My gut history (IBS, SIBO + more!) - Part III

The incredible thing about our bodies is that they adapt and change over time (in fact every 7 years you are a completely different human on a cellular level - WOW!). In addition to changes in our bodies, our circumstances (physical environment, stress, family and home situations, etc) are also always changing. So especially when it comes to gut health, and especially for those with more sensitive systems, what works and makes us feel good in one moment may not work a few months or years later.

In this third post of my gut health history series, I’m sharing where I’m at right now with my gut and gut healing. As I shared in the first post in this series, my symptoms began to worsen the last year, and so I’ve made it my priority to focus on what these symptoms are telling me.

In case you missed it, check out the first two posts in my gut history series here:

My Gut History (IBS, SIBO + MORE!) - Part 1 - How it all Started + Symptoms

My Gut History (IBS, SIBO + MORE!) - Part 2 - What I’ve Tried in the Past

Quite a bit of this post will talk about SIBO, or Small Intestinal Bacterial Overgrowth. SIBO is HOT right now in the digestive health world - people are being diagnosed left and right. Like with gluten intolerance or IBS, I’m not sure if the increase in diagnoses is because there’s more information available about this condition, or if it’s become the new catch all condition, but many many people are dealing with similar symptoms and protocols.

Side note: I’m not 100% sure that I have or had SIBO. I’ll talk about this more below but most all digestive disorders are tough to clearly diagnose AND often issues overlap. IBS can cause SIBO, SIBO can cause IBS. A food allergy can manifest as a skin condition, as can a parasite, or straight up anxiety.

Please do not let the nuances and complexity of the gut and your symptoms deter you from moving forward. Please do not let “failed” treatments rob you of hope. Instead I encourage you to take each step of your healing process in stride, each protocol or supplement regime or test an opportunity to gather more information from which you can build a stronger, happier, more balanced foundation.

As always, I share not as a doctor or medical professional, but as a human having a human experience in hope that what I write may provide you with a spark of insight or inspiration or hope that supports your own healing process. Please read my full disclaimer here.

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Small intestinal bacterial overgrowth (SIBO) is defined as the presence of excessive bacteria in the small intestine.

Bacteria in our bodies is not a bad thing; in fact, there are more bacterial cells in your body than human cells (there are roughly 40 trillion bacterial cells in your body and only 30 trillion human cells). Your microbiome (the community of bacteria that live inside and on our bodies) plays a crucial role in many bodily functions including digestion and nutrient absorption, immunity, metabolism and brain health.

Most of the bacteria in your digestive tract is located in the large intestine (also called your colon). This is where these bugs assist in the final stages of the digestive process. With SIBO, too much bacteria has found it’s way into the small intestine, where it neither has a place nor a function.


Symptoms of SIBO include:

  • Abdominal bloating**

  • Abdominal pain and cramps**

  • Constipation, diarrhea or both**

  • Gas (belching and flatulence)**

  • Heartburn and/or acid reflux**

  • Nausea**

  • Food sensitivities**

  • Headaches**

  • Joint pain

  • Fatigue**

  • Eczema, rosacea or skin rashes**

  • Anxiety and depression**

  • Malabsorption / nutrient deficiency (especially iron or B12 deficiencies)

  • Weight Loss**

**All symptoms I’ve experienced as shared in the first post of this series

The main symptoms of SIBO are those of IBS (Irritable Bowel Syndrome), which is why more and more people who were told they have IBS and there’s not too much they can do about it are now being diagnosed with SIBO (which can be a good thing, since with SIBO there are more treatment options).

SIBO is also related to many other disorders such as leaky gut, Crohn’s, ulcerative colitis, Hashimoto’s and more, both as an underlying cause or as the effect of the pre-existing disease - which can make treating it complicated, individualized and nuanced.

For a full list of symptoms and associated conditions, click here.


Sure, diet can trigger SIBO symptoms to flare, but the underlying cause of this condition often is not just a result of the food you’re eating.

One cause of SIBO is low stomach acid. We’ve been taught to think that stomach acid is bad, and it is in excess, BUT acid plays an important role in both the digestion of food and how our body rids itself of harmful bugs and pathogens. Regular or frequent use of antacids can result in reduced stomach acid, which means it’s harder for your body to digest your food, and that you’re more susceptible to harmful invaders.

Another cause of SIBO is a dysfunction in the migrating motor complex (MMC).

What is the migrating motor complex? The MMC are waves of electrical activity that sweep through the intestines in a regular cycle during fasting. These motor complexes trigger peristaltic waves, which facilitate transportation of indigestible substances such as bone, fiber, and foreign bodies from the stomach, through the small intestine, past the ileocecal sphincter, and into the colon.

