How IBS and SIBO Can Affect Periods and Hormones

IBS, SIBO, and period problems.

Did you know that what’s happening in your gut can affect your periods and hormones?

In episode twelve of my podcast and YouTube video, I discuss small intestinal bacterial overgrowth (SIBO) and its role in IBS; how SIBO can drive or worsen endometriosis, insulin resistance, premenstrual mood symptoms, and the fibromyalgia of perimenopause; plus how to treat SIBO.

Also available wherever you get your podcasts.


Welcome back to the podcast. I’m your host, Lara Briden, a naturopathic doctor and author of the books Period Repair Manual and Hormone Repair Manual. It’s autumn in New Zealand, and I’ve just come back from a multi-day walk in Abel Tasman National Park, where I even managed a couple of ocean swims. It was a welcome break because I’ve been working really hard on my third book, which is all about troubleshooting metabolic health for women. Not just diet and exercise but all the factors, including, of course, digestive health—which is the topic of today.

In my latest podcast and YouTube video, I look at IBS and SIBO and how they can affect women’s health problems such as endometriosis, PCOS, premenstrual mood symptoms, and perimenopause.

Now, when it comes to IBS or irritable bowel syndrome and the menstrual cycle, there’s lots of information out there about how IBS symptoms can worsen during the premenstrual phase of the menstrual cycle. Which makes sense because falling estrogen and progesterone at the end of the cycle alter gut motility, change the microbiome, and increase inflammation, all leading to worsened IBS symptoms.

But in this podcast, I want to look at it all in the other direction. Specifically, I want to look at how an underlying problem with IBS or SIBO can drive or worsen certain women’s health conditions, especially endometriosis, PCOS, premenstrual mood symptoms, and the fibromyalgia of perimenopause.

If you have not heard of SIBO, it means small intestinal bacterial overgrowth and is the common situation of having too many bacteria in the small intestine where they’re not supposed to be. Most healthy gut bacteria are supposed to be down in the large intestine, doing their jobs there. Having a lot of bacteria—even the good kind in the small intestine can cause pain, bloating or distention, and—importantly—can cause increased intestinal permeability, also called “leaky gut,” which is the partial leaking of intestinal contents, including bacterial toxins, into the body. We’ll come back to intestinal permeability in a minute.

But first, let’s acknowledge that the symptoms of SIBO—namely pain and distension — are quite similar to the symptoms of IBS. And indeed, SIBO and other types of intestinal dysbiosis appear to be the underlying cause of a lot of IBS, but not all IBS. And that’s because IBS is not one thing but is instead an “umbrella diagnosis,” which means the term IBS really just describes a set of digestive symptoms that can result from different underlying biological drivers or mechanisms.

In that sense, a diagnosis of IBS does not really mean anything but is merely a label for symptoms. The best strategy for IBS is to try to identify and address the underlying biological driver, such as food sensitivities and/or the topic of today: SIBO.

Now, I mentioned that SIBO can increase intestinal permeability. Please understand that increased permeability can, in turn, cause immune dysfunction and inflammation. And that is the mechanism by which SIBO can drive or worsen women’s health conditions.

Especially endometriosis, which we looked at in episode 4 of the podcast, called “Endometriosis is a disease of immune dysfunction.” In that episode, I talked about the new research that found that endometriosis may be driven by immune dysfunction caused, in part, by bacterial toxins entering the pelvis via “intestinal permeability and gut microbiota-derived extracellular vesicles” — i.e. intestinal permeability. That makes sense because most women with endometriosis also have IBS, or, in many cases, SIBO, which, according to that research, could be driving their endo. Although, to be fair, the tight relationship between endo and IBS can also work in the other direction, with endometriosis lesions themselves affecting the gut and causing IBS symptoms.

Next, SIBO and intestinal permeability can contribute to the insulin resistance of PCOS or polycystic ovary syndrome. That’s because of something called metabolic endotoxemia, which is a low-level elevation of circulating bacterial toxins—called endotoxins—that can drive or worsen insulin resistance. And, of course, insulin resistance can be a big part of PCOS. Bigger picture, metabolic endotoxemia can drive or worsen insulin resistance in everyone—including people without PCOS. Which makes addressing SIBO and intestinal permeability a key part of a metabolic health or weight loss strategy potentially for anyone with insulin resistance, but especially for women in our 40s —or perimenopause—when we’re more vulnerable to intestinal permeability, insulin resistance, and abdominal weight gain.

