If the level of oestrogen declines in the vagina, bladder and pelvic floor, this in turn affects the growth of vaginal epithelial cells and the availability of glycogen (a stored form of glucose is made up of many connected glucose molecules and is called glycogen). Because glycogen is the main nutritional source for lactobacillus, the beneficial bacteria in the vagina, this results in lower production of lactic acid which keeps the vaginal PH acidic and creates a higher more alkaline vaginal PH in which lactobacilli strains cannot survive. This leads to the level of lactobacilli in the vagina dramatically decreasing alongside the production of lactic acid and hydrogen peroxide.

When the level of lactobacilli is disrupted and the vaginal flora becomes imbalanced, the risk of developing an infection is increased. If the vagina is not acidic enough, then fungi such as candida, vaginal infections such as bacterial vaginosis (BV), vaginitis and ‘bad’ bacteria such as coliforms, enterobacter, gardnerella, mycoplasma, streptococci and staphylococci are able to reproduce more than they usually would.

Low oestrogen can also affect the structure of the delicate mucous membranes, or muscles, that line many parts of the body, including the urinary tract, making infections more likely. Thinning of the vaginal and vulval mucosal lining also affects the mucosal wall of the bladder allowing bacterial permeability – in other words it becomes easier for bacteria to become established on or within the cells of the bladder and vaginal walls. Further, the walls of the vagina, urethra and bladder rely on oestrogen as one way to stay toned and able to manage the flow of urine from the bladder. With less oestrogen, these organs lose tone and some degree of function.

Too much synthetic progesterone weakens the lining of the bladder, urethra, and vagina leaving them more susceptible to injury and inflammation and can cause urogenital/vaginal/urethral atrophy because oestrogen levels cannot compensate and help to rebuild healthy tissue.

High levels of progesterone can also cause frequent urination as progesterone acts like a diuretic. The sacral nerve which controls the pelvis and its organs is full of oestrogen receptors. Research published in The International Urogynecology Journal in 1993 showed a change in hormone levels, in particular that of progesterone, may affect the excitability of the nerves and make you feel like you have to urinate more frequently. This may also be the reason for frequent urination during the second half of the menstrual cycle as progesterone levels are higher than those of oestrogen.

A study published in Science Translational Medicine in 2013 noted that oestrogen also encourages production of natural antimicrobial substances in the bladder. The hormone also makes the epithelium of the bladder wall stronger by closing the gaps between cells that line the bladder wall. They also noted that by “gluing” together the cells of the bladder wall, it helps to prevent bacteria from penetrating to the deeper layers of the wall and may help prevent too many cells from shedding from the top layers of the bladder wall thus preventing exposure of the deeper bladder wall tissues to bacteria.

The pill’s synthetic hormones can cause the development of an imbalance between the Th1 branch and Th2 branch of the immune system. Th1 cells can release inflammatory chemicals in response to viruses and some bacteria while Th2 cells kickstart the production of antibodies. If the immune system is functioning well, both types of cell work to protect the body. But when either Th1 or Th2 cells become dominant due to use of oral contraceptives, one branch of immune cells are overactive and the other branch can be underactive. This can lead to issues with recurrent infections. Women using a progesterone only contraceptive were found in a study published in Fertility and Sterility in 2001 to have more exposure to the risk of vaginal infections because progesterone can enhance a type of immune cell. Viruses can manipulate these cells to increase the infection risk but in the presence of oestrogen combined with progesterone this is decreased. Other research published in AIDS in 2014 shows that progestins decrease the activity of other immune cells. The effects being on hormonal contraceptives can also have an effect on the body’s nutrient stores. Oral contraceptives are thought to contribute to draining stores of vital minerals including Vitamin C, B vitamins and Zinc, all of which have an important role in supporting the immune system and therefore the ability to keep on top of infections.

Research shows that being on the pill can increase infections and changes in the structure of the urinary tract. Oral contraceptive users were about around twice as likely to suffer from vaginal thrush in comparison to women who did not use a hormonal contraceptive in a study published in Infection and Immunity in 2000.

One theory for this is that significant drops in oestrogen could be having a part to play. Especially when it comes to oestrogenic forms of the pill, i.e. the combined pill, the drop off in oestrogen that are experienced at the end of the month could be making urogenital tissues more prone to vaginal infections due to changes in the vaginal PH.

Read more about changes in vaginal PH and how they can increase infection risks.

Research in the American Journal of Obstetrics and Gynaecology in 2002 shows that increased oestrogen levels in the blood is associated with increased growth of Candida in the vagina, and that growth of Candida appears to be stimulated by oestrogen in a study publicised in Clinical Infectious Diseases in 2002. A study published in the American Society of Microbiology in 2006 found, if certain types of oestradiol (a specific type of oestrogen found in birth control pills) are added to candida cells, this oestrogen has been shown to increase the number of germ tube and length – developments that support candida overgrowth. After starting the birth control pill, many women complain of developing chronic thrush and bloating and flatulence due to the candida overgrowth in their gut.

Oestrogen promotes production of glycogen (glucose) within the vaginal cells, and increased glycogen acts as an ideal source of food for growing Candida. Oestrogen also acts on Candida yeasts and promotes its growth, and improves its ability to cling onto vaginal epithelial cells as shown by this study in PLOS Pathogens published in 2014.

These changes together can encourage the overgrowth of Candida, and further studies are being conducted to gain a better understanding of these mechanisms.

This explains why pregnant women, and those who are on the combined oral contraceptive pill (COCP) or hormone replacement therapy (HRT) are more at risk of developing thrush, as all these situations can be associated with potentially high oestrogen levels.

The body has inbuilt mechanisms to try to maintain homeostasis (aka the natural body balance). It also has many feedback systems and can alert someone as to when levels of chemicals in the body are getting out of balance. This protective mechanism also applies to your reproductive hormones. When taking daily doses of synthetic hormones, the body registers that it is getting unusually high levels of oestrogen and progesterone throughout a monthly cycle. As the brain perceives an upset in hormone balance, it will try to correct any excess by shutting down production of natural oestrogen and progesterone. This shut-off may be why some women complain that their menstrual cycle takes years to return to normal after they come off the contraceptive pill.

Women taking birth control pills release more of a substance called Thyroid Hormone Binding Globulin (THBG), which binds to thyroid hormones so that there is less to enable the body to function well (such as energy and immune system response). Oral contraceptives (OCs) also cause depletion of nutrients needed for healthy thyroid function and thyroid hormone production. Progesterone for example is shown to change mood, cause bloating and affect the thyroid by binding to the glucocorticoid receptor.  This is the same receptor which cortisol utilises – stimulating our flight or fight response when we are stressed. Prolonged periods of stress has been shown to lower the immune system, a key component of our ability to fight off infections such as UTIs.