How the Vaginal Microbiome Differs from the Gut

By Monazza Ahmad, B.Pharm, MSc

A healthy genital tract makes some of the most important phases in a woman’s life more enjoyable and easier to manage. Menstruation, intimacy, giving birth, and embracing menopause are all significant milestones. But you may not realize that good vaginal health plays a fundamental role in reaching these milestones with minimum hurdles.

Importance of gut health is well-researched and well-understood for our overall health, concluding that the gut is vital to the health of most organs in our body. Gut health is defined by the microbiome that resides in it and influences the absorption and digestion of everything we consume. These microorganisms constantly and selectively translocate to different parts of the body, creating a unique microecosystem in each organ.1

Curious how the vaginal microbiome differentiates from the gut microbiome? To understand this concept better, we will briefly explore the diversity of the microbiome in the human body.

Diversity of human microbiome

Microbiome diversity in our body depends on factors like diet, environment, genetics, and early exposure to microbiota, meaning at birth. Just like skin and scalp, the female genital tract is also represented by its own community of microorganisms. The vaginal microbiota is evolved through a continuous translocation of species from gut to vagina or from a mother to child at birth.1

Driven by hormonal changes, the complex vaginal microbiome is continuously transformed throughout various cycles of the female lifetime—from birth to puberty, menstruation, pregnancy, menopause, and postmenopause.1

Difference between gut and vaginal microbiome

Simply put, gut microbiota is more diverse while vaginal microbiota is more selective in healthy bacterial strains. This means using the same interventions to protect vaginal flora as that for the gut may not always be optimal. Recognizing the difference between the native microbiome of gut and vagina helps us find the right and safe solutions to help avoid undesirable genital conditions.1

It is important to understand that the physiological and biochemical characteristics of microorganisms remain the same in the gut and vagina; however, their immune responses vary considerably between the two environments.1 In other words, the way each environment detects a substance as harmful or safe is different.1

For example, where the by-products of bacterial fermentation (such as short-chain fatty acids) have shown to prevent damage to the gastrointestinal tract, they have shown unfavorable effects in the genital tract, leading to negative outcomes in the reproductive and gynecological system.1

When the undesirable bacteria from the gut invade the vaginal or urethral area, they create an imbalance that may lead to various female concerns.

What is the gut-vagina axis?

Modern research has revealed a collection of intricate pathways, namely gut-vagina axis, which connects the vaginal tract to our gut.

Despite the difference between intestinal flora and the vaginal flora, the former is found to be involved in the development of some vaginal imbalances. For example, bacteria from the gut pass to the rectum, from where they can travel to the vagina due to the close proximity, resulting in unfavorable conditions. Therefore, it is important to keep the communication smooth between the gut and vagina.2

Effects of vaginal microbial imbalance

Vaginal microbial imbalances may result in several unfavorable conditions.

  1. The vaginal tract is dominated by specific species of bacteria. Loss of these particular bacteria can lead to imbalances that may cause vaginal discomfort.3
  2. A woman’s reproductive health also depends on feminine microbial balance. The depletion of beneficial bacteria can cause microbial imbalance that can extend to fallopian tubes affecting reproductive outcomes.4
  3. Vaginal microbiome disruptions may also affect sexual health and female organ health.5,6

It is evident that there could be some serious consequences associated with poor vaginal health. Taking care of feminine health should be the top priority for every woman and shouldn’t be overlooked.

Factors affecting the vaginal microbiome

The intricate and dynamic female genital tract requires special attention to care. Here are some of the factors that can create imbalance in the vaginal microbiome.

  1. Menstrual cycle and hormones: Fluctuations in reproductive hormones, especially estrogen, throughout the menstrual cycle influence the composition of vaginal organisms.4 Clinical evidence shows that elevated estrogen levels are linked to increased chances of vaginal microbial disruption.7 Estrogen is involved in a process important for healthy microbial colonization and maintaining low vaginal pH. Any alteration in this process can affect vaginal health.8 Therefore, women with higher estrogen levels, such as women in reproductive years, those taking high doses of birth control pills, or those undergoing hormone therapies, are more prone to vaginal microbial imbalances.9
  1. Contraceptives: Some birth control methods have shown to alter the healthy vaginal microbiome. Hence, it is advised to use contraceptive methods under the care of a physician.10
  1. Menopause and aging: As much as we wouldn’t like to admit it, aging impacts vaginal health negatively. Vaginal aging is associated with low levels of estrogen that can cause changes in the microbiome. In postmenopausal women, the decrease in vaginal flora results in lesser microbiome diversity and higher pH levels.4,11
  1. Lifestyle: Personal hygiene practices seem to affect the vaginal microbiome composition, such as the type of cleansing agents, undergarments, and body sprays used. Types of intimate activities and absence of protection have all been associated with the reduction of healthy vaginal bacteria.6 Stress is another lifestyle factor that may result in microbial disruption by increasing cortisol levels that ultimately cause estrogen changes, leading to higher pH levels.4
  1. Diet: Poor eating habits are associated with almost all chronic conditions. Highly processed food rich in dietary fat and carbohydrates negatively impact the vaginal environment, whereas dietary fiber intake seems to support vaginal health. Micronutrients such as vitamins A, C, E, beta carotene, calcium, and folate also play an important role in improved vaginal health.12,13

Overall, eating a well-balanced diet that contains phytonutrients and healthy proteins can support vaginal microbial health. Using proper hygiene products, practicing safe intimacy, managing stress and taking a high-quality probiotic can help women can enjoy each phase of their lives with optimal health.


1. Amabebe E et al. Front Immunol. 2020;11:2184.
2. Brannon JR et al. Nat Commun. 2020;11:2803.
3. Han Y et al. Front Micriobiol. 2021;12:643422.
4. Lehtoranta L et al. Front Micriobiol. 2022;13:819958.
5. Gholiof M et al. Front Reprod Health. 2022;4:963752.
6. Lewis FMT et al. Obstet Gynecol. 2017;129(4):643–654.
7. Cheng G et al. Eukaryot Cell. 2006;5(1):180–191.
8. Mirmonsef P et al. PLoS One. 2014;9(7):e102467.
9. Mayo Clinic. Accessed December 5, 2022.
10. Gupta K et al. J Infect Dis. 2000;181(2):595-601.
11. Szymański JK et al. Int J Environ Res Public Health. 2021;18(9):4935.
12. Neggers YH et al. J Nutr. 2007;137(9):2128-2133.
13. Tohill BC et al. Am J Clin Nutr. 2007;85(5):1327-1334.

Monazza Ahmad, B.Pharm, MSc
Monazza Ahmad obtained her Bachelor of Pharmacy from University of Karachi, Pakistan, and MSc in Health Communication from Boston University. She has experience working at community pharmacies, nonprofit health organizations, and nutrition companies dealing with both patients and practitioners. These experiences developed her interest in improving public health literacy for which she initiated a Community Health Education program at a local community center in Southern California. She is currently working in internal sales at Metagenics providing product consultation to practitioners. She is also pursuing Integrative Nutrition Health Coach certification from the Institute of Integrative Nutrition.

She loves cooking and is always looking for healthy recipes. She also enjoys singing, hiking, reading a good book, and traveling with her husband and kids.

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