Gut Health and Your Menstrual Cycle: What Women Need to Know

Dr. Jolene BrightenPublished: Last Reviewed: Digestion, Leaky Gut, Menstrual Cycle Leave a Comment

Your microbiome is the community of bacteria, fungi, and viruses that live in your body, mostly in your large intestine and skin. These guests (and their genes) play a huge role all throughout the body, including digestion, immunity, and even your mood. Your gut microbiome takes cues from your hormones and can even influence your menstrual cycles.

What Does Your Gut Health Have to Do With Your Menstrual Cycle?

Like any community, one of the most important factors in gut health is diversity. Without a diverse cast of friendly bacteria, it’s easy for the bad bugs to overpower the good bugs. This kind of imbalance is called dysbiosis, and can throw a wrench in your mood, metabolism, immunity, and yes, menstruation.

But how are your hormones and your gut really connected? After all, those are two completely separate systems in the body, right? 

As a naturopathic physician, I’m here to tell you that everything in your body is connected. Your hormone health influences every system in your body, and as growing research shows, your microbiome just might too. Your hormones and your gut each affect the other, and taking care of these systems can be key to optimal health.

I can’t stress this enough, a happy gut and balanced hormones are pillars for your overall health.

Estrogen and your gut

Certain bacteria in your gut community are tasked with managing estrogen metabolism. This community within your microbiome is called the estrobolome

Estrogen is produced mainly in your ovaries and circulated all throughout your body where it acts on other tissues and organs. Eventually, that active estrogen gets filtered through the liver, which deactivates it, then sends it off to your gut. With a balanced estrobolome, most of that deactivated estrogen gets excreted with your stool, leaving the body.

But what if your gut doesn’t do its job? Certain gut bacteria can actually reactivate inactive estrogen in your gut, by producing an enzyme called beta-glucuronidase. If too many of these bacteria are present in your gut, active estrogen is getting sent back into circulation at way higher levels than your body intended. This means trouble, because now the system designed to reduce estrogen is doing just the opposite. 

Is Excess Estrogen a Problem?

The state of having too much estrogen, especially relative to progesterone, is called estrogen dominance. It’s actually one of the most common issues I treat as a women’s hormone expert. 

Don’t get me wrong, estrogen is both necessary and awesome, but when it overpowers your other hormones, it spells bloating, headaches, mood swings, and more. In fact, when estrogen and progesterone levels are properly balanced, PMS is almost non-existent!

Recent research even links gut dysbiosis to the development of breast cancer through this same pathway of elevated estrogens released from the gut. 

Symptoms of estrogen dominance look different for every woman, but can include:

Concerned you may have estrogen dominance? Get the free Hormone Balancing Starter Kit and start loving your hormones today!

Can gut health impact my period?

Yes. Your gut health and microbial diversity affect how well your gut excretes or recirculates Estrogen. If your estrobolome is in dysbiosis (unbalanced), and producing too much beta-glucuronidase, your overall estrogen levels can be too high. This estrogen dominance can result in heavier, more painful periods with worse PMS symptoms. 

Can Birth Control Hurt My Gut?

Likely, yes. There’s no shame in using the pill if you decide it’s best for you, but I want you, and everyone, to fully understand the risks before deciding. Using hormonal birth control can harm your gut by causing intestinal hypermobility, more commonly called leaky gut. When your gut is “leaking,” proteins from your food can make their way past your intestinal lining, triggering autoimmune responses and food sensitivities. The pill can also cause imbalances and overgrowth in your microbiome, leading to SIBO and yeast infections.

If you're struggling with your gut or using hormonal birth control, check out my free birth control detox guide, or my hormone-balancing starter kit I mentioned above, to start taking the steps your body needs to rebalance your hormones. 

@drjolenebrighten Plant based breakfast for gut & hormone ❤️. #learnontiktok #tiktokpartner #guthealth #guthealing #hormones #pms #periodproblems ♬ Yummy – Justin Bieber

Period Symptoms vs. Gut Health Issues

Your menstrual cycle can also affect your gut, and diseases you may not think are related to hormones. irritable bowel syndrome, inflammatory bowel disease, Crohn's Disease, and other digestive symptoms may worsen or change throughout your menstrual cycle.

