What’s happening in your gut can affect your hormones, metabolism, and thyroid function — and gut inflammation is often the hidden driver behind symptoms women assume are “just” thyroid, PMS, or menopause. Today I want to challenge how we classify these symptoms, because so often the real cause is a gut-related problem.
Let’s look at why we investigate gut health with our patients, rather than stopping at hormones or thyroid function alone.
IBS and intestinal permeability affect:
IBS and intestinal permeability become a problem for thyroid hormone function, largely because T4 converts into Free T3 through the gut (see the diagram below). If there is intestinal permeability, constipation, diarrhoea, autoimmune dysfunction, or poor immune function, this affects the T4 conversion into active Free T3.

Active Free T3 is the active metabolic hormone that is important to every organ and cell in the body — it provides energy and a strong metabolism. Poor gut function can also lead to poor absorption of essential nutrients important to thyroid function, like iron, B vitamins, zinc, and many others.
Nutrient deficiencies have a major draw-down effect on the metabolising function of the thyroid and can leave many women feeling depleted. This is why, when treating patients with thyroid problems, we look at the conversion from T4 to active Free T3 (something T4 medication doesn’t necessarily do) and at micronutrients. We even see patients with hyperthyroidism who are suffering weight gain — poor gut function and nutrient malabsorption are often key parts of the puzzle.
IBS symptoms can worsen during the premenstrual phase. Falling oestrogen and progesterone alter gut motility, change the microbiome, and increase inflammation, which can worsen IBS symptoms. Vice-versa, underlying IBS can worsen hormonal symptoms — many women with IBS experience constipation or diarrhoea the day before and the first two days of their bleed.
Bacteria overgrowth can lead to pain, bloating or distention, increased intestinal permeability, diarrhoea, fatigue, nausea, reflux, and feeling full or uncomfortable shortly after eating. IBS is an umbrella diagnosis describing a set of digestive symptoms that can result from different underlying drivers — it’s typically diagnosed when people suffer from diarrhoea, constipation, alternating between the two, and bloating. IBS is often caused by bacteria overgrowth or increased intestinal permeability.
There are two key reasons women are sensitive to gut inflammation between 38 and 65 years of age:
We’ve written more about what triggers bacteria inflammation during peri and post menopause — you can read that here.
Intestinal permeability causes inflammation and contributes to gut dysbiosis (an imbalance of good and bad bacteria). For example, it’s often the leading cause of insulin resistance and increased androgens in PCOS, because of metabolic endotoxemia — a low-level elevation of circulating bacterial toxins that drive insulin resistance. But it’s not exclusive to PCOS; metabolic endotoxemia is quite common in women over 40 because of increased intestinal permeability.
Metabolic endotoxemia is when increased intestinal permeability allows particles — bacteria, waste, and antigens like undigested food proteins — to flow into the bloodstream where they have no business being. Lipopolysaccharides (LPS) are large complex molecules found only in gram-negative bacteria. LPS are endotoxins, and when absorbed they can cause a very strong overreaction of the immune system. Remember, 80% of your immune system lives in the gut. When LPS leaks into the bloodstream through a leaky gut, it causes metabolic endotoxemia — LPS levels two to three times higher than normal.
Symptoms of metabolic endotoxemia include:
A lot of these sound like thyroid or menopause symptoms, right? Yet many women overlook the connection between digestive symptoms and vitality, hormones, or inflammatory pain — or there are three or four doctors each looking at one issue, rather than connecting everything to the whole body.
Metabolic endotoxemia matters because it increases insulin resistance at a time when women are already becoming more sensitive to it. It also raises many inflammatory cytokines (pain) in the body, such as Interleukin-1, Interleukin-6, and Tumor Necrosis Factor-alpha. It’s believed LPS is a trigger for the onset of insulin resistance, obesity, and diabetes. This is why IBS and intestinal permeability need to be addressed from 40, when women are already more susceptible to insulin resistance as oestrogen declines.
Histamine is a stimulating neurotransmitter that can cause anxiety, agitation and headaches. Bacteria overgrowth can cause mast cell activation and histamine activation too, which produces these commonly labelled “PMS” symptoms. In our presentation on the Brain-Body Recalibration: The 4 Stages of Menopause, the third phase (between 50 and 57 years of age) is mast cell activation and high histamines as oestrogen decreases. This makes women vulnerable if they have intestinal permeability or IBS, and more likely to experience inflammation symptoms and weight gain due to metabolic endotoxemia. Combined with decreasing oestrogen, many women are diagnosed with osteopenia, arthritis, or osteoarthritis — which is why we encourage women to pay attention to their body at this time.
The gut microbiome strongly influences the metabolism of oestrogen. By fixing what’s happening in your gut, you can improve a lot of your symptoms. Gut dysbiosis bubbles underneath the surface and is more common than most women think. Rather than labelling the symptoms, we encourage you to ask, why?
If there’s something happening in the gut, like metabolic endotoxemia, then by supporting the digestive lining and secretory function of the gut, many symptoms — weight gain, pain, or digestive discomfort — stop. Metabolic hormones reset because the underlying cause has been addressed. The gut is so responsive it can be a game changer for general health.
When working with our patients, we look to:
To learn more, I encourage you to watch our webcast, A Deeper Look Into Thyroid: How Active Free T3 Conversion, Adrenal Function & Gut Function Affect the Thyroid. You can reserve a spot here: https://naturalhormonebalance.co/free-training-thyroid-gut-adrenal/.
If you’re ready to get help and want to learn more about how we can support you, please organise a free introductory consultation with us here.
Warmly,
Tiaan