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Probiotics and Prebiotics

How Different Birth Control Options Affect The Microbiome

Published on 04/15/2022
Probiotics and PrebioticsMicrobiomeMind and BodyWomen's Health
Birth Control Options

Key Points (Why You Should Care)

  • Imbalances of the vaginal microbiome can lead to decreased innate defenses and increase the risk of vaginal infections
  • Birth control may be the reason for recurrent vaginal infections
  • Oral contraceptives, injections, intrauterine devices and rings can all affect the vaginal microbiome

The Vaginal Microbiome

Just like the gut, the vagina is full of good bacteria referred to as the vaginal microbiome. The vaginal microbiome is comprised of a diverse community of microbes that plays a synergistic role in maintaining vaginal health.

A healthy vaginal microbiome should have an abundance of lactic-acid-producing bacteria from the genus Lactobacillus. Lactic acid is produced as a fermentation product that lowers the vaginal pH to an acidic environment at a pH of 3.5-4.5.[1] This acidic environment is an innate defense mechanism that helps prevent ascending urinary infections, yeast infections, sexually transmitted infections, and bacterial overgrowth.[1,2]

One of the most common vaginal dysbiosis in women is bacterial vaginosis (BV). Bacterial vaginosis occurs when the proportion of beneficial Lactobacillus in the vagina decreases allowing other bacteria to grow and thrive, such as Gardnerella vaginalis and Atopobium vaginae.[3]

The effects of contraceptives on the vaginal microbiome can significantly impact women who suffer from infections associated with imbalances and disruptions in the vaginal flora, particularly bacterial vaginosis.

Combined Oral Contraceptives (COCs)

Also known as “the pill,” combined oral contraceptives (COCs) are the most commonly prescribed form of contraception in the United States, with approximately 25% of women ages 15-44 using this method.[4]

The pill is composed of both estrogen and progesterone taken daily to help prevent unwanted pregnancy.[4] The progesterone is responsible for preventing the pregnancy by preventing ovulation. No ovulation means that an egg will not be released to be fertilized by sperm. Progesterone also thickens the cervical mucus, making entry into the uterus difficult for the sperm. Estrogen is responsible for regulating and controlling the monthly menstrual bleeding.[4]

How do COCs affect the vaginal microbiome?

Not only is this form of birth control 91% effective in preventing pregnancy, but research also shows that it can actually improve the vaginal microflora. In fact, several studies have demonstrated that the use of COCs increase the abundance of healthy vaginal flora (Lactobacillus crispatus and Lactobacillus jensenii) and decrease the amount of bacterial vaginosis-associated bacteria.[5]

The increase in Lactobacillus results from the effect estrogen has on glycogen accumulation in vaginal epithelial cells. Increased glycogen in genital fluid is associated with a Lactobacillus-dominant vaginal flora.[6] This data suggests that glycogen is important for maintaining vaginal health since an increase in Lactobacillus promotes the natural defenses of the vagina, which reduces flora imbalances that promote infection.

Based on this research, women who have recurrent bacterial vaginosis infections may benefit from switching their birth control to combined oral contraceptives which improves their vaginal microbiome and reduces the risk of vaginal infections.

Progestin-Only Oral Contraceptive Pill (POP)

The progestin-only pill (POP) is another type of oral contraceptive taken daily. Instead of containing both estrogen and progesterone like combined oral contraceptives, it only contains progestin, as its name implies. POP is often referred to as the “mini pill” since it does not contain estrogen.

As with all the other forms of birth control containing progesterone, progestin prevents pregnancy by inhibiting ovulation (the release of an egg), and also thickens the cervical mucus so that the sperm cannot enter the cervix and into the uterus.

This formulation is beneficial to women who may be unable to tolerate estrogen due to an underlying medical condition, a sensitivity, or unwanted side effects.

How does it affect the vaginal microbiome?

Studies have shown that women on the progestin-only pill have an increased likelihood of developing atrophic vaginitis (vaginal thinning, dryness, itching), which naturally occurs in postmenopausal women due to the decline of estrogen.[7] This side effect can negatively impact sexual function and a woman’s quality of life.

The same study also demonstrated that women on the mini pill have a lower rate of Candida infections when compared to women using an intrauterine device (IUD).[7] This study concluded that if women have a history of recurrent vulvovaginal candidiasis (RVVC) infections, the progestin-only pill may be beneficial in reducing the recurrence of these infections.[7]

Progesterone Injection

Instead of taking a daily pill, an injection containing progesterone is another common option for birth control. Depo medroxyprogesterone acetate (DMPA) is an injectable progestin given as an intramuscular or subcutaneous injection every 3 months. It maintains a contraceptive concentration of progestin for at least 14 weeks, providing a safety net if the injection is not repeated precisely at 12 weeks.[8]

DMPA prevents pregnancy by thickening the cervical mucus so that the sperm cannot center the cervix and into the uterus, decidualization of the endometrium, and maintains an adequate amount of circulation progestin to lock luteinizing hormone surge, and thus, ovulation.[8]

The injections may be beneficial to women who frequently forgot to take the pill or are sensitive to estrogen.