Some women experience flu-like symptoms with PMS, including nausea or diarrhea, that could be confused with gut issues. If you notice patterns in these symptoms related to your period, take notes to talk with a specialist, as this could help you clue in to certain hormone imbalances. 

Your hormones can also change the way you poop! Yes, period poops are a regular thing, and you’re not alone if things move differently throughout your cycle. In the week leading up to your period, increased progesterone levels can relax the muscles around your digestive tract. This might help ease PMS, but can also lead to constipation. On the other hand, if you find yourself running to the loo more often during your period, this could be a result of elevated prostaglandins. While these hormones are intended to cause uterine contractions (hello, cramps), they also cause contractions in the digestive tract (hello, diarrhea).

While these symptoms can easily be confused with a bad stomach bug, they aren’t necessarily a result of gut issues. That said, supporting a healthy gut microbiome can help your body properly regulate other hormone levels. Your gut is responsible for absorbing nutrients, helping you make the hormones you need, and breaking down the hormones you don’t.

How to Support your Microbiome and Balance your Hormones

The connections between hormone health and gut health are so vast, I actually have an entire chapter and protocol dedicated to this in my book, Beyond the Pill.

Taking control of your gut health is seriously key to balancing your hormones. And because so many factors affect both your microbiome and hormone health, making healthy changes to support one will often help you support both. Lifestyle changes like reducing stress, eating high-fiber veggies and fermented foods, and reducing your intake of refined sugars and alcohol are all first steps that build the foundation for balanced hormones and a thriving microbiome.

With that foundation in place, probiotic supplements are a great way to start building a diverse, healthy community of beneficial bacteria. After years of research, I’m excited to show you our new, specialized Women’s Probiotic, designed entirely around supporting healthy gut and vaginal microbiomes. I specifically formulated this supplement with Lactobacillus acidophilus and Lactobacillus rhamnosus, plus 3 key spore probiotics, to support vaginal health and estrogen levels. 

If you’re already starting with elevated estrogen, and want to support your gut and liver in properly breaking it down, Balance Women's Hormone Supplement could also help. This supplement packs B vitamins, DIM, and broccoli seed extract to support the liver's role in breaking down estrogen, plus calcium d-glucarate to help your gut send it on its way. 

Related Reading:

The Gut Hormone Connection – Dr. Jolene Brighten 

Does Alcohol Affect Your Period? – Dr. Jolene Brighten

Why Do I Poop So Much On My Period? – Dr. Jolene Brighten

Is Birth Control Bad for Your Gut – Dr. Jolene Brighten

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  1. d'Afflitto M, Upadhyaya A, Green A, Peiris M. Association Between Sex Hormone Levels and Gut Microbiota Composition and Diversity-A Systematic Review. J Clin Gastroenterol. 2022. 56(5). 384-392.
  2. Alexandra Kautzky-Wille. The relationship of the intestinal microbiome and the menstrual cycle - full text view. 2022.
  3. Ervin SM, Li H, Lim L, et al. Gut microbial β-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens. J Biol Chem. 2019. 294(49). 18586-18599.
  4. Khalili H.. Risk of Inflammatory Bowel Disease with Oral Contraceptives and Menopausal Hormone Therapy: Current Evidence and Future Directions. Drug Saf. 2016. 39(3). 193-197.
About The Author

Dr. Jolene Brighten

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Dr. Jolene Brighten, NMD, is a women’s hormone expert and prominent leader in women’s medicine. As a licensed naturopathic physician who is board certified in naturopathic endocrinology, she takes an integrative approach in her clinical practice. A fierce patient advocate and completely dedicated to uncovering the root cause of hormonal imbalances, Dr. Brighten empowers women worldwide to take control of their health and their hormones. She is the best selling author of Beyond the Pill and Healing Your Body Naturally After Childbirth. Dr. Brighten is an international speaker, clinical educator, medical advisor within the tech community, and considered a leading authority on women’s health. She is a member of the MindBodyGreen Collective and a faculty member for the American Academy of Anti Aging Medicine. Her work has been featured in the New York Post, Forbes, Cosmopolitan, Huffington Post, Bustle, The Guardian, Sports Illustrated, Elle, and ABC News. Read more about me here.