5 signs your good gut bacteria are struggling in menopause

Gut red flags to look out for!



Menopause Advisor
eileentalksmenopause
Ask Eileen


05 August 2025

Why your gut microbiome matters during menopause

Your gut microbiome is made up of communities of bacteria that play a vital role in many areas of your health—including hormone regulation. Some gut bacteria produce enzymes that help recycle and reactivate oestrogen, a process known as the estrobolome function. This helps to maintain healthy oestrogen levels and supports hormonal balance throughout the body.

However, studies show that during and after menopause, many women experience a drop in both the number and diversity of friendly gut bacteria (1)

So, how do you know if your gut microbiome is out of balance? Here are five common signs that your friendly bacteria may need some support.

1. Digestive problems

One of the first signs of gut dysbiosis (an imbalance in gut bacteria) is digestive discomfort. You may start noticing:

These symptoms often indicate that the bacteria helping to break down your food and regulate bowel function are struggling. As a result, you may not be absorbing nutrients as efficiently, which can leave you feeling sluggish and uncomfortable.

2. Fatigue and brain fog

Surprisingly, your gut bacteria can even influence your mental clarity. This is due to the gut-brain connection—a well-established relationship between your digestive system and your brain.

Certain friendly bacteria produce neurotransmitters and fatty acids that help support brain function. If these bacteria are in short supply, you may experience:

While it’s easy to blame menopause for these symptoms, your gut health may be playing a significant role.

3. Inflammation

When your gut microbiome is out of balance, it can lead to increased inflammation throughout the body. This might show up as:

  • Joint and muscle aches
  • Gum inflammation
  • Generalised pain and stiffness

These symptoms are often written off as part of menopause or even early arthritis, but they may be directly linked to gut health.

4. Weight gain and trouble losing weight

Friendly bacteria help with digestion, fat storage, and metabolism. When these bacteria are diminished, you may find that:

Again, this isn’t always “just menopause.” Supporting your gut can help bring your metabolism back into balance.

5. Mood swings and anxiety

The gut is often called the second brain, and for good reason. It’s home to a large number of serotonin receptors—key players in mood regulation.

If your gut bacteria aren't producing the right “feel-good” chemicals, you may experience:

This connection highlights how deeply intertwined your gut health is with your emotional well-being.

How to support your gut through menopause

The good news is that there are simple, daily habits you can adopt to nourish your friendly gut bacteria—especially during and after menopause.

1. Eat more fibre-rich, plant-based foods

Focus on fibre from vegetables rather than from processed carbs. Cruciferous vegetables like broccoli, onions, and leafy greens contain lignans—compounds your gut bacteria can convert into phytoestrogens that support hormonal balance.

Include moderate amounts of whole grains such as brown rice, wholemeal bread, and wholemeal pasta—but be mindful of any bloating they may cause.

2. Try fermented foods

Fermented foods are a fantastic way to reintroduce beneficial bacteria into your gut. Examples include:

  • Kimchi
  • Kefir
  • Sauerkraut

Taken daily, in small amounts, they can help restore balance and improve digestion.

One option I’ve personally used for years is Molkosan Fruit, a fermented whey drink that supports gut health. I take two teaspoons in the morning—just once a day—and it works wonders for me and my friendly bacteria.


A.Vogel Molkosan Fruit | Prebiotic Formula Providing Gut Health Support | Ariona Berry & Pomegranate | 200ml


£8.99 (200ml) In Stock Get it tomorrow, 8th August.

3. Manage stress

Stress produces chemicals that can disrupt your gut flora. Regular stress management practices—like deep breathing, yoga, or even a short daily walk—can help protect your microbiome.

4. Stay hydrated

Water supports every aspect of your health, including digestion. Aim to drink regularly throughout the day.

5. Cut back on processed foods

High-sugar, high-salt foods can harm your friendly bacteria. Focus on whole, natural foods to keep your microbiome thriving.

6. Consider probiotics

A probiotic course twice a year can give your gut a helpful boost—especially if you’re going through a particularly stressful time or recovering from illness.

Final thoughts:

The connection between your gut and hormones is an exciting and rapidly growing area of research. By supporting your gut microbiome, especially through menopause, you can feel more in control of your health and symptoms.

Have you tried any of the gut-friendly strategies mentioned above? Have you noticed a difference in your bloating, mood, or energy levels after changing your diet?

I’d love to hear your stories—please feel free to share them below.

Take care xx

References:

https://pmc.ncbi.nlm.nih.gov/articles/PMC11658944/

https://pubmed.ncbi.nlm.nih.gov/35675542/

https://pmc.ncbi.nlm.nih.gov/articles/PMC9343210/ 

A.Vogel Molkosan Fruit | Prebiotic Formula Providing Gut Health Support | Ariona Berry & Pomegranate | 200ml

200ml

£ 8.99

Buy now

A.Vogel Molkosan Fruit Digestion | Contains L+ lactic acid | Suitable for Vegetarians | 200ml
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