While there is no exact definition of a “healthy” microbiota, it is generally characterised by a state of symbiosis – a balanced and diverse microbial environment that remains stable over time and is resilient to disturbances such as antibiotic use.  

On the other hand, when the balance of the gut microbiota is disrupted, it is said to be in a state of dysbiosis. This can involve a decrease in beneficial microbes, an increase in potentially harmful microbes or a loss of overall microbial diversity.   

The gut microbiota begins to develop at birth, influenced by factors like mode of delivery (i.e. vaginal or Caesarean section) and infant feeding methods (i.e. breastfed or formula fed). Babies born vaginally and those who are breastfed typically have a higher abundance of Bifidobacterium and Bacteroides.¹^,2

By the age of three, the gut microbiota stabilises and begins to resemble that of an adult.³ This makes the period from birth to age three, a critical window for shaping a baby’s gut microbiota composition. Factors like diet, antibiotic exposure and environment influences such as pollution, hygiene practices and even owning a pet can significantly affect microbial diversity during this formative stage.⁴

As a woman enters puberty, fluctuating levels of oestrogen and progesterone begin to exert noticeable effects on the gut. Throughout the menstrual cycle, many females can experience gastrointestinal symptoms such as bloating, constipation or diarrhoea. These changes are mediated by sex hormones receptors located in gastrointestinal cells, which affect gut motility (i.e. movement of food through the digestive tract) and gut permeability.⁵   

This can manifest as cyclic gastrointestinal symptoms during different phases of the menstrual cycle. For example, around ovulation, when progesterone levels are rising, gut motility may slow, leading to harder stools or constipation. Whereas during menstruation, when progesterone levels drop sharply, gut motility tends to speed up, often resulting in looser stools or diarrhoea.  

A key player in the bidirectional relationship between the gut microbiota and female hormones is the oestrobolome – a specific subset of gut microbes that can metabolise and recycle oestrogen. Oestrogen circulates the body and is inactivated in the liver before moving to the intestines for excretion in stools. However, certain gut bacteria such as Bacteroides and Firmicutes, produce an enzyme called beta-glucuronidase which reactivates oestrogen and allows it to re-enter circulation. This means that the composition and diversity of the gut microbiota can influence oestrogen levels in the body.  

A balanced and diverse gut microbiota supports a healthy oestrobolome, which can help regulate oestrogen levels effectively, potentially leading to reduced menstrual symptoms. In contrast, dysbiosis may impair oestrobolome function, leading to reduced oestrogen recycling and possibly more severe menstrual symptoms. However, more research is needed to fully understand these connections.  

Although research investigating the role of the gut microbiota in fertility is still in its infancy, some studies suggest that gut dysbiosis may be linked to infertility in both men and women. Specifically in women, gut dysbiosis may lead to vaginal and uterine dysbiosis which negatively affects endometrial receptivity, interfering with embryo implantation.^6,7  

During pregnancy, rising levels of oestrogen and progesterone can slow digestion, leading to constipation and an increased risk of haemorrhoids (also known as piles).^8,9 Meanwhile, the maternal microbiome undergoes significant changes to support foetal development, particularly during the later stages of pregnancy when oestrogen levels peak. The composition and diversity of the gut microbiota have been shown to differ between healthy and complicated pregnancies, with dysbiosis linked to conditions such as gestational diabetes, pre–eclampsia and restricted foetal growth.^10,11

After childbirth, attention turns to the relationship between the gut microbiota and postpartum depression (PPD) via the gut-brain axis. PPD affects around 10-15% of women after childbirth and is marked by symptoms such as sadness, irritability, low mood and, in severe cases, suicidal thoughts.^12,13 Research shows that women with PPD tend to have a different gut microbiota when compared to those without, which may disrupt important signalling pathways in the body, including those associated with mood-regulating compounds such as short-chain fatty acids (SCFAs) and tryptophan.^14,15

Probiotics could potentially be used during and after pregnancy to support maternal mental health and reduce the risk of PPD. For example, one study found women who consumed a lactobacillus-containing probiotic during pregnancy and 6 months postpartum had significantly lower depression and anxiety scores in the postpartum period.¹⁶ While more research is needed to confirm these effects and identify the most effective strains, probiotics may be a promising tool for supporting perinatal mental health.  

Menopause is defined as the absence of menstrual periods for 12 consecutive months, which typically occurs between the ages of 45 and 55. During and after this transition, levels of oestrogen and progesterone decrease, which is accompanied by symptoms such as hot flushes, sleep disturbances, low mood and joint pain. 

Postmenopausal women tend to have lower gut microbial diversity and altered overall composition that more closely resembles that of men, compared to premenopausal women.¹⁷

Hormone replacement therapy (HRT) has shown promising potential in restoring microbial diversity and mitigating dysbiosis, but more research is needed to confirm long-term benefits and mechanisms.¹⁸

Through the oestrobolome, gut microbes can continue to influence oestrogen levels, which may help counteract the drop that comes with menopause. This makes maintaining a diverse gut microbiota especially important during menopause to support hormone regulation and symptom management.  

Download our Gut Health Habit Tracker, to keep yourself (or your patients) accountable for these gut health habits!  

The gut microbiota is emerging as a key player in women’s health.  

While research is ongoing, the current evidence shows that maintaining a balanced and diverse gut microbiota can support hormonal changes, symptom management and overall wellbeing.  

Small, consistent nutrition and lifestyle habits – such as eating more fibre, getting quality sleep, staying active and managing stress – can make a big difference when it comes to supporting the female gut microbiota across all stages of life.  

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2. Ma et al. (2020) Sci Rep 10(15792). 
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14. Zhang et al. (2023) Ann Gen Psychiatry 22(1), 36 
15. Liu et al. (2020) J Agric Food Chem 68(47): 13697–13710 
16. Slykerman et al. (2017) EBioMedicine 24: 159-165 
17. Peters et al. (2022). mSystems, 7(3), pp.e00273-22 
18. Jiang et al. (2021) Front Endocrinol 12: 794496