How does it affect the vaginal microbiome?

Similar to combined oral contraceptives, progestin injectable contraceptives have been shown to decrease bacterial vaginosis associated taxa, however, they do not possess the same increased abundance of protective natural vaginal flora (H2O2-producing lactobacilli) as seen in combined oral contraceptive users.[5]

In short, research indicates that the progesterone injection does not increase the abundance of BV-associated microorganisms leading to bacterial vaginosis. However, it was associated with higher levels of some BV-associated species, including Atopobium vaginae and Prevotella bivia.[5]

Similarly, a study on South African women compared the association between injectable progestin contraception and risk of infection with Neiserria gonorrhoeaChlamydia trachomatis, bacterial vaginosis, and Trichomonas vaginalis. They concluded that injectable progestin contraception can alter the vaginal microbiome in the following ways:

  • Slight, but not significant, increase in the risk of cervical infection with Chlamydia and gonorrhea[9]
  • Appears to be protective against Trichomonas vaginalis[9]
  • Decreased risk of bacterial vaginosis[9]

However, this evidence is not enough to definitively conclude that injectable progestin contraception will cause sexually transmitted diseases. Sex without a condom while opting to use injectable progestin contraception may put patients at an increased risk of sexually transmitted diseases.

Hormone Free Intrauterine Device

An intrauterine device, sometimes simply referred to as an IUD, is a small device shaped like a “T” that is anchored to the myometrium at the uterine fundus to prevent pregnancy. There are two forms of IUDs: hormonal and non-hormonal. In this section, we will refer to non-hormonal IUDs, more commonly known as the “copper IUD.”

Copper IUDs effectively prevent pregnancy because copper is toxic to sperm. Copper will effectively interfere with sperm movement, egg fertilization, and possibly prevent implantation.[10] This explains why it can also be used for emergency contraception if inserted within 120 hours of unprotected intercourse.[10]

Aside from sterilization, this is the longest lasting form of intrauterine devices. The copper IUD (ParaGard) can prevent pregnancy for up to 10 years. However, if a woman chooses to get pregnant, the IUD can be removed and fertility is not affected.

How does it affect the vaginal microbiome?

According to a few studies, women with the copper intrauterine devices have an increased risk of developing bacterial vaginosis. One study noted the prevalence of BV-associated bacteria increased over 6 months after the initiation of the copper IUD from 27% at baseline, 35% at 30 days, 40% at 90 days, and 49% at 180 days.[11] This was contrasted with women utilizing a hormonal birth control method which had no notable change in BV associated bacteria over 180 days.[11]

The link between the copper IUD and an increased risk of BV is likely attributed to the heavier and longer menstrual flow associated with copper IUD users. An increased flow can deplete the vagina’s natural defenses, Lactobacillus, which permits the overgrowth of Gardnerella and other BV associated taxa.

In addition to heavier flows affecting the microbiome, intrauterine devices are also known to foster growth of bacterial biofilms, causing recurrent infection and antibiotic resistance in IUD users.[12] Moreover, the tail of the IUD that extends below the cervix and into the vagina has also been shown to transfer yeast cells from the vagina (external environment) into the uterus (internal environment).[13] These additional factors may also contribute to recurrent vaginal infection observed in copper IUD users.

Women with recurrent BV may prefer to opt for a hormonal method rather than a copper IUD for contraception to minimize recurrence risk.

Hormonal Intrauterine Device

Hormonal IUDs prevent pregnancy by releasing a small amount of progestin called levonorgestrel every day. This type of IUD is also referred to as the levonorgestrel-releasing intrauterine-system (LNG-IUS). Compared to women who use other forms of progesterone containing birth control, the progesterone released from the IUD acts locally within the uterus resulting in less hormones within the blood steam.

Similar to the copper IUD, the hormonal IUD is also reversible, and is a long acting contraceptive that can be worn for several years before it needs to be replaced. However, it cannot be used as an emergency contraceptive option like the copper IUD.

How does it affect the vaginal microbiome?

Studies investigating the influence of the levonorgestrel-releasing intrauterine-system (LNG-IUS) on the vaginal microflora were ultimately contradicting.

One study comparing the vaginal flora of hormonal IUD users to combined oral contraceptives, found that women using the hormonal IUD had significantly greater BV-associated bacteria than that of combined oral contraceptives users. Analysis specifically detected Gardnerella vaginalis and Sneathia amnii in hormonal IUD users.[5]

Similarly, another study found that over the course of 6 months after insertion of the IUD, the vaginal flora was observed to have an increase of Gardnerella vaginalis and Atopobium vaginae between baseline and 30, 90, and 180 days after initiation.[11] There was no change in vaginal lactobacillus concentration during that time period.[11]

Contradicting the other research, a study of 406 vaginal, cervical, and uterine samples obtained at nine time intervals, from 1 week before to 12 after the LNG IUS insertion on 11 women found a significant increase in vaginal Lactobacillus crispatus (48.9% of over 6 million total reads).[14] This study concluded that the LNG IUS has little negative impact on the vaginal microbiome.

