Menopause & Microbes - can the microbiome be your secret weapon?

Start a conversation about menopause and the talk will be of hormones and all of the unpleasant symptoms that are thrust upon women during mid-life. But there's another story, quietly unfolding, one that involves the microbiome, the trillions of microbes that live not just in your gut, but in your mouth, on your skin, and in the vagina.

Research is discovering that these microbes are changing in some surprising ways during menopause. Hormonal shifts appear to have an influence on the delicate balance that exists in the vast ecosystems that occupy our bodies, reshaping them and creating a ripple effect that can affect your digestion, immunity, mood, metabolism and more.

In this post, you'll discover the connection between menopause and the microbiome, why it matters and what you can do to take care of yours.

Hormones & Microbes - friends or foe?

As you move through the different stages of menopause and oestrogen and progesterone fluctuate and decline, the environment in the gut changes. This influences the speed at which food moves through the digestive system, the immune function of the gut, the signals sent to the brain affecting mood and cognition and the effectiveness of the gut barrier which prevents microbes escaping from the gut and into the blood stream.

This environmental shift also affects a particular group of bacteria known as the estrobolome. The estrobolome comprises different microbial species that are primarily responsible for the metabolism and regulation of oestrogen. This specific group of microbes regulates and maintains hormonal balance by deciding how much oestrogen should be reabsorbed by the body and how much should be removed. Declining oestrogen levels during menopause disrupts these microbes, meaning that they work less efficiently, potentially worsening symptoms such as bloating, fatigue, weight gain and low mood.

And so it does appear as though there is a relationship, sometimes friendly and sometimes not, between hormones and the microbiome with one influencing and affecting the efficiency of the other.

What is research telling us?

Microbiome research is fast moving and the evidence is still emerging and while more human studies are needed, research is pointing to some meaningful links between menopause, microbial changes and health risks. Here's what the studies are suggesting so far:

• Reduced microbial diversity and composition - microbial diversity tends to decline after menopause with shifts in the abundance of some of the particularly beneficial species. Some of these changes also mirror those that are seen in metabolic disease.

• Bone health - research suggests that the microbiome can influence mineral absorption and systemic inflammation, both of which can affect bone density, along with declining levels of oestrogen.

• Metabolic health - weight gain, especially around the mid-section, and insulin resistance tends to increase during menopause. Emerging evidence suggests that, although this may partly driven by hormones , microbial changes may play a role in the way that we use energy and store fat.

• Vaginal and urogenital microbiome changes - it's not just the gut microbiome that is changing. Declining levels of oestrogen increase vaginal pH, creating an environment that can increase the risk of UTI's, yeast infections, and symptoms such as dryness and irritation.  

• Mental health - the gut microbiome produces and regulates compounds that affect the function of the brain and so changes in the microbial community may be contributing to anxiety, low mood, brain fog and difficulties with memory in menopause.

• Inflammation - loss of microbial diversity can be the fuel on the fire of low-grade, chronic inflammation, which is linked to an increased risk of cardiovascular disease, joint pain and cognitive decline.

What are the signs of a disrupted microbiome?

These symptoms, especially if clustered together, might hint at a shift in the microbiome, whether you are in menopause or not. It goes without saying that if you are experiencing any of these symptoms, you should discuss them with your GP before making any changes to your diet.

• Persistent bloating, flatulence, persistent constipation or diarrhoea

• Persistent sugar cravings

• Recurring UTIs or vaginal discomfort

• Skin issues such as eczema, rosacea or a new sensitivity

• Low mood, especially if accompanied by gut symptoms

• Abdominal weight gain

• Fatigue

• Joint pain

Supporting the microbiome during menopause

There isn't a magic pill that will "reset" the microbiome but there are simple ways that you can nurture your microbiome to make it more resilient to hormonal shifts during menopause.

Support Diversity First:

• A high fibre, plant-rich diet - different microbes thrive on different types of fibre so variety in your choice of plant foods matters. If you've not already done so, take our 30 Plant Challenge to see how many plants you are including each week to help your microbiome thrive.

• Include resistant starches - these are great prebiotics that feed your microbes. Cooked and cooled potatoes and rice, oats, legumes and some wholegrains will keep your microbes well fed.

