Gut microbiome dysbiosis and women's hormones

March 2022
By Talida creator of Hazel & Cacao

Talida of Hazel & Cacao

The field of gut health is relatively new in science and recently microbiome research has exploded, however there is still much that is unknown. My aim for this article is to outline the main types of gut imbalances that can occur and the consequent hormone imbalances that usually follow.

The gut microbiome is a collection of trillions of different micro-organisms living inside the intestinal tract. While bacteria have been the main focus of research in the last few years there are also viral, fungal, protozoa biomes as well, all of which should live in harmony with one another and our bodies. The microbiome is responsible for digesting the foods we eat as well as absorbing and synthesising nutrients. It also plays a huge role in regulating hormones, metabolism, immunity as well as mood and brain health (10). Any imbalance in the gut microbiome or “dysbiois” can lead to digestive discomfort and influence many different disease states.

So how does the microbiome become imbalanced? Some people may be born with a disadvantaged microbiome eg. by being born via c section (so they are not exposed to the beneficial bacteria within the vaginal canal) or were not breastfed (as breastfeeding feeds and diversifies the microbiome). Other things that can interfere with the microbiome is the widespread and repetitive use of antibiotics (1) as well as pain relief drugs like NSAID’s and other medications like PPI’s, antidepressants (2) and hormonal birth control, specifically oestrogen-containing hormonal birth control and HRT methods (3). Diet and lifestyle factors such as stress, anxiety, depression, alcohol, smoking and exercise also impact and change the gut microbiome, in fact, the diet itself is the largest contributing factor to gut dysbiosis (4). Generally speaking diets high in sugar, animal protein and saturated fat starve the microbiome or cause an overgrowth of unwanted microbes. Furthermore, people who do not eat enough e.g. eating disorders or undergo elimination diets or restrictive weight loss diets for prolonged periods of time also starve the microbiome of beneficial bacteria (11). In contrast, a diet rich in a wide variety of fibre containing plant foods and resistant starch (prebiotics) and a small amount of fermented foods (probiotics) feed beneficial gut bacteria and improve microbial diversity (10). Fibre and resistant starch feed the microbes in the gut which in turn create various compounds known as short chain fatty acids. These short chain fatty acids create a myriad of different healthful affects on the body including strengthening and maintaining the integrity of the gut lining and improving immune function. A diverse microbiome has been consistently associated with health and prevention of many chronic diseases (10).

There is no perfect microbiome because every microbiome is unique however problems can arise when there is variability in the quantity of some microbes in comparison to others. Broadly there are two main types of imbalances that can occur: 1. overgrowth of some bacteria or yeasts 2. absence or insufficiency of some types of beneficial bacteria or low overall microbial diversity.

Often but not always these imbalances feed and influence each other. For example an overgrowth of some bacteria will compete with nutrients needed from other bacteria to thrive, this then starves the other bacteria leading to lower diversity. IBS is a blanket term that relates to any number of these imbalances. In my opinion the term IBS can be considered interchangeable with dysbiosis.


Dysbiosis generally starts in the large intestine because the large intestine houses the largest number and concentration of microbes. An overgrowth of opportunistic bacteria (usually gram negative bacteria which secrete endotoxins called LPS) (15) can move up and down the GI tract. It can lead to a disrupted vaginal microbiome which can cause recurrent vaginal infections eg. thrush or can move up and cause SIBO (small intestinal bacterial overgrowth. SIBO is defined as a bacterial population in the small intestine that exceeds the norm (5) the type of bacteria present can influence the type of symptoms felt. An overgrowth of bacteria in the small intestine is one of the factors that can sometimes lead to “leaky gut” or “increased intestinal permeability.” Leaky gut occurs when the integrity of the gut lining in the small intestine is compromised, this means that different food particles and byproducts that should remain in the intestines can leak through the intestinal wall and into the blood stream. This causes wide spread inflammation and activates the immune response.

