5 Gut Bacteria That Influence Progesterone Balance (And What Science Reveals)

Key Insight:

Emerging research confirms that gut bacteria don’t just respond to hormones—they actively metabolize and regulate them, including progesterone, through enterohepatic ( of both the liver and the intestine) circulation. Some species enhance progesterone activity, while others may diminish its effectiveness, making the gut microbiome a critical player in female hormonal health.

Your Gut: The Hidden Hormone Laboratory

Most people think of hormones as something the ovaries, adrenal glands, and thyroid manage. But here’s what’s rarely talked about: your gut microbiome acts as an endocrine organ, actively modifying and regulating hormones, including progesterone.

How? Through bacterial enzymes that influence hormone metabolism.

Progesterone, like other steroid hormones, undergoes a recycling process called enterohepatic circulation. It’s metabolized in the liver, sent to the gut, and reabsorbed back into the bloodstream. This process depends on specific gut bacteria, some of which help maintain progesterone levels, while others speed up its breakdown.

Here’s what recent studies reveal:

• Gut microbes metabolize 15-30% of circulating progesterone through bacterial β-glucuronidase activity.

• Microbial progesterone metabolites influence ovarian function and endometrial receptivity, affecting fertility and menstrual cycle regulation.

• Gut (dysbiosis) imbalances can reduce progesterone bioavailability by up to 40% in animal models, suggesting that an imbalanced microbiome could contribute to hormone-related disorders.

This means that a well-balanced gut microbiome is beneficial for digestion and essential for hormonal stability, fertility, and overall reproductive health.

The Progesterone-Microbiome Connection: What We Now Know

Certain bacterial species directly affect progesterone metabolism. Some promote progesterone stability, while others may deplete or alter it. Understanding which bacteria influence hormonal health is key to optimizing your gut for better progesterone balance.

1. Clostridium innocuum: The Progesterone Reducer

This bacterium is known for breaking down progesterone into a different form, epipregnanolone, which has little to no progesterone-like activity in the body.

Mechanism: Converts progesterone into epipregnanolone, a neurosteroid with minimal progestogenic activity.

Impact: Reduces bioactive progesterone levels by 58% in human trials.

Clinical Significance:

1. Associated with 32% higher IVF failure rates in fertility studies.

2. Disrupts follicular development and may contribute to irregular ovulation.

🚨 Why it matters: High levels of Clostridium innocuum could be silently disrupting your hormonal balance. A microbiome test can help identify overgrowth.

How to reduce it:

• Increasing fiber intake, particularly from prebiotic-rich foods like onions, leeks, and asparagus, has been shown to reduce Clostridium levels by 33%.

• Consume resistant starches like cooked and cooled potatoes to boost gut integrity.

• Take partially hydrolyzed guar gum to inhibit Clostridium species growth.

• Limit processed foods and antibiotics that encourage Clostridium overgrowth.

2. Bifidobacterium longum: The Hormone Stabilizer

This beneficial bacteria helps regulate progesterone metabolism by supporting liver function. It produces acetate, a short-chain fatty acid that enhances the liver’s ability to conjugate (bind) progesterone for better circulation.

Action: It produces acetate, which supports liver function and enhances hepatic progesterone conjugation.

Trial Data: Supplementation with B. longum increased serum progesterone by 18% in PCOS patients.

Dietary Support:

Jerusalem artichokes (rich in inulin) increased Bifidobacterium populations by 4.7x in randomized controlled trials.

Why it matters: Bifidobacterium longum acts as a natural hormonal stabilizer, helping women with PCOS, PMS, and fertility concerns.

How to increase it:

1. Consume fermented dairy products like yogurt and kefir.

2. Eat prebiotic-rich foods like bananas, oats, and garlic.

3. Consider a high-quality Bifidobacterium probiotic supplement.

3. Lactobacillus spp.: The Estrogen-Progesterone Balancers

Dual Function: 

• Lactobacillus bacteria help balance estrogen and progesterone by:

  1. Reducing estrogen dominance through β-glucuronidase inhibition.

  2. Enhancing progesterone receptor sensitivity by producing short-chain fatty acids (SCFAs) that improve hormonal signaling.

Clinical Impact:

• Lactobacillus reuteri supplementation decreased PMS symptoms by 41% in a 3-month study.

• Women with low Lactobacillus levels were more likely to have irregular cycles and hormone imbalances.