• Limit processed foods and added sugars - these feed the less beneficial microbes, allowing them to overgrow and reduce the diversity of the microbiome.

Introduce Probiotic Foods Mindfully:

• Choose fermented foods - whole yoghurt, sauerkraut, kimchi, miso, tempeh, kefir, kombucha are all foods containing live microbes that can help to populate the microbiome with beneficial species.

• Start slowly - start low and slow to prevent bloating and flatulence. A tablespoon every couple of days to begin with and progressively build up to 2 tablespoons daily.

• Keep it varied - each food has its own collection of microbes and you'll want to benefit from as many as possible.

Take Care of your Vaginal & Urogenital Microbes:

• All of the above - it's not just your gut microbiome that thrives on plants and fermented foods, the microbes that populate the vagina, and in fact all of your microbiomes, love them too!

• Stay hydrated - this will support the vaginal lining to be more elastic, help to maintain the mucosal layer in which the microbes live, support a healthy vaginal pH and reduce the risk of UTIs.

• Choose the right products - these can be really helpful if there is dryness and irritation. We love Yes products and you can find a link to their page here.

• Don't be shy - if you are struggling with vaginal discomfort, speak to your GP. Yes products are available on an NHS prescription and there are other products available that your GP may recommend.

Move for your Microbiome:

• Make it moderate - especially with aerobic exercise. Walking, cycling and swimming at a moderate pace supports microbial diversity.

• Train for strength - strength training is crucial in menopause to preserve muscle mass. Fascinating and emerging research talks about certain types of gut bacteria that have the ability to support and maintain muscle mass.

• Don't overtrain - consistent overtraining has been shown to increase the risk of damage of the gut lining, activating the body's stress response, altering the balance and diversity of the microbiome.

Manage Sleep & Stress:

• Maintain a regular sleep / wake rhythm - the microbiome is directly linked to the circadian rhythm, our internal body clock, having its own daily rhythms that are synchronised to the body's circadian clock while the circadian clock regulates microbiome composition and function so support the body's daily needs. A regular sleep / wake cycle will help to maintain microbial balance.

• The impact of stress - it is thought that 70% of menopausal women suffer with chronic stress although this number is likely to be higher. Stress can trigger a shift in microbial balance and alter the function of the gut barrier, creating an environment that can lead to digestive issues and changes in mood and anxiety.

• Prioritise yourself - remember the oxygen mask analogy, put your own on before helping others. To support hormone balance and a healthy microbiome, take some time out each day to focus on yourself, use some gentle yoga or breathing exercises, go for a walk, make a cup of coffee and just sit and drink it quietly, anything you like but it's got to be some time to focus on yourself.

It's gradual and sustainable changes that have the most impact.

Microbial communities adjust slowly so be patient and you may find it useful to track your symptoms as you make changes to your diet and lifestyle. It is important to remember that your microbiome is unique to you and what works for one, won't necessarily work for another. If you feel that you are doing everything right but still suffering from symptoms of menopause, please have a chat with us about how bespoke nutrition and lifestyle advice can support you during midlife.

Sources:

Becerra-Cevera, A et al (2025). Gut microbiota changes in postmenopausal women with low bone density linked to serum amino acid metabolism. Front. Cell. Infect. Microbiol. Sec. Intestinal Microbiome, 15

Gaber, M et al (2024). Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia. Microbiome 12, 192

Nieto, M.R et al (2025). Menopausal shift on women's health and microbial niches. npj Womens Health, 3, 3

Liaquat M et al (2025). The gut microbiota in menopause: Is there a role for prebiotic and probiotic solutions? Reproductive Health, 31(2): 105-114

Wan-Qiang, L et al (2021). Human gut microbiome impacts skeletal muscle mass via gut microbial synthesis of the short-chain fatty acid butyrate among healthy menopausal women. J Cachexia Sarcopenia Muscle, 12(6): 1860-1870

Wang, H et al (2025). Gut Microbiota has the potential to improve health of menopausal women

by regulating estrogen. Front. Endocrinol., Sec. Gut Endocrinology, 16

Xinyuan, X et al (2024). Study on gut microbiota and metabolomics in postmenopausal women. BMC Women's Health, 24, 608