The Difference Between Gut and Vaginal Microbiomes

Conversations surrounding the microbiome and how it impacts our health have gained significant attention. But what exactly does it mean when we talk about the human “microbiome”? The microbiome is a community of microorganisms, such as bacteria, viruses, and fungi that reside in our skin, gut, and vaginal tract.1 The microbiome aids in digestion, supports vaginal health, improves cognition, and promotes general wellbeing.1

Not all microbiomes in our body’s system are exactly the same. The gut and vaginal microbiomes differ, and understanding this difference helps us find the right solutions to avoid unwanted women’s health issues.2 The gut microbiome is more diverse, while the vaginal microbiome is more selective in bacteria strains that keep the vagina balanced and healthy. In other words, what may be good for the gut may be harmful to the vagina.2

Bacteria that help keep our gut healthy, or any bacteria that are harmful in general, can cause problems if they find their way to the vagina.3 This can occur when certain bacteria travel through the gut-vagina axis— a collection of intricate pathways connecting the vaginal tract to our gut.3  This can upset the balance in the vaginal and/or urinary tract and lead to women's health problems.3

Effects of imbalance within the vaginal microbiome

Any imbalance in the vaginal microbiome can impact a woman’s gynecological health, including:

  • Overall vaginal health and wellbeing: The vagina is home to specific types of bacteria. When these bacteria are lost, it can upset the balance and lead to physical discomfort.4
  • Fertility: A decline in beneficial bacteria that leads to imbalance may affect fertility and reproduction.5
  • Sexual health: Vaginal imbalance may also affect intimacy and sexual health. Sexual activity may be uncomfortable.6,7

Factors affecting the vaginal microbiome

Throughout a woman’s lifecycle, different factors can upset the balance of bacteria in the vagina, including:

  • Menstrual cycle and hormones: Estrogen helps maintain a healthy environment in the vagina, including keeping a low pH level, which is important for vaginal health. If you have high estrogen levels, you're more likely to experience an imbalance.8 This can happen to women who are in their reproductive years, those who take strong birth control pills, or those receiving hormone therapies.9
  • Contraceptives: Some birth control methods have shown to alter the healthy vaginal microbiome. It’s a good idea to discuss contraceptive methods that are right for you with your physician.10
  • Menopause and aging: When estrogen levels drop during menopause, it can impact the vaginal microbiome by decreasing vaginal flora, leading to imbalance.5,11
  • Lifestyle: Everything from the soap you use, choice of undergarments, and the choice to practice safe sex can impact your vaginal health.7 Also, the stress in our daily lives can affect our body's balance as well. Stress can increase levels of a hormone called cortisol, which in turn can affect our estrogen levels.5,7
  • Diet: Eating processed foods loaded with fats and carbs can compromise your vaginal health. It’s important to eat a balanced diet with plenty of fiber, vitamins, and minerals.12,13 And don't forget about the potential benefits of high-quality probiotics!

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1. Ogunrinola GA et al. Int J Microbial. 2020; 2020:8045646.
2. Amabebe E et al. Front Immunol. 2020;11:2184.
3. Brannon JR et al. Nat Commun. 2020;11:2803.
4. Han Y et al. Front Micriobiol. 2021;12:643422.
5. Lehtoranta L et al. Front Micriobiol. 2022;13:819958.
6. Gholiof M et al. Front Reprod Health. 2022;4:963752.
7. Lewis FMT et al. Obstet Gynecol. 2017;129(4):643–654.
8. Cheng G et al. Eukaryot Cell. 2006;5(1):180–191.
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.

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