Why it matters: This bacterial genus helps regulate the estrogen-progesterone ratio, reducing symptoms like bloating, mood swings, and irregular periods.

How to boost Lactobacillus levels:

1. Eat fermented foods like sauerkraut, kimchi, and kombucha.

2. Consume polyphenol-rich foods such as berries, green tea, and dark chocolate.

3. Take a multi-strain probiotic containing Lactobacillus.

4. Bacteroides spp.: The Bile Acid Modulators

Role: Convert primary bile acids into secondary forms that upregulate hepatic progesterone synthesis.

Key Finding: Women with Bacteroides-rich microbiomes had 27% higher luteal progesterone levels.

Why it matters: These bacteria support progesterone production indirectly by optimizing bile acid metabolism.

How to maintain balance:

1. Eat a Mediterranean-style diet rich in fiber, healthy fats, and fermented foods.

2. Avoid processed foods, as they can disrupt bile acid metabolism.

5. Enterobacteriaceae: The Double-Edged Sword

This bacterial family has a dual effect on progesterone:

• Low levels = Beneficial: At low levels, they assist in progesterone conjugation.
• High levels = Harmful: Overgrowth produces endotoxins that:

• Increases progesterone metabolism by 22%, depleting levels too quickly.

• Trigger’s inflammation, impairing ovarian function and fertility.

🔥 Why it matters: Chronic inflammation caused by Enterobacteriaceae overgrowth is linked to hormone imbalances, gut permeability issues, and even endometriosis.

How to regulate it:

• Increase intake of polyphenols (found in green tea, pomegranate, and turmeric).

• Take a high-quality spore-based probiotic to control overgrowth.

• Avoid excess sugar and processed foods, which encourage Enterobacteriaceae overgrowth.

• Eat fermented foods that promote good bacteria to keep them in check.

The Gut-Progesterone Diet: Evidence-Based Recommendations

• 

  Top Foods for Progesterone Balance

1. Resistant Starches

• Cooked-cooled potatoes increase butyrate (a progesterone-supporting SCFA) by 3.1x.

• Green bananas boost beneficial gut bacteria like Faecalibacterium populations by +137%.

2. Polyphenol-Rich Foods

• Pomegranate: Reduces progesterone-metabolizing Clostridia by 41%.

• Green tea (EGCG): Enhances Lactobacillus adhesion to intestinal mucosa.

3. Fermented Foods

• Kimchi contains 12 strains of β-glucuronidase-inhibiting Lactobacillus.

• Kefir: Reduces Enterobacteriaceae overgrowth by 5.8x in IBS patients.

The 28-Day Microbiome Reset Protocol (That Is Science-Backed)

Phase 1 (Days 1-7): Microbial Reshaping

Morning: 2 cups of roasted chicory root tea (inulin increases Bifidobacteria 4.3x).

Evening: 1 tsp partially hydrolyzed guar gum (reduces Clostridia 33%).

Phase 2 (Days 8-21): Hormone-Supportive Feeding

Daily:

2 tbsp ground flaxseed (lignans increase Lactobacillus 2.9x).

1 cup cruciferous vegetables (helps balance estrogen and progesterone).

Phase 3 (Days 22-28): Gut Barrier Optimization

Supplements:

• L-glutamine (5g/day): Tightens intestinal junctions by 27%.

• Zinc carnosine: Reduces microbial translocation by 41%.

Final Thoughts:

Your gut bacteria play a direct role in hormone balance. By understanding how gut bacteria affect progesterone metabolism, women struggling with fertility, PMS, or hormone imbalances, addressing gut health might be the missing piece.. By optimizing your gut microbiome with diet and targeted probiotics, you can support your hormonal health naturally.

Always consult a functional medicine practitioner before implementing significant dietary changes. Hormone testing and microbiome analysis are recommended for personalized protocols.

(Citations reflect current research as of March 2025)

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[15] Purdue Nutrition Science researcher uncovers connection between hormones, gut microbiome and metabolic dysfunction commonly seen in postmenopausal women – News | College of Health and Human Sciences https://www.purdue.edu/hhs/news/2024/04/purdue-nutrition-science-researcher-uncovers-connection-between-hormones-gut-microbiome-and-metabolic-dysfunction-commonly-seen-in-postmenopausal-women/

[16] Natural progesterone: Products, food, remedies and benefits https://www.medicalnewstoday.com/articles/321919

[17] The Gut Microbiome and Female Health - MDPI https://www.mdpi.com/2079-7737/11/11/1683