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In this study, vaginal microbiota composition was determined in twenty-one women with BV, before and after treatment with metronidazole or clindamycin. Microbiota composition varied greatly between women and defining a (un)healthy vaginal microbiota state remains elusive, challenging BV diagnosis and treatment. While relative abundance of <jats:italic>Lactobacillus<\/jats:italic> increased after antibiotic treatment in two-third of women, its abundance was not associated with treatment outcome. 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These companies had no role in the research described in this manuscript. All other authors declare that they have no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"The study was approved by the local medical ethics board (METC Zuidwest Holland, The Hague, The Netherlands).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}},{"value":"Written informed consent was obtained from all participating subjects.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent to participate"}},{"value":"Written informed consent was obtained from all participating subjects.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"Raw sequencing data was analysed using free, open source software NG-Tax () and R ().","order":6,"name":"Ethics","group":{"name":"EthicsHeading","label":"Code availability"}}]}}