). Endocervical swabs were collected 3\u00a0months prior to treatment and at 3\u00a0months post\u2010treatment for bacterial 16S rRNA gene pyrosequencing and for HPV DNA testing. There was an increase in the number of <jats:italic>Lactobacillus<\/jats:italic> bacterial species present after the clinical treatments, and the community state type (CST) profiles were shifted from dysbiotic CSTs II and IV to <jats:italic>Lactobacillus<\/jats:italic>\u2010dominated CSTs I and III. Specifically, the composition of <jats:italic>Geobacter<\/jats:italic> and <jats:italic>Prevotella<\/jats:italic> before treatment and <jats:italic>Lactobacillus secaliphilus<\/jats:italic> after treatment might have been related to CIN I, the composition of <jats:italic>Burkholderia<\/jats:italic> before treatment and <jats:italic>Lactobacillus iners<\/jats:italic> after treatment might have been related to CIN II\/III, and the composition of <jats:italic>Atopobium<\/jats:italic> and <jats:italic>Aerococcus<\/jats:italic> before treatment and Bacilli after treatment might have been related to SCC. Further functional predictions revealed that the composition differences were linked to infectious disease\u2010 and cancer\u2010related genes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our study provides an illustration of the changes in CSTs and the cervicovaginal microbiota before and after HPV16 clearance in each disease state.<\/jats:p><\/jats:sec>","DOI":"10.1002\/cam4.4801","type":"journal-article","created":{"date-parts":[[2022,5,15]],"date-time":"2022-05-15T13:14:55Z","timestamp":1652620495000},"page":"5037-5049","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Changes in the cervicovaginal microbiota composition of <scp>HPV16<\/scp>\u2010infected patients after clinical 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