When I was in the thick of my SIBO journey, my hormones were cray cray. My thyroid hormones were in the tank, my cortisol levels were through the roof and my period had been absent for over a year!

This pattern of low thyroid hormones, high cortisol levels and low sex hormones is so common in my SIBO clients. The connection between hormonal health and gut health is indisputable. This leads to the question, does hormone dysfunction cause SIBO or does SIBO cause hormone dysfunction?

The hormone-gut connection is a prime example of a chicken or egg scenario. It can be very hard to determine which came first. But, you can anticipate that if your gut is out of balance then your hormones will be out of balance and vice versa.

Addressing hormone imbalances with diet and lifestyle interventions should be a top priority during SIBO treatment. Many SIBO sufferers and even practitioners get too wrapped up with a killing and clearing mentality that they fail to address the underlying root causal factors. One of the biggest of these missed factors is hormone imbalances.

Not only is the hormonal piece of the puzzle ignored, many SIBO sufferers hop on restrictive SIBO diets to starve the bacteria which can create imbalances and exacerbate any pre-existing hormone issues. There are 2 main reasons why SIBO diets are hard on your hormones:

  1. Many SIBO diets are too low carb in an effort to starve the bacteria

  2. Many SIBO diets are overly restrictive, which can lead to unintentional undereating

Low Carb Problems

Having enough dietary carbs is crucial for proper levels of cortisol, thyroid and sex hormones. Woman tend to be even more sensitive to hormonal imbalances when on low carb diets compared to men.

Here is what happens when you eat too few carbs.

First, your blood sugar can dip and your body addresses this by releasing cortisol, aka your fight or flight hormone. Cortisol promotes a process called gluconeogenesis, which involves breaking down protein to make glucose.

Second, your ability to activate thyroid hormones will be blunted leading to leading to hypothyroid symptoms. Insulin is a hormone that is released when we eat carbs and it is also responsible for converting the inactive thyroid hormone (T4) into its active form (T3). With lower levels of active thyroid hormones, you can feel fatigued, depressed, bloated and constipated. Hair loss, weak nails, dry skin and weight gain are also symptoms of low thyroid hormones.

Third, your sex hormones will be down regulated. Sex hormones are highly sensitive to metabolic reserves. Making a baby is the most metabolically expensive process that a human experiences. Your body will shut down reproduction if it believes the necessary amount of fuel is not present to sustain a healthy pregnancy.

Insulin serves as a signal to the brain that their is enough available short term resources for you to produce a baby. Like I said before, insulin is released in higher amounts when we eat carbohydrates. Low carb diets produce a much lower insulin response. Low levels of insulin will tell the brain that you don’t have enough short term fuel to produce a baby.

Lara Briden, a hormone expert, discusses on this podcast how woman need the right amount of carbs and calories to ovulate and to be fertile. She explains that the hypothalmus in our brain actually has glucose sensing receptors that require a certain level of carb intake to ovulate.

That is why many woman will not have periods or lose their sex drive when they are eating too low carb. This carbohydrate set point varies from woman to woman, but many SIBO diets easily slip below the amount of carbs you need to have balanced sex hormones.

Carbs are not the enemy and having the right amounts in your diet can help keep you your hormones healthy.

When restrictive diets lead to undereating

Unintentional under eating is quite common when you are on a restrictive diet and can lead to further hormonal troubles. If you aren’t eating enough food, your body has been evolutionarily programmed to conserve fuel. Your thyroid hormones start to down regulate, cortisol rises and reproductive function starts to shut down. Your body is trying to help you survive, but these shifts will make you feel awful.

Chronic undereating is often more obvious in woman, because like eating too low carb, underrating will cause irregular periods. While insulin is a signal of your short term energy, leptin signals that you have enough long term energy stored for reproduction.