Next, SIBO and intestinal permeability can drive or worsen premenstrual mood symptoms. I discuss that in episode 7 of the podcast when I talk about the role of mast cell activation and histamine in premenstrual mood symptoms. With the understanding that histamine is not only an immune signalling amine; it’s also a stimulating neurotransmitter that can cause anxiety, agitation, and headaches, i.e. premenstrual symptoms. And yes, SIBO can cause mast cell activation and high histamine, thereby contributing to premenstrual mood symptoms. What’s especially interesting is the relationship between mast cell activation, histamine, and estrogen. See my blog post, The curious link between estrogen, mast cells, and histamine—link in the show notes.

As I describe in the episode about premenstrual mood symptoms, histamine is not the only thing going on. There are also some very interesting dynamics with other neurotransmitters such as GABA and serotonin, but even they can be strongly influenced by what’s happening in the gut via the gut-brain axis. There’s also the fact that the gut microbiome strongly influences the metabolism of estrogen, which is a topic for another day.

Finally, I’ll say a few words about perimenopause, specifically about the muscle pain or fibromyalgia that can arise during women’s 40s, i.e. perimenopause. Some of that tendency to muscle pain could simply be the result of perimenopausal disturbed sleep and/or the loss of the natural anti-inflammatory benefits of progesterone and estrogen.

But SIBO and intestinal permeability can also play a role, especially because:

  1. intestinal permeability has been proposed as a primary underlying cause of fibromyalgia (I’ll put that citation in the show notes), and
  2. changing hormone levels— specifically falling estrogen — can significantly increase the risk of intestinal permeability. That’s because estrogen normally helps to maintain a healthy intestinal barrier via several mechanisms, including by thickening the mucus layer.

So. If you’re suffering in a later phase of perimenopause with weight gain, mood symptoms, and fibromyalgia, please consider whether SIBO and intestinal permeability could be playing a role. And know that by fixing what’s happening in your gut, you could improve a lot of symptoms.

Diagnosis of SIBO is primarily based on symptoms such as pain, diarrhea, constipation, fatigue, nausea, reflux, and most commonly, bloating or abdominal distension shortly after eating, especially after eating fermentable carbohydrates, ie. FODMAPs. That’s why SIBO is the most common cause of a FODMAP intolerance.

SIBO diagnosis can also be made by a breath test, which measures levels of hydrogen and methane, the gases produced by the bacteria.

In terms of treatment of SIBO, well, that would be its own episode! And also quite a large section in my upcoming book.

Broad strokes, conventional SIBO treatment usually involves a 10 to 14-day course of the antibiotic Rifaximin, followed, in some cases, by a prokinetic or motility agent.

Natural SIBO treatment is more multi-pronged and diverse, using antimicrobial strategies such as the famous herbal medicine berberine, as well as with antimicrobial probiotics such as Saccharomyces boulardii and antimicrobial diet changes like a low FODMAP diet. Followed by or in conjunction with strategies to reduce inflammation, such as curcumin and strategies to promote healthy gut motility, such as HCl digestive enzymes and/or fasting for at least four hours between meals. Fasting improves motility by activating something called the migrating motor complex, which helps to clear the small intestine of any remaining food or bacteria that may be present after digestion and absorption have occurred.

Another natural strategy for SIBO is to boost the neurotransmitter acetylcholine, which improves intestinal motility—just one of many interesting ways that acetylcholine improves metabolic health, by the way. If you follow me on social media, you might have seen some of my posts about the nutrient choline and how it boosts acetylcholine. Other ways to boost acetylcholine include getting enough thiamine or vitamin B1 plus supporting the vagus nerve and parasympathetic tone. Finally, one of the more popular natural prokinetic or motility agents is the herbal mix Iberogast, which, if you’ve had IBS, you may have tried.

In closing, I’ll just say how great it is that fixing the gut can improve problems with periods and metabolic health. Because the gut is so accessible and so responsive and fixing it can really be a game changer for general health.

As always, there’s a section in my forum at to discuss the episode. Chime in there with your knowledge, experience, questions, and your favourite SIBO resources and treatment protocols.

I hope that’s been helpful, and thanks so much for listening. Please share and leave a review. And I’ll see you next time when I’ll discuss the oh-so-controversial topic of food addiction.

IBS, SIBO, and endometriosis.
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