How Your Gut Health Shapes Your Hormones (and Your Cycle)

When we think about hormones and menstrual cycles, we often focus on the ovaries, uterus, or maybe even stress levels, but your microbiome plays a surprisingly powerful role, too. In fact, supporting your digestive health may be one of the most overlooked ways to support your hormones.

Let’s take a closer look at how your gut and hormones work together, and what you can do to keep both in balance.

Your Gut: More Than Just Digestion

Your gut isn’t just where food gets broken down. It’s also a command center for metabolism, immunity, and hormone regulation. Housing trillions of microbes (collectively known as your gut microbiome), your digestive system influences everything from estrogen detoxification to insulin sensitivity, two major players in menstrual health. 

3 Ways Gut Health Affects Hormones

Here are three key ways your gut influences your cycle:

1. Estrogen Recycling (The Estrobolome)

Your liver packages up used estrogen and sends it to your gut for elimination. But if your microbiome is imbalanced or sluggish, certain bacteria (through an enzyme called beta-glucuronidase) can re-activate and reabsorb that estrogen, sending it back into circulation.

The result? Estrogen dominance can lead to symptoms like PMS, irregular cycles, heavy bleeding, and mood swings.

2. Insulin Resistance and PCOS

A disrupted gut microbiome can contribute to inflammation and insulin resistance, a condition where the body has trouble using insulin effectively to manage blood sugar, two major drivers of PCOS. But it goes deeper than that. 

Studies show that women with PCOS have distinct changes in their gut bacteria, including lower microbial diversity and higher levels of certain strains like Catenibacterium and Kandleria (source). These specific microbes may contribute to the inflammation and hormonal imbalances common in PCOS. For example, Catenibacterium has been linked to inflammatory conditions and tends to flourish on high-carbohydrate, Western-style diets (source). Kandleria, on the other hand, has been associated with increased levels of androstenedione, a male hormone frequently elevated in women with PCOS (source). These gut-related imbalances are even more pronounced in women with PCOS who are also obese. (source)

3. Inflammation and Nutrient Absorption

Chronic gut inflammation (what some call “leaky gut”) and even genetics can impair the absorption of key nutrients like magnesium, zinc, and inositol, all of which play vital roles in hormone balance. If your body can’t absorb these well, your menstrual cycle can become irregular or more symptomatic.

How Your Microbiome and Hormones Interact

Hormones Shape the Microbiome, and Vice Versa

Hormones like estrogen and testosterone don’t just influence your reproductive system; they also shape the bacteria in your gut. These hormone-microbe interactions are complex, but understanding them is key to supporting hormonal health through gut care.

Estrogens' Positive Influence

In one study, higher estrogen levels in healthy women (like during the follicular phase of your cycle or with estrogen-based contraceptives) are associated with (source):

• An increase in beneficial bacteria like Bacteroidetes
• A decrease in Firmicutes and Ruminococcaceae, which are often linked with inflammation
• An overall boost in gut microbiome diversity, which is a marker of better gut and immune health

Testosterone Tells a Different Story

In men, higher testosterone can support microbial diversity. But in women, elevated testosterone (as seen in conditions like PCOS), can disrupt the balance. Research links high testosterone in women to: 

• More Escherichia and Shigella (potentially harmful bacteria) (source)
• Less Ruminococcus, which is key for digestion and inflammation regulation (source)

One Nutrient You Might Be Missing: The Inositol-Gut Link

One nutrient especially impacted by gut health is myo-inositol, a natural compound that supports insulin sensitivity and ovulation. Some women, particularly those with PCOS or chronic gut issues, may not absorb it well, leading to what’s called inositol resistance (source).

The good news? Emerging research shows that alpha-lactalbumin, a natural milk protein, may improve inositol absorption by enhancing gut permeability and reducing inflammation (source). For women who haven’t responded to inositol alone, this combination may be a game-changer.

Tips to Support Your Gut (and Your Cycle)

1. Eat more fiber – Fiber feeds the good bacteria that help regulate estrogen.
2. Limit processed sugars – They feed harmful microbes and increase inflammation.
3. Include fermented foods – Yogurt, kimchi, sauerkraut, and kefir support microbial diversity.
4. Support inositol absorption – Consider pairing it with alpha-lactalbumin for better results.
5. Look for signs of dysbiosis – Bloating, constipation, skin issues, or fatigue can all point to gut imbalances.

Bottom Line

If your periods are irregular, painful, or missing altogether, it’s worth asking not just what’s going on with your hormones, but also what’s happening in your gut. By nurturing your digestive health and improving nutrient absorption, you can create a more balanced internal environment for your hormones to thrive.

Want to take the first step? Use this gut health checklist to evaluate your current habits and start supporting your hormones from the inside out.