Leptin is produced by fat cells and you must have a body fat percentage high enough to produce enough leptin to signal that long term reserves are adequate. Many SIBO patients lose weight on restrictive diets and from malabsorption, which can lead to  depletion of body fat and lower leptin levels. Therefore, having too low body fat leads to absent periods and low sex drive.

For woman, having your period every month is like a report card for your health. If you are not having your cycle regularly, then a stressor is preventing ovulation. Missing a cycle every once in awhile due to some sort of stress isn’t a huge deal, but when you are regularly experiencing irregular cycles you need to dig to the bottom of why your cycle is absent.

For men, hormonal imbalances may not be quite as obvious, but there are definitely signs that your hormones may be running low like fatigue and low sex drive.

Tracking your calories to ensure you are achieving an adequate intake level is a good first step to supporting your hormonal health through SIBO treatment. Working with a practitioner can also be important to help you determine the right amount of calories and carbs you need to eat to support your hormones.

Above we have discussed how diets can effect hormones, but lets dive deeper into how inflammation in the gut, SIBO and general dysbiosis can have negative effects on your hormones.

Thyroid-Gut Connection

I have written extensively about the thyroid and gut connection in the past. But, I would like to briefly touch on this again.

If your gut is imbalanced and inflamed, your thyroid function will be suppressed in a couple different ways.

First, 20% of your thyroid hormones are activated in the gut. Bacteria along your GI tract produce a special enzyme that can convert T4, the inactive thyroid hormone, into T3, the active thyroid hormone. If your gut bacteria are off, the conversion to the active hormone will be reduced.

Second, endotoxins (LPS) produced by gut bacteria have been shown to negatively effect thyroid function. When you have poor gut barrier function (leaky gut), these endotoxins enter the bloodstream in high amounts and these toxins can then reduce the conversion of T4 to T3 in the bloodstream. These endotoxins can also reduce the number of thyroid receptors on your cells, which prevents thyroid hormones from producing their desired physiological effects.

Third, inflammation from the gut will raise cortisol levels. Cortisol downregulates thyroid hormone synthesis and activation.

Thyroid dysfunction can also be a root cause of SIBO. Like I said before it’s hard to tell what comes first, hormone imbalances or gut problems! Hypothyroidism can cause disturbed motility and inhibit MMC activity.

Dietary factors like iodine, selenium, iron, zinc, vitamin A, tryptophan and enough carbs/calories also are needed for healthy thyroid function.

Cortisol-Gut Connection

The connection between the brain and the gut can alter our cortisol levels and our response to stress. The bacteria in your gut communicate messages to the brain via the vagus nerve.

As I have mentioned in previous posts, the vagus nerve mediates our stress response by activating our parasympathetic nervous system aka our “rest and digest” system. This counteracts our sympathetic nervous system, which is responsible for our “fight or flight” response. This fight or flight response will shut down the digestive process and cause inflammation in the gut.

Patients with IBS and IBD have been shown to have weaker vagus nerve function compared to those without gut issues. This weak vagus nerve functioning can stem from perceived stress from the brain and/or from inflammation and dysbiosis in the gut.

To cultivate healthy vagus nerve function you need to address emotional stress/trauma while also addressing inflammation in the gut. The brain gut axis is a two way street.

Let’s first look at how the gut environment effects the stress response. Dysbiosis, leaky gut and inflammation in the GI tract will cause cortisol dysregulation and activate your sympathetic nervous system in a number of ways.

Toll Like Receptors in the gut can scan the environment of the gut sensing endotoxins (LPS) and metabolites levels. This information is then relayed to the brain via the Vagus Nerve. Endotoxins (LPS) have been shown to activate the hypothalmus-pituitary adrenal (HPA) axis, which will raise cortisol levels.

The SCFA butyrate has also been shown to directly activate the Vagus Nerve. SCFA are metabolites produced when gut bacteria ferment fiber. It is important to have a healthy population of gut bugs to produce enough butyrate levels to activate the Vagus Nerve.