The MMC occurs every 45–180 minutes during the interdigestive phase (i.e., between meals) and is responsible for the rumbling experienced when hungry. It also serves to transport bacteria from the small intestine to the large intestine and to inhibit the migration of colonic bacteria into the terminal ileum. [Wikipedia]

In other words, your MMC is responsible for "housekeeping" in your gut - it sweeps residual undigested material and toxins through the digestive tube so that they’re properly eliminated.

Get this: the most common cause of low MMC function is food poisoning. When harmful bacteria enter the small intestine they release a toxin that kills the immune cells that trigger your MMC. Symptoms of this may take weeks or months to show up, which is why doctors don’t always link symptoms to SIBO or the food poisoning.

The second cause of MMC dysfunction is structural - a kinking of the intestines, a stricture (narrowing) from abdominal surgeries (hernia, C-section, appendectomy, endometriosis, etc) or other organs pressing on the intestines. Think of your intestines like a garden hose - if the hose gets kinked, folded or pressured, waste cannot flow freely through.

Additionally, while I have NOT found solid research on this, I believe another cause of of MMC dysfunction can be prolonged use of laxatives or fiber supplements. Why? If you’re FORCING yourself to go (either through the use of these medications, or by excessive pushing in the bathroom), you’re not allowing the MMC or your digestive muscles to do their jobs. Eating disorders such as anorexia and bulimia can also result in low MMC function, known by some as “lazy bowel syndrome.”

When I learned this, a LOT of things clicked into place: my first major belly issues happened after I had eaten a questionable egg salad sandwich during a time in my life when my system was likely extra sensitive (freshman year of college). And after that I did tend to get constipated and relied on laxatives and supplements to go #2. I rarely allowed my belly to relax, and I didn’t trust it to do it’s job.

Finally, as mentioned above, SIBO can be linked to many other disorders. It’s still unclear in many cases whether it’s the cause or effect, but if you’ve suffered from IBS, leaky gut or hormonal imbalances such as Hashimoto’s, they may be connected to MMC dysfunction.


SIBO diagnoses have increased in the last few years - this apparent increase in prevalence may have occurred because readily available diagnostic tests have improved our ability to diagnose SIBO.

The main test for SIBO is a breath test that you can do from the comfort of your own home over a 2 or 3 hour period. You fast overnight and then drink a sugar solution (either glucose or lactulose). The test measures the levels of hydrogen and methane (gas!!) in your breath as the sugar solution makes its way through various parts of your intestines.

The SIBO breath test kit

The SIBO breath test kit

Two things to note about testing:

  1. There is no definitive consensus about what constitutes a positive result, so your diagnoses may depend on your doctor and which test you take. Glucose can only provide information on the first two to three feet of the intestines, because after that it’s absorbed into the body. Lactulose is the safer bet if you want to test for bacteria beyond that point, but can provide less clear results.

  2. False negatives are possible. There can be another bacteria in your gut that eats the hydrogen and methane gas, so gas levels will not show up as elevated even if in fact they are.

This is what happened when I took the test: my hydrogen and methane levels were not elevated enough to clearly conclude that I had SIBO. But my doc and I decided to move forward with SIBO treatment because of my history and symptoms, and the fact that if SIBO was in fact the case, we would need to treat that before addressing any other issues.


Digestive issues are complicated. There is SO much we don’t understand, and SO much more than simple science. I say that not to discourage you, but rather to empower you. If you’ve been diagnosed with SIBO this may just be step one in your healing journey - I know it is for me. Use this as an opportunity to learn more about your body and yourself, to truly examine your habits, but know that one round of antibiotics, or herbal antibiotics, may not be the cure all.

While a SIBO diagnosis and treatment plan may provide physical and emotional relief, this is rarely the only issue and there’s rarely a one-size-fits-all healing protocol

With treating SIBO, you have options. First, I recommend working with a practitioner (a doctor or naturopath) that you’re comfortable with and trust. I DO NOT recommend going at this alone - it’s important to have a professional who’s dealt with many cases and can see things in your tests and symptoms that you may not.

Additionally, I encourage you to go with your gut. If you’re not feeling great about taking antibiotics, find someone who will support you through a herbal protocol. And if your doc is pushing the herbal route but you’d rather just go at it with drugs, do that.

When I shared on social media that I was taking the antibiotic route (versus herbal) I got some push back. Why would someone like me who promotes holistic health and healing choose medication over herbs? Aren’t I so against antibiotics since they kill the good bacteria in your gut?

This was a personal decision and ultimately my body and heart knew that I needed to go this route. It’s also what my doctor suggested, especially given my history and the long term nature of my symptoms, and I trust her. There is a time and place for Western medicine, and even though I’d prefer natural solutions 99% percent of the time, for ME this felt like a situation where I wanted to use the power of stronger drugs.

