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February 6, 2026

Hormones and The Gut

Hormones and The Gut

During perimenopause, gastrointestinal symptoms are common and often caused by hormonal imbalances and erratic swings; this is because there are hormone receptors all throughout the digestive tract.  Symptoms common during this transition include constipation, diarrhea, reflux, indigestion, and bloating or gas.  Women may have experienced this during their luteal phase or menstrual cycles throughout their cycling years during which time GI symptoms are common.  Digestive symptoms can also arise when on menopausal hormone replacement therapy (MHT) which can often be remediated by adjusting the dose, route of administration or the type of hormone replacement.

So how do our hormones affect the gut?

Motility:

Estradiol speeds up gastrointestinal motility while progesterone slows gut motility.  When progesterone is high in the luteal phase, this can lead to constipation and bloating.  Progesterone relaxes the smooth muscle of the intestinal lining.  This is one of the mechanisms behind constipation.  If you are experiencing constipation on HRT, you want to first optimize your estradiol level per the labs.  This means a minimum serum estradiol level of 60pg/mL.

If symptoms persist, you can consider lowering the progesterone dose.  The minimum uterine protective dose is 100mg nightly or cycling 200mg nightly for 12 days of the month.  Other alternatives would be to consider vaginal progesterone vs oral or a progestin-only IUD (Mirena).

If you are having persistent diarrhea, you may consider if your estradiol dose is too high, although this is much less common.

Gallbladder function:

Estrogen enhances bile production and helps with fat absorption.  When estrogen decreases in menopause, this can cause difficulty digesting fatty foods or post meal bloating.  Hormone replacement therapy, particularly oral estradiol tablets can also have effects on the gallbladder.

Oral estrogen goes through the first pass effect, meaning it is absorbed right into the hepatic duct; high levels of estradiol here increase the cholesterol content of bile and decrease bile flow leading to gallstones.  This is one of many reasons transdermal estradiol (a patch or a gel) is recommended over oral therapy.  

Progesterone hormone therapy also slows gallbladder function, leading to bile stagnation and consequently gallstones – I don’t see this often, but something to think about if you’re on high dose therapy.  

Reflux:

Progesterone relaxes the lower esophageal sphincter which can lead to reflux and heartburn.  This combined with slower gastric emptying can cause burning pain in the chest and feeling overly full after meals.  

To remediate this when on BHRT, you might consider a lower dose, i.e. 100mg vs 200mg nightly or perhaps switching to a vaginal progesterone if symptoms don't improve with a dose change.  We also recommended not taking progesterone with a large meal.


Microbiome:

Estradiol increases microbial diversity.  This means there are more types of beneficial bacteria, which make for a healthier gut overall. Estradiol promotes beneficial bacteria growth like lactobacillus and bifidobacteria and inhibits pro-inflammatory bacteria like proteobacteria.  

Estradiol maintains this healthy mix of gut bacteria, and a healthy microbiome leads to stable levels of estradiol, through balanced estrogen recycling.  If there is intestinal dysbiosis, too much or too little estrogen is recycled.  If too much, this causes estrogen-dominant symptoms (breast tenderness and migraines).  If too little, a woman may have estrogen deficiency symptoms (brain fog, joint pain, hot flashes).  

This interrelationship of the gut microbiome and estrogen is called the estrobolome.  Estrogen also decreases leaky gut through strengthening tight junctions which decreases bad bacteria crossing the intestinal lining into the blood circulation.  

Progesterone’s relationship to the gut is less studied, but we do know that too much can cause overgrowth of methanobacteria, common with constipation issues and SIBO.

How can you support your digestive system during perimenopause?

New IBS symptoms may be one of the many signs of perimenopause which can be remediated with hormone balancing or hormone replacement.  When a woman is ready, transdermal estradiol can help increase the diversity of the microbiome, which supports stable, healthy levels of estrogen recycling and lowers inflammation.  

Eating 30g of fiber daily (oats, chia, flax) and incorporating polyphenols which are prebiotics (berries, pomegranate, green tea, cocoa) further support diversity, a healthy microbiome, and healthy estrogen levels throughout the menopause transition.  Other prebiotic foods or (probiotic fertilizer) are bananas, honey, resistant starches (cooled and reheated potatoes), asparagus, leeks, onions, and garlic.