The good news is that altering the terrain in the gut with probiotic supplementation appears to helps tame the fight or flight response. Research on animals has shown that probiotics can reduce the stress response and stress hormones through vagus nerve activation. Probiotics also reduce inflammation and help strengthen the intestinal barrier, which will further blunt endotoxin release into the bloodstream that promotes systemic inflammation and cortisol release.

While a healthy gut is necessary for healthy cortisol levels, emotional and mental stress will also inhibit the vagus nerve and the sympathetic nervous system. This fight or flight activation will effectively shut down digestion, increase permeability and inflammation in the GI tract(which will only further exacerbate your stress response).

Addressing both stress and the gut is necessary to optimize cortisol levels.

Sex Hormones-Gut Connection

It is very common for SIBO sufferers to have symptoms like low sex drive, vaginal dryness, irregular cycles, infertility and horrible PMS. Like thyroid and adrenal hormones, sex hormones will be effected when your gut is not healthy.

An unhealthy and inflamed gut will indirectly influence sex hormone levels because thyroid hormones and cortisol levels become imbalanced. These hormones need to be balanced to have healthy sex hormone levels.

But, what surprises a lot of people is that gut bacteria directly influence metabolism of sex hormones.

There are certain bacteria in the gut that play a role in estrogen metabolism and these bacteria are collectively called the estrobolome. These bacteria produce an enzyme called beta glucuronidase that activate estrogen freeing it to be used by our cells.

Therefore, to maintain a healthy level of estrogen in the body, you need to have a healthy level of beta-glucuronidase producing bacteria. If you have too much of these bacteria, estrogen dominance develops and all the nasty symptoms that comes with it. But, not having enough of these bacteria has been associated to PCOS (polycystic ovarian syndrome), a condition marked by low estrogen levels and high androgen levels.

Estrogen isn’t the only hormone that can become imbalanced. Testosterone levels can often become effected when your gut is inflamed. Leaky gut can lead to trans mucosal migration of endotoxins from the gut to the testes, which will result direct decrease in production of testosterone. If your sex drive has been non-existent, low testosterone levels may be at play.

Bottom Line

If your gut is imbalanced, then your hormones will be too. Treating SIBO and fixing large intestine imbalances will help you regain hormonal harmony.

You also need to make sure that your pursuit of SIBO clearance is not exacerbating hormonal issues. It is so so crucial to support hormones during treatment.

Need help finding hormonal balance while addressing your gut?

Contact me to schedule a free 20 minute consult to see if I can help!





  • Hey Amy, I read your posts about spore probiotics and I’m considering trying out one. I came across some articles about how spores might actually turn pathogenic in the gut if there’s not enough good bacteria to keep the spores under control. I also read that the spores might be harmful because we’re not normally consuming them anymore. What are your thoughts? The spore probiotics seem really intriguing but I’m scared of possibly causing more harm.

    Another question: I’m currently treating dysbiosis and a possibly pathogenic bacterial overgrowth in the large intestine with herbals. I know feeding sibo with prebiotics makes it easier to eradicate, do you think this applies to large intestine bacteria aswell? 🙂 I tried to google it but didn’t find anything. Thanks!

    • Spore forming bacteria are the most widely used probiotics in the world (not in the states, but worldwide). In my opinion, they are very safe. It is great that you are researching up on them! I have never seen them become pathogenic in any clients. If you are still having apprehensions you can try Bifido Maximus probiotic that is D lactate free and usually well tolerated instead of the spores.

      In terms of your LI overgrowth, that is a good question. I am not 100% sure. But, prebiotics tend to be very helpful balancing out the GI tract with good bugs versus bad ones.

      • Do you have any idea if saccharomyces boulardii or streptococcus thermophilus are D-lactate free? What about water kefir? Do you have experiences with s.boulardii in general? I’m suspecting I have an issue with D-lactate-producers so I’m trying to find a safe one.