While SIBO protocols vary, my doctor (Dr. Aliza Cicerone, ND FABNO, amazing human and founder of Spark Health) recommended her unique 4 phase protocol for me:

  • Phase 1: Treat SIBO. This is when you’ll be actively killing the overgrowth of bugs through an antibiotic or herbal antimicrobial. Most often there are no dietary restrictions during this time, with the exception of foods that may interact with the drugs or herbs you’re taking.

  • Phase 2: Restricted diet. During this phase you’ll be on a restricted food protocol and likely an extensive supplement routine. The purpose of this phase is to continue to starve off any bacteria overgrowth while also supporting your digestive processes.

  • Phase 3: Re-introduce and re-build. During this phase you’ll start adding restricted foods back in. The purpose is 1) to start to re-build the good bacteria in your gut through the introduction of new foods and 2) observe if there are any foods that trigger your symptoms. You’ll likely re-test for SIBO before starting this phase - if it hasn’t improved, you may go through another round of phase 1 and phase 2.

  • Phase 4: Maintenance. Ultimately the goal is to get you to a place of “I can live here.” Through the reintroduction phase it may become clear that there are other issues at play that need to be explored (food intolerances, hormone imbalances, etc).

SIBO is a chronic condition. If symptoms comes back, it’s not an indication that the treatment plan didn’t work, but instead that the root cause was not dealt with properly, or there wasn’t an appropriate maintenance plan.


As I write this, I’m just over 3 months into my SIBO healing protocol. What I’ve found is that while the medications, supplements and dietary shifts are essential to me feeling better, the lifestyle changes and healing practices have been just as essential.

Before we get into those practices and healers, I want to share an outline of the protocol I’ve been on. This is NOT a recommendation for you to follow this protocol. I purposefully have not included dosages. As I mentioned previously, I strongly encourage you to work with a professional (someone with extensive SIBO experience - I’ve linked my doc below!) and together craft a plan that works for your body.

  • Phase 1 - Treat SIBO - As stated above, my doctor and I decided to go with traditional antibiotics. During this phase I was on two antibiotics to kill off the bacteria overgrowth (Rifaximin and Metronidazole), along with Naltrexone which supports gut motility. No diet modifications at this point except no alcohol because it can interact with the drugs. I started to take my supplements during this period including support for fat, starch and protein digestion; vitamin D and an energy support blend.

  • Phase 2: Restricted diet - After the course of antibiotics, I started the restricted diet phase of my healing. I had a very specific foods list and everything had to be cooked (and homemade to ensure no restricted foods were included). My list included a handful of fruits and vegetables (but again, everything had to be cooked), all proteins (except a few high mercury fish) and a few fats/oils. It was similar to a low FODMAP plan except a bit stricter, with no grains or dairy and everything had to be cooked. I could have tahini and winter squash which basically saved me during this phase, which ended up lasting for 45 days (we originally planned for 30 days but I wanted to go a bit longer since my symptoms weren’t improving as much as I would have liked). This was definitely a challenge, especially since I traveled during this time, but it wasn’t THAT hard. I stuck with basically the same supplement plan except I was taken off the energy support blend, and added in an additional enzyme support and gut lining repair support in between meals. I also continued the Naltrexone

  • Phase 3: Re-introduce and re-build - This is the phase I’m currently in! My foods list has expanded so I’m gradually adding back in specific foods (one at a time!) and monitoring my symptoms. I’m also allowed to have raw foods, which I am SO happy about since it’s the middle of summer here in NYC. My supplements will shift some during this phase - the plan is to scale back some of the digestion support (ideally we want my body to do this all on it’s own)! The energy blend supplement comes back in thought, which I’m glad about because I felt it helped in Phase 1. If all goes well with food re-introduction, I will start adding in a probiotic in a few weeks to start to re-build my gut bacteria.

My first time taking antibiotics in over 10 years

My first time taking antibiotics in over 10 years

Throughout all of the phases, I’ve been working on specific lifestyle changes and with certain healing modalities to support my gut healing. All of these practices were recommended by my doctor, and every single appointment she has checked in with my, gently reminding me that stress reduction and being kind to myself is just a crucial part of the process as the foods and drugs.

  • Stress reduction

  • Allowing 3-4 hours between meals

  • Mindful eating (ie chewing and being present with food)

  • Quality SLEEP! Especially during the antibiotic phase

  • Daily low intensity exercise (walking, hiking, yoga, light runs, stretching or rebounding)

  • Sauna and salt baths

  • Manual therapy (at some point I will write a whole post on this because I feel it has been SO supportive to my healing process)

  • Acupuncture

  • Lots of therapy, sessions with my own coaches and long talks with good friends

What next?

One of the most frequent questions I’ve gotten over the past few months is “So how are you feeling??”

That is the million dollar question, isn’t it?

Am I feeling better than I was 3 months ago? Definitely.

Am I feeling totally healed? No.

As I mentioned above, I do believe SIBO and SIBO