Lastly, another study found a temporary decrease in lactobacillary dominance, and an increase in bacterial vaginosis and aerobic vaginitis after 3 months of LNG-IUS insertion, when compared to pre-insertion.[15] However, after 1 to 5 years with the LNG-IUS, vaginal flora returned to pre-insertion levels, but candida colonization remained twice as high in that same time period.[15] Increased candida was also noted in another study analyzing the vaginal flora of hormonal intrauterine device users.[7] Researchers concluded that LNG-IUS use may not be an ideal form of long term contraception in women who are at risk for recurrent vulvovaginal candidiasis.[15]

Contraceptive Ring

The birth control ring is a small flexible ring designed to be manually inserted into the vagina once a month. It is removed after three weeks, allowing menstruation to occur on the fourth week of the month once it has been removed (due to the lack of progesterone).

The ring prevents pregnancy by releasing localized amounts of progestin and estrogen, which prevents ovulation and thickens cervical mucus, similar to oral contraceptives and other progestin containing contraceptives.

How does it affect the vaginal microbiome?

Similar to other estrogen containing birth control, contraceptive rings also appear to increase the abundance of Lactobacillus species.

One study analyzed 120 women’s vaginal microbiome before and after NuvaRing use for 12 weeks. At baseline, bacterial vaginosis prevalence was 48%. With use of the NuvaRing, Lactobacillus species increased significantly, and consequently the BV associated bacteria (G. vaginalis and A. vaginae) substantially decreased.[16] Although BV decreased, there was an associated increase of biofilm accumulation on the ring.[16]

They concluded that overall, the NuvaRing can increase the abundance of lactobacillus and consequently decrease the amount of BV associated bacteria within the vaginal microbiome.

Why Should We Care?

If the vaginal microbiome becomes comprised of an imbalance of healthy bacteria to unhealthy bacteria it can render the vagina susceptible to infections.

In order for the vaginal microbiome to stay healthy, lactobacillus must be present. A decrease in vaginal lactobacillus can ultimately lead to an increase risk in developing infections as well as bacterial and yeast overgrowth. This can cause a multitude of complications:

  • Bacterial Vaginosis can cause preterm labor in pregnant women[17]
  • Colonization of Neisseria gonorrhoeae and Chlamydia trachomatis can lead to pelvic inflammatory disease, and even infertility if not treated[18]
  • Bacterial vaginosis and yeast vaginitis cause vaginal changes that could increase susceptibility to human immunodeficiency virus (HIV)[19]
  • Women with bacterial vaginosis are more susceptible to herpes simplex virus type 2 (HSV-2), which also significantly increases the risk of acquiring HIV[19]
  • Women with bacterial vaginosis are at a higher risk of getting the Human Papilloma Virus (HPV)[19]
Table 1. Contraceptive Effect on the Vaginal Microbiome
Type Brand Names Effect on Vaginal Microbiome

Combined Oral Contraceptive

Mircette, Aviane, Natazia, Estrostep, Levora, Levlite, Lessina, Enpresse, Aranelle, Lo/ovral-28, Ortho Tri-Cyclen, Ortho-Novum, Alesse, Levlen, Loestrin, Apri, Yaz, Yasmin, Nordette

Increased abundance of healthy vaginal flora (Lactobacillus crispatus and Lactobacillus jensenii) and decreased the quantity of BV-associated bacteria[5,19]

Progestin-Only Oral Contraceptive

(“Mini Pill”)

Micronor, Camila, Errin, Jolivette

May cause atrophic vaginitis, but also decrease Candida species contributing to recurrent yeast infections[7]

Progesterone Injection

Depo Provera

Does not directly increase the risk of bacterial vaginosis, but is associated with higher levels of some BV-associated species, including Atopobium vaginae and Prevotella bivi[5]


Associated with a slight increased risk of cervical infection with Neiserria gonorrhoeaChlamydia trachomatis, and protection against Trichomonas vaginalis[9]

Hormone Free IUD (“Copper IUD”)


Increased BV-associated microbiota, Gardnerella vaginalis, and Atopobium vaginae[11]

May foster growth of bacterial biofilms on IUD[12]

May transfer yeast cells from the vagina into the uterus via IUD tail[13]

Increased Candida colonization[7]

Progesterone IUD

Skyla, Liletta, Mirena, Kyleena

Increased BV-associated species including Gardnerella vaginalis, Sneathia amnii, and Atopobium vaginae[5,11] and a temporary increase in aerobic vaginitis flora[15]


May increase Lactobacillus crispatus[14] or temporarily decrease Lactobacillus within the first 3 months of insertion[15]

Increased Candida colonization[7,15]

Contraceptive Rings


Biofilms containing BV-associated bacteria easily form on vaginal ring within three weeks[3]

Increased Lactobacillus abundance, with an associated decrease in Gardnerella vaginalis and Atopobium vaginae[16]

Key Takeaways

  • Different forms of birth control may have different effects on the vaginal microbiome
  • Estrogen-containing contraceptives may be protective against vaginal microbiome imbalances
  • Women who experience recurrent bacterial vaginosis should talk to their healthcare provider about different birth control options

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