SIBO and Problems with Gut Health

Remember, this is educational information only and not medical advice (and I am not a doctor nor an expert on endometriosis). Always check with your qualified medical professional before making any changes to your treatment plan.

SIBO and Problems with Gut Health

Digestive problems are common in people with endometriosis

Many of us with endometriosis have digestive problems. According to the CEC’s website, they have their patients fill out a pre-operative questionnaire, and here are some statistics: “intestinal cramping and painful bowel movements occur in approximately 25% of patients; constipation occurs in 35% of patients and diarrhea occurs in more than 60% of patients.”

However, we don’t need to have endometriosis on our bowel to have digestive problems or problems with our gut health. It’s hard to know the exact number of people with bowel endometriosis, but I’ve seen some estimates put it at 10-20%. There are a variety of reasons why we can have digestive problems or problems with gut health. Some of these are related directly or indirectly to endometriosis, and some aren’t:

  • food intolerances
  • endometriosis inflammation
  • adhesions or endometriosis lesions on or near the bowel
  • low stomach acid
  • co-conditions like Crohns, colitis, gastritis, gut dysbiosis, or SIBO
  • chronic stress and not being in “rest and digest mode”
  • taking NSAIDS for pain management
  • and more
Scroll below for sections on SIBO as well as tips for helping your microbiome.

For more info

SIBO – Small Intestinal Bacterial Overgrowth

What is it?

While the large intestines have trillions of bacterias in them, the small intestines have relatively few. SIBO is as the name implies: the small intestines have an overgrowth of bacteria when they shouldn’t.

Contributing factors to SIBO can be NSAIDs, chronic stress, inflammation, constipation, bowel surgery, and more. For some of us, SIBO can be a co-condition of endometriosis and contribute to our endobelly, digestive problems, or non-digestive problems (as I saw in my own case, explained further below!) One very small study of 50 people with endometriosis found that 40 of them had SIBO.

With SIBO, it’s important to work with a qualified doctor who has experience with SIBO.

Testing for it

The most common way to diagnose SIBO is typically through a breath test which measures levels of different gases such as hydrogen and methane. Unfortunately, these tests are not very reliable and can be falsely negative at times, which means that you could still actually have SIBO even if the test shows as negative.

In my own case, because of this and the fact that I had symptoms associated with SIBO as well as many of the common contributing factors that may lead to it, my doctor didn’t do any SIBO testing on me and instead we did a treat-and-see approach. When the first round of treatment reduced my symptoms, she gave me a working diagnosis of SIBO and we did several rounds of treatment until my symptoms were gone.


Generally, there are 3 treatments for SIBO: antibiotics, antimicrobials, or an elemental diet. Some doctors may also put the patient on a low FODMAP diet while treating with antibiotics or antimicrobials.

While each treatment type had been shown to reduce SIBO, they have different pros and cons, costs, accessibility, etc. Some doctors find antimicrobials to be a helpful first-line treatment, because these can also address gut dysbiosis in the colon as well.

Unfortunately, SIBO may need multiple rounds of treatment, as it can often recur in patients.

For more info

  • SIBO Info“The place for all things SIBO”, an educational website by Dr. Allison Siebecker, ND, MSOM, LAc, a leader in the field of SIBO.

  • Low FODMAP diet -This diet has been beneficial to many people with IBS or SIBO and may be worth researching if you have digestive problems, although it’s not recommended to follow this diet more than a few months. Cutting out FODMAPs long term hurt gut health. Monash University is one of the leaders in this diet and their app is helpful!

  • All about SIBO: Small Intestinal Bacterial Overgrowth – from Lucy Mailing PhD

Tips for helping your gut microbiome

What is the gut microbiome?

The gut microbiome varies from person to person. People may have 300-1000 species of bacteria in their gut microbiome, and it’s estimated that the gut has about 100 trillion bacteria total! Lucy Mailing PhD says that if we pick any 2 people, on average they will only have about 1/3 of the same gut bacteria. The other 2/3 will vary drastically due to their genetics, environment, diet, antibiotic use, mode of birth, and other factors. Due to that variation, there probably isn’t a specific universally healthy microbiome. She says “At the moment, a healthy microbiome is probably the microbiome you have when you’re healthy!”

While scientists are still working to understand more about the microbiome, we do know that gut infections are not part of a healthy microbiome. Things like parasites, fungi, and pathogenic and opportunistic bacteria, etc, need to be treated.

How do we try and keep our microbiome healthy?

That’s going to be individual to each person depending on their microbiome and what it needs, but there are some general ways we can help our gut:

-Treat any gut infections.

-Reduce our stress, especially chronic stress, so that our body is in rest-and-digest mode rather than fight-or-flight mode.

