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Background  Local treatment for cervical intraepithelial neoplasia (CIN) by Loop Electrosurgical Excision Procedure (LEEP) has been correlated with reproductive morbidity, while the cervicovaginal microbiota is also known to affect the risk of preterm delivery. CIN and treatment by LEEP might change the cervical microbiota. The main aim of this study was to describe the cervical microbiota before and after LEEP and assess its associaton with cone depth and HPV persistence. Further, we aimed to compare the microbiota to references with normal cervical cytology.    Methods  Between 2005 and 2007, we prospectively identified 89 women planned for LEEP in a Norwegian hospital and recruited 100 references with a normal cervical cytology. Endocervical swabs were collected prior to treatment and at six ( n  = 77) and 12 months ( n  = 72) post LEEP for bacterial culture and PCR, and post LEEP for DNA testing for human papillomavirus (HPV). We compared the cervical microbiota composition before and after treatment and between women planned for LEEP vs references.    Results  There was a reduction in the number of non- Lactobacillus  bacterial species six and 12 months after LEEP compared to before treatment and a tendency towards a concomitant increase in  Lactobacillus . No association between the detection of cervical bacteria, HPV persistence or cone depth was found.  Women planned for LEEP carried significantly more  Bacteroides  spp.,  Gardnerella vaginalis, Mycoplasma hominis  and  Ureaplasma parvum  as well as a greater number of bacterial species than the references.    Conclusions  Local excisional treatment appears to alter the cervical microbiota towards a less diverse microbiota. Women with CIN have a more diverse cervical microbiota compared to women with normal cervical cytology.    Electronic supplementary material  The online version of this article (10.1186/s12905-019-0727-0) contains supplementary material, which is available to authorized users.

Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study