Oral Contraceptives & the Microbiome

IFM’s Advanced Practice Modules (APM) offer insight into a range of clinical conundrums and provide useful clinical pearls on approaching care through the functional medicine lens. Below is a question that is frequently asked by attendees during the program.

How do oral contraceptives affect the microbiome?
Oral contraceptive pills (OCPs) affect both the vaginal and gut microbiome. OCPs decrease the risk for bacterial vaginosis but can increase the prevalence of vaginal candida infections. Vaginal cultures have shown an increase in Lactobacillus fermentum, Candida spp, and E. coli in women (31-40 yo) using OCPs.1 This most likely occurs because estrogen affects the glycogen accumulation in vaginal epithelial cells, increasing lactobacilli.2 In terms of the gut microbiome, OCPs have been found to decrease microbial metabolites, TMAO and its precursors, in patients with PCOS.3

OCPs may also increase the risk for IBD, although conflicting evidence exists. A 2017 review found that there was a 24% higher risk for developing Crohn’s disease and a 30% higher risk for developing ulcerative colitis in patients using OCPs.4 A more recent case control study found no association between OCP use and IBD.5

Clinical takeaway: Oral contraceptives disrupt both the vaginal and gastrointestinal microbiome. The consequences are not completely clear.

At the upcoming Hormone Advanced Practice Module, expert educators will provide insightful discussion on approaching care from a variety of clinical angles. Explore novel diagnostic and therapeutic opportunities for supporting hormone production and function.



  1. Kazi YF, Saleem S, Kazi N. Investigation of vaginal microbiota in sexually active women using hormonal contraceptives in Pakistan. BMC Urol. 2012;12:22. doi:1186/1471-2490-12-22
  2. Brooks JP, Edwards DJ, Blithe DL, et al. Effects of combined oral contraceptives, depot medroxyprogesterone acetate and the levonorgestrel-releasing intrauterine system on the vaginal microbiome. Contraception. 2017;95(4):405-413. doi:1016/j.contraception.2016.11.006
  3. Eyupoglu ND, Caliskan Guzelce E, Acikgoz A, et al. Circulating gut microbiota metabolite trimethylamine N-oxide and oral contraceptive use in polycystic ovary syndrome. Clin Endocrinol (Oxf). 2019;91(6):810-815. doi:1111/cen.14101
  4. Ortizo R, Lee SY, Nguyen ET, Jamal MM, Bechtold MM, Nguyen DL. Exposure to oral contraceptives increases the risk for development of inflammatory bowel disease: a meta-analysis of case-controlled and cohort studies. Eur J Gastroenterol Hepatol. 2017;29(9):1064-1070. doi:1097/MEG.0000000000000915
  5. Sanagapalli S, Ko Y, Kariyawasam V, et al. The association between new generation oral contraceptive pill and the development of inflammatory bowel diseases. Intest Res. 2018;16(3):409-415. doi:5217/ir.2018.16.3.409