-Make sure we have good digestion, which involves having enough stomach acid.

-Look at our diet. Our diet greatly affects our gut microbiome, and over consumption of ultra-processed foods, sugar, and highly refined carbs can inflame the gut, so limiting these and instead prioritizing a variety of nutrient dense food. It’s not about never eating dessert (for example) again – it’s about our overall eating pattern. We don’t need to be scared of a donut or chips, but instead we can limit these, prioritizing and eating much more nutrient dense food as the foundation of our diet.

-Eat enough fiber. Fiber is vital for gut health and also is associated with health benefits outside of GI tract. Eating enough fiber can help with constipation, bowel regularity, diarrhea, and more. If we can, eat more plant foods and a diversity of them. Fiber is found in foods like vegetables, fruits, nuts, legumes, and whole grains. We can buy fruits and vegetables frozen or canned – we don’t need to just buy raw produce.

There’s different types of fiber like fermentable and unfermentable fibers, soluable and insoluble. Different types of fiber may cause GI upset for some people, so if we have digestive problems, we may need to figure out which types of fiber are the easiest for us to digest. If we’re increasing our fiber intake, it’s recommended to do so slowly, as well as increase our water intake and this may help avoid or minimize GI upset

-Doing major health behaviors like getting enough sleep, getting enough daily movement, getting sunshine, socializing, etc.

It’s easy with our health to think that we aren’t doing enough, or to put too much focus on what we think we are doing “wrong” vs what we are doing well. The goal isn’t to go down every single rabbit hole, or blame ourselves, or stress ourselves out trying to make 100 changes to our lifestyle at once, but rather to have more awareness of how our lifestyle impacts our health.

For example, if we have trouble getting adequate sleep, we can identify that as an area we want to work on, but without blaming or judging ourselves. We can spend the time it takes to address that and figure out what works for us: what feels natural and easy to follow. Once we’ve made that into our new habit/way of living, then (should we choose to) we can look at another aspect of our health. It’s important to have patience and compassion with ourselves while making any changes, because modern life can be hard and we are doing the best we can.

Should I get a stool sample?

Not everyone needs a stool sample. That’s something you can speak to your doctor about and decide depending on your symptoms and situation.

There is a difference between a comprehensive stool sample vs a standard stool sample. A comprehensive stool sample will go a lot more in depth than a standard stool sample. Depending on the test, they can look for bacterial and pathogenic overgrowth, parasitic pathogens, fungi/yeast, inflammatory markers, immune markers, beneficial bacteria, and more. Different stool tests can have pros and cons (in terms of what they look for, the method used, their reliability, etc), and some doctors use a combination of different stool tests along with other methods and your symptoms to get a big picture of a person’s gut health.

A stool sample is just a snapshot of the bacteria in your stool, and this may not be reflective of the bacteria in your actual microbiome. That science is just not there yet, so be wary of the different claims that certain tests or practitioners make.

What doctor can help me with my gut health?

It will depend on what you are looking for. Some people may see a GI doctor, naturopath, or functional medicine doctor – but the important thing is the person you work with has experience and expertise in addressing gut health, SIBO, or whatever you are trying to treat. There is often a lack of evidenced-based medicine with naturopaths and functional medicine doctors, so make sure to research before choosing one of those doctors should you go down that path.

Taking probiotics

Probiotics are defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host” (Hill et al, 2014).

We hear often that probiotics are supposedly great for XYZ, so one might wonder if they need to take probiotics? And the answer is no, you don’t have to. What you need is individual and depends on your own gut microbiome and gut health.

There’s actually conflicting opinions on whether probiotics are even needed for healthy individuals, with some researchers now saying that they aren’t needed. We often hear that we should take probiotics alongside antibiotics, but new research suggests that probiotics may actually slow recovery of the normal microbiome after antibiotics. I’ve linked a write up below on this from Lucy Mailing PHD.

Probiotic benefits are strain specific

Evidence is actually showing that the benefits a person can get from probiotics are disease specific and strain specific. Various probiotics have been studied in randomized placebo controlled human trials for their efficacy and safety for IBS, skin conditions, anxiety, depression and more.

So I think an important question if you are thinking about probiotics is “Why do I want to take probiotics? Am I looking to help a certain condition?” If so, look to see if a specific strain has been found in studies to be beneficial for it.

If you are using a probiotic that claims to have certain health benefits, there should be evidence on that strain to back up those claims, and hopefully even on that specific product. However, my understanding is that there’s not a general consensus on which specific probiotics are the best for which conditions.

Fermented foods

Some fermented foods can have microorganisms in them. My understanding is that the ones that have been properly fermented and contain live bacteria may be beneficial for gut health for some people. You don’t have to eat fermented foods, but if you like them, things like raw sauerkraut, kimchi, kefir, kombucha, etc, can be a delicious way to potentially help your gut microbiome.