The large intestine is home to the estrobolome, which is a specific subset of bacteria responsible for managing the excretion and absorption of oestrogen. An enzyme called beta-glucuronidase is responsible for unpacking the inactive oestrogen that was packaged by the liver reactivating it and sending it back into the circulation. If there is too much of the bacteria that produce beta glucuronidase then too much oestrogen can re enter the circulation (9). The liver and the gut are the main organs responsible for excess oestrogen, the ovary very rarely produces too much oestrogen. SIBO has also been shown to create B vitamin deficiencies, in particular vitamin B12 and potentially vitamin B6 (18) which is needed to help metabolise oestrogen properly in the liver, another reason why an overgrowth of bacteria leads to oestrogen dominance.

An overgrowth of microbes can lead to oestrogen dominance conditions like PMS, fibroids, tender breasts, heavy and painful periods. Leaky gut is greatly associated with autoimmunity and can lead to conditions like celiac disease, hashimotos thyrodities, graves disease and diabetes (13). Endometriosis is considered an autoimmune condition by some researchers and is greatly associated with SIBO and leaky gut (14).

Low diversity

low diversity of good bacteria is common even in the presence of an overgrowth of bacteria. Often the two occur together. Low diversity either of particular types of beneficial bacteria or low diversity on the whole is the basis of most gut imbalances. When there is low microbial diversity, certain fibres in plants become difficult to digest leading to digestive upset. The FODMAP’s approach identifies foods that contain certain type of fibres that people with IBS or digestive upset are most likely to react to. A reaction to any of the FODMAPS (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) usually means the certain subset of bacteria needed to digest any of the FODMAP fibres is in low supply or absent. Before much was understood about the microbiome a reaction to a FODMAP was generally seen as a “food intolerance” and many people were advised to avoid these foods altogether through elimination diets. (gluten containing grains are one of the most common FODMAPS, read my article on gluten and hormone health here)
We now know that elimination diets starve the microbiome of beneficial bacteria and lower microbial diversity leading to poorer health outcomes. The general thought process now is to carefully and slowly introduce dosed portions of FODMAPS allowing the body enough time to assimilate and adjust to the introduction of a new fibre and the microbes attached to it. Probiotics may also be beneficial although I believe the research on probiotics is still in its infancy.

In contrast to overgrowth, low diversity can lead to lower oestrogen and progesterone states. If there is not enough of the bacteria in the estrobolome to produce beta glucaronidase then it may be hard for the gut to create any additionally required oestrogen from plant foods. Low oestrogen is a problem for mood, vaginal integrity bone and heart health. Interestingly underweight women or women with eating disorders have much lower oestrogen levels likely due to caloric restriction and an unvaried diet. Women with PCOS have also been shown to have lower gut diversity than women without, and the higher the androgen count, the lower the diversity (16). Insulin resistance which is usually a driving mechanism behind PCOS is also associated with lower microbial diversity (17).

It can be very difficult to navigate dysbiosis, but we know that the gut plays a huge role in both hormone balance and metabolism. Based on the best available research that we have, the best way to ensure optimal gut health long term is to avoid microbiome disrupting agents like certain drugs, pesticides and herbicides, alcohol and tobacco, lower stress and focus on a diet that has a wide variety of different plant fibres and a small amount of probiotic foods like kimchi and yogurt etc. At a minimum experts are recommending 30 different plants a week, however different fibres should be introduced slowly and thoughtfully as to not create major digestive upset. The microbiome needs time to repopulate with beneficial bacteria. High fibre diets is one the main reasons people struggle in transitioning to a plant-based diet as the microbiome is not used to all the new plant fibres coming in. Following regular eating times (usually 3 meals a day) is also important to set the circadian rhythm of the microbiome and also giving the digestion adequate time in between meals to break down food properly. In the case of overgrowth of negative bacteria sometimes treatments are necessary either with herbal antimicrobials or pharmaceutical medicines. Probiotics can also be utilised but all of this should be done under the guidance of a professional.


Recipes to explore:

Resistant starch:
Breakfast recipes:

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