Your Gut Health May Be Affecting your Menstrual Cycle

Disclaimer: No information in this article is to be taken as personal medical advice. Please consult your personal registered dietitian, medical doctor, or other health professional regarding any information in this article.

Your Gut Health May Be Affecting Your Menstrual Cycle

This may blow your mind! But your gut health can affect your period in a very interesting way!

There are actually groups of bacteria in our colon that can help us metabolize estrogen! And as you may know estrogen is a key player when it comes to regulating out period.

The groups of bacteria that directly effect estrogen are known as members of the “estrobolome” .

We excrete varying amounts of estrogen in bile when we eat, a compound that helps us digest fat. Depending on factors such as your diet, estrogen can make it’s way to the colon to be excreted via feces.

How cool is that!!? 

But sometimes your gut flora interferes with this process.

Estrogen arrives in the colon as conjugated estrogen, a slightly different form of estrogen that essentially gets "trapped" in the colon so it can be fully excreted. However, bacteria that make up the estrobolome have enzymes that can "de-conjugate" estrogen. This process frees estrogen and allows it to renter the bloodstream.

How Gut Bacteria May Be Effecting Your Period?


Having excess amounts of bacteria capable of "de-conjugating estrogen" could result in high estrogen levels. This could worsen conditions such as endometriosis, where sensitivity to estrogen encourages increased growth of endometrial tissue. 

Menstrual irregularity:

Estrogen levels should be at their lowest point during menstruation, so having gut flora that can increase estrogen levels could interfere with your body's ability to lower estrogen in a timely manner for your period.

Menopause and PCOS:

On the other hand, having low amounts of  bacteria able to deconjugate estrogen, may result in too much estrogen excretion. This could worsen the hormonal imbalances seen in women with PCOS and in some women who are menopausal. In fact, studies show that women with PCOS, and women who go into menopause prematurely, commonly have a poor diversity of gut bacteria.

Digestive problems before and during your period

In theory, the progressive decrease in estrogen that should occur as you near your period could result in a temporary, yet noticeable shift in your estrogen metabolizing bacteria. This shift could allow for other species of bacteria to become more or less dominant as a result. These new predominating bacterial strains may metabolize the food you eat differently. 

This means that the food you eat during your period may no longer be encountering the same exact distribution of bacteria it would ordinarily. So that yummy pizza that usually does not give you excess gas might make you feel gassy and bloated close to your period.

Can you test your gut flora to analyze your ability to metabolize estrogen?

Yes! Even though the estrobolome and its effects are a new science (especially when it comes to how it affects men), we are now able to test for some of the identified strands and groups of bacteria that are capable of metabolizing estrogen. Some tests can even show you how much estrogen you excrete in your stool. At 3 In 1 Nutrition, we often recommend such testing if you have painful or irregular periods that are especially characterized by GI symptoms. We then create a tailored food-based protocol to encourage shifts in the gut biome. Interested? Book a free call here. 

What Can You Do If Your Gut Bacteria is to Blame ?

1.Trial an elimination diet

Gas and discomfort during and right before your period may be a sign of an over-nourished estrobolome. One of the first things you can do to mitigate the gastrointestinal side effects that may come around your period, is to trial an elimination diet to help you identify problem foods that you can limit or avoid prior to and during your period. 

You can start by keeping a daily record of foods that generally result in excess production of gas or bloating the week leading up to your period and during your period.  Once you identify these foods you can try to eliminate or limit each foods until your period ends. This option may be hard to implement if your period is not regular.

If you would like to explore how nutrition therapy can make your period more regular, and trial an elimination diet with professional guidance, please reach out via our contact page as I would love to help!

2. Promote a diversity of gut flora 

The more we can diversify your gut flora the higher the probability is that your gut microbiota is not over or under populated with bacteria that can metabolize estrogen. Infact, promoting bacterial diversity has been shown to improve symptoms of PCOS and menopause, in part due to this very reason.


Here are 3 Ways to Diversify Your Gut Microbiome

1. Eat Fermented Foods

home-made kimchi (credit to "Portuguese gravity")

We have yet to discover all the bacteria that exist within our world. There are billions of cultures that we have yet to identify that may have wonderful health benefits. One of the best and most natural ways to encounter such bacteria in addition to bacteria that we have already discovered to be healthful, is to eat foods that have been naturally fermented.

  • Kimchi
  • Fermented pickles or sauerkraut
  • Yogurt (Always buy organic yogurt!!) 
  • Kombucha
  • Organic Kefir (always buy organic)
  • Organic Tempeh (always buy organic)
  • Organic Miso (always buy organic)
  • Homemade sourdough bread

A great starting goal could be to have at least 1-2 fermented foods per day that are at least 1/2 cup in volume. You do have to be careful with fermented foods as many can be high in sodium! Diversifying your sources of fermented foods can help make sure you do not get all of your fermented foods from one source (i.e have a pickled fermented food one day, dairy-based fermented food the next, and a fermented  drink like kombucha the next day). 

2. Consider a Probiotic

Many people ask me " Can a probiotic effect your period?". And the answer is yes!

Some Probiotics that include bifidobacterium and lactobacillus acidophilus have been shown to help improve clinical outcomes and symptoms associated with several menstrual disorders such as PCOS and Endometriosis, two conditions which are affected by the estrobolome.  