Gut problems can cause non-digestive symptoms too

The gut is involved in more than just digestion and can influence conditions that we don’t normally associate with the gut, such as obesity, skin problems, rheumatoid arthritis, autoimmune problems, anxiety, depression, brain fog, histamine intolerance, and mast cell activation syndrome. (Although this doesn’t mean the gut is playing a role for every person with these conditions).

In fact, what recently led me to address my gut health was mast cell activation syndrome. After taking antimicrobials for gut dysbiosis, and then doing several rounds of SIBO treatment, my racing heart, migraines, anaphylaxis, insomnia, and rosacea either greatly diminished or ceased. And interestingly, both my IC pain and my fibromyalgia pain vanished after treating SIBO! Although I will say that I was using Curable (a pain psychology app) over those same 8 months so I can’t be sure if it was the SIBO treatment or the pain psychology app or both, but I strongly suspect it was treating SIBO because food has always been my biggest fibromyalgia trigger. And now food that previously caused me fibromyalgia flares doesn’t cause me any fibro pain at all! (And 2 years has gone by and I’m still pain free!)

Gut health can play a huge role in different symptoms, but it doesn’t mean it’s playing a role in your symptoms

There’s a lot of talk nowadays about gut health, “healing your gut”, and that the gut is related to various health problems. For some of us with endometriosis, addressing our gut health might be a big puzzle piece to improving our quality of life, but for others, our gut health may be fine, and therefore our time, energy, and money may be better spent doing pelvic floor therapy, or seeing a trauma-informed mental health professional, or going on HRT, or something else that will make a bigger impact.

When it comes to endometriosis, excision surgery continues to be the gold standard treatment for endometriosis and the cornerstone to a multidisciplinary approach to treatment. Also, poor gut health is not a root cause of endometriosis. In spite of what some misinformed websites say, addressing your gut health will not heal the disease.

Addressing gut health is individual

If you think your gut health might be playing a role in some of your symptoms, that’s something you can explore. But remember that the way you address your gut health will be individual and depend on what your body needs, so don’t feel pressure to do every single suggestion that you come across, like taking probiotics, eating fermented foods, drinking bone broth, etc.

I’ve worked on my gut health 3 different times over the last 15 years, and each time the reason why and the steps I took to help my gut health were different. The following are examples of how varied my gut problems have been over the years and how the approach to each problem was different. However, I’m not implying that anyone with similar problems do the exact things I did. Again, what each person will need for their gut health is individual.

In my late teens, I was having diarrhea 25x a day.

I still don’t know what caused this, but it went on for almost 2 years until I changed my diet (I went Paleo). This drastically reduced my diarrhea down to a few times a day, and over the next few years, my diarrhea decreased even further as I brought bone broths and fermented foods into my diet. I also learned to make a relaxing environment around eating with no rushing to help myself into a state of rest-and-digest at mealtimes.

In my late twenties, I was diagnosed via endoscopy with gastritis.

I believe this was from taking NSAIDs often for endometriosis pain management. For the next few months, I helped my mechanic digestion by only having soups and smoothies, and I used digestive enzymes and HCL to help with chemical digestion. I also used other supplements like DGL and aloe. I had to stop taking NSAIDS too. The gastritis healed within a few months, but I can no longer take NSAIDs because it still causes me acute gastritis symptoms.

In my mid 30s, I had the onset of mast cell and histamine intolerance.

In my case, this has multiple contributing factors that I’m working on, but one of the biggest ones seems to be my gut health. A stool sample which showed I had gut dysbiosis and an overgrowth of opportunistic bacteria, as well as giardia. Working with a doctor, we did 2 months of herbal antimicrobials and then 2 months of probotics. This diminished my symptom severity but they didn’t go away completely.

Based on my symptoms, my doctor gave me a working diagnosis of SIBO, and we did a treat-and-see approach using a different set of antimicrobials. With each treatment round, my symptoms continued to improve, so we did 6 rounds total over a year.

I believe part of my gut dysbiosis/SIBO was due to endometriosis lesions/inflammation affecting my peristalsis, and having bowel surgery.

I always had painful bowel movements during my period.

These became excruciating as I got older. I also would have bowel spasms and during the first few hours of my period, I’d poop 15-20 times. The year prior to excision, I started throwing up during those bowel episodes too. During my excision surgery, the surgeon found that part of my intestines were fused to my pelvic back wall and narrowed to a third of their width, causing a partial bowel blockage. After the surgeon excised my bowel endometriosis as well as fixed my distorted anatomy, I no longer have any bowel spasms nor painful bowel movements, nor do I vomit anymore during my period!

For more info