🧬 Gut Check: The Basics of Your Microbiome

Your gut microbiome is made up of bacteria, viruses, fungi, and other microorganisms. Most of them live in the large intestine, and they’re essential to your health. We’re talking nutrient production (hello, B vitamins and vitamin K), gut lining integrity, metabolism regulation, and immune balance.

But the gut’s biggest claim to fame? It’s part of the gut-brain axis—a communication superhighway between your belly and your brain that uses neurotransmitters like serotonin, dopamine, and GABA. Up to 95% of your serotonin is made in your gut. That’s not a typo. Ninety. Five. Percent. Source

So what happens when your hormones jump on this delicate system like a hormonal wrecking ball? Buckle up.

Estrogen and the Estrobolome

You’ve probably heard of the microbiome—but have you met the estrobolome? It’s the collection of gut bacteria that metabolizes estrogen. These bacteria produce an enzyme called β-glucuronidase, which helps recycle estrogen in your body. Sounds helpful, right?

Well, only if the balance is right.

When your gut bacteria are healthy and diverse, estrogen metabolism flows like Beyoncé on stage—graceful, powerful, and on point. But when the gut is imbalanced (due to antibiotics, processed food, stress, or hormone changes), that β-glucuronidase activity can go haywire. This can lead to excess circulating estrogen (which may fuel fibroids, PMS, breast tenderness, or mood swings) or not enough estrogen (cue vaginal dryness, low libido, or hot flashes). Source

💡 Fun fact: Estrogen also feeds certain types of gut bacteria—so fluctuating levels during perimenopause or menopause can cause shifts in microbiota composition and diversity.

Progesterone: The Microbial BFF

While estrogen can be dramatic (and we love her for it), progesterone is your chill friend—the one who brings snacks and reminds you to breathe. It’s anti-inflammatory, supports GABA (your calming neurotransmitter), and helps modulate the immune system.

Turns out, progesterone also supports gut barrier function—aka keeping your gut lining strong and preventing leaky gut. And it helps nurture “good” microbes, including Lactobacillus species, which play a major role in maintaining vaginal and gut health. Source

When progesterone drops (like it does in perimenopause or with chronic stress), the gut becomes more vulnerable to inflammation and dysbiosis. Which means… not-so-happy microbes, more bloating, more brain fog, and less serotonin.

Testosterone: Not Just for the Bros

Let’s not forget about testosterone, which women have too—especially in early midlife. This hormone is linked to energy, mood, and muscle mass. Some gut bacteria actually help regulate testosterone metabolism, and there’s evidence that a disrupted microbiome can reduce androgen levels. Source

And here’s the kicker: testosterone also affects the gut by modulating immune responses and inflammation, meaning it can shape which bacteria flourish and which flounder.

Cortisol: The Stress Hormone with a Gut Complex

Now let’s talk about the elephant in the hormonal room: cortisol.

Cortisol is your body’s main stress hormone, and it’s meant to save your life in danger (like from a bear… or a toddler tantrum at Target). But when stress is chronic, cortisol stays elevated, and this messes with the gut in three major ways:

1. Thins the gut lining, contributing to leaky gut
2. Reduces microbial diversity, favoring pathogenic strains
3. Disrupts serotonin and GABA production, fueling anxiety, depression, and irritability

High cortisol also suppresses immune function in the gut, making it easier for bad actors (like Candida or E. coli) to overgrow. Source

And remember: your gut makes neurotransmitters. So if stress hits your gut hard, you may feel it in your mood, your sleep, and your ability to stay emotionally afloat when your favorite jeans don’t fit.

The Gut–Hormone–Neurotransmitter Triangle

Let’s connect the dots:

• Hormones (estrogen, progesterone, cortisol) affect the gut microbiome
• The microbiome influences neurotransmitter production
• Neurotransmitters shape your mood, focus, motivation, and stress resilience

In other words, your hormone chaos isn’t “just in your head”—it may be in your gut. And healing the gut could mean better hormone balance, and yes, better brain chemistry.

Here’s what the gut helps make:

So… What Can You Do About It?

Let’s get to the good stuff: action steps. Because nobody wants a blog that leaves them bloated and hopeless.

1. Support Estrogen Detoxification

• Eat cruciferous veggies (broccoli, kale, cauliflower)
• Consider DIM or calcium-D-glucarate supplements (talk to your provider)
• Poop daily. Yep. Estrogen is excreted in the stool.

2. Feed the Friendly Flora

• Eat prebiotic fibers (leeks, onions, bananas, oats)
• Add fermented foods (yogurt, kimchi, sauerkraut, kefir)
• Take a diverse, clinically backed probiotic

3. Balance Cortisol

• Get serious about sleep
• Use adaptogens (ashwagandha, rhodiola) if needed
• Try breathwork, vagus nerve toning, or even a brisk walk

4. Topical Hormone Support

Many women find relief using bioidentical progesterone or estriol creams, which may help support the microbiome indirectly by calming inflammation, improving sleep, and balancing estrogen. (Always work with a trained provider.)

💥 Final Thoughts

Perimenopause and stress don’t just mess with your hormones—they mess with your microbes. And when your gut is unhappy, it can’t make the neurotransmitters you need to sleep well, think clearly, or keep it together when someone eats the last of your almond butter.

Your hormones, your microbiome, and your brain are having a constant group chat. Make sure you’re not feeding them drama.

References:

• Gut Microbiota’s Effect on Mental Health
  
• The Estrobolome and Estrogen Metabolism
  
• Progesterone and Immune Modulation
• Androgens and the Microbiome
  
• Stress, Cortisol, and Gut-Brain Axis