I am personally an advocate for a whole foods based approach in addition to probiotics. I will also add that in clinical practice, I have found that choosing specific probiotic strains based on a person’s symptoms, stool analysis, and full clinical picture can yield better results than choosing any over the counter probiotic. This is because there is a chance that you can get a probiotic that further disturbs the estrobolome in some cases.

3. Eat a diversity of plant-fiber:

You can eat all the probiotics and fermented foods you want, but if you are not providing your existing and “new bacteria” with a consistent source of fuel, then you will not be able to effectively diversify your gut flora. The best way to do this is to eat plenty of fiber rich foods. Fiber are carbohydrates that we don't have the enzymes to digest, but many of our bacteria do!

Soluble Fiber:

Specific fibers known as soluble fiber serve as a great food source for a broad spectrum of bacteria. They can be found in several whole grains, vegetables, legumes, nuts and seeds. 

Soluble fiber also helps bring estrogen to the colon. Remember when I noted earlier that bile contains some sex hormones like estrogen ? Well, soluble fiber forms a thick, viscous solution during digestion that traps bile, eventually carrying it to the colon. Without fiber trapping estrogen in bile, estrogen could makes it's way back into circulation higher up in the GI tract.

Insoluble Fiber:

Insoluble fibers, are also important. These are the fibers that your grandma commonly called “roughage”, and they too can also be digested by some bacteria.  Hence why many people can eat a bowl of roughage rich salad greens, and still see very few undigested plant particles in their stool. These fibers are important for "stool bulk" and encouraging you to use the bathroom regularly.


There are also more detailed categories of fiber known as prebiotics. This is a very important group of fibers to focus on if you plan to diversify your gut biome. Prebiotics are technically soluble fibers, but are categorized separately since they cause bacteria to produce specific biproducts that are especially healthful to the human host. You  can read a more about the distinctions between general dietary fiber and prebiotics here .

Whole food sources that are rich in prebiotic fibers include:

  • Oats
  • Barley
  • Wheat
  • Jerusalem artichoke
  • Garlic
  • Leeks
  • Onion
  • Dandelion Greens
  • Asparagus
  • Bananas (especially bananas that are not fully ripe)

There are plenty of other whole grains, fruits, and vegetables that contain prebiotic fiber. However, the foods highlighted in the list above are particularly high in specific prebiotics. This ist could also challenge you to experiment with some fruits and vegetables that perhaps you don’t include ordinarily. 

How do you know if you are getting enough fiber overall?

To get the health benefits to your gut biome, it is best to eat a variety of foods from each plant food group per day which will ensure you get a great distribution of all fiber types. 

The American Dietetic Association suggest aiming for at least 25-30 grams of fiber a day, so aiming for this range can be a great goal. If you are not use to eating a high fiber diet, it may be best to aim a bit lower. Perhaps you aim for 10 grams of fiber per day, and work your way up to 25-30g per day depending on how you feel. 

Another good start is to try to meet the basic dietary guidelines and serving sizes for the following plant foods per day:

Whole Grains (aim for 3, ½ cup servings per day)

* I encourage my clients to make sure these are whole, intact grains such as quinoa or oats

Fruits (aim for 2 servings per day)

Vegetables (aim for 2-3, 1/2 cup servings per day)

*Ensuring you include vegetables that are high in prebiotics such as onions and garlic can help diversify the gut biome

Nuts (1-2 oz per day)

Seeds (1-2 oz per day)

Legumes (beans) ( minimum ½ cup per day)

However, as noted earlier, trialing a high fiber diet close your period may lead to excess bloating and more gas. This is why it may be best to taper your fiber intake close to your period days to limit excess gas production

What if I have IBS?

Some people are very responsive to certain fibers found in food. Especially prebiotic fibers. This is especially true for individuals with IBS. If you have IBS or find that you are very sensitive to certain fibers, you may want to note which fiber rich foods you can tolerate, and only eat an array of fiber with in those foods. Working with a dietitian can help you systematically note which foods and specific fibers you are reactive to can help. If you are interested in talking with an RD specialized in this area, click here.

Conclusion: Gut health Affects Your Menstrual Cycle!

You may have bacteria that is interfering with estrogen excretion, and allowing excess estrogen to re-enter circulation. This could be playing a role in conditions such as PCOS, menopause, endometriosis, missing or absent periods and GI discomfort during menstruation. Introducing new bacteria via probiotics or fermented foods, and eating a variety of plant foods such as beans, nuts, seeds, fruits, vegetables, and whole grains, which are naturally rich in fiber,  may help diversify your gut flora and improve hormonal shifts throughout your menstrual cycle.


Baker JM, Al-Nakkash L, Herbst-Kralovetz MM. Estrogen-gut microbiome axis: Physiological and clinical implications. Maturitas. 2017 Sep;103:45-53. doi: 10.1016/j.maturitas.2017.06.025. Epub 2017 Jun 23. PMID: 28778332.

Rizk MG, Thackray VG. Intersection of Polycystic Ovary Syndrome and the Gut Microbiome. J Endocr Soc. 2020 Nov 16;5(2):bvaa177. doi: 10.1210/jendso/bvaa177. PMID: 33381671; PMCID: PMC7757431.

Markowiak P, Śliżewska K. Effects of Probiotics, Prebiotics, and Synbiotics on Human Health. Nutrients. 2017 Sep 15;9(9):1021. doi: 10.3390/nu9091021. PMID: 28914794; PMCID: PMC5622781.

Written by
Ciara Dove-Reid, RDN
Registered Dietitian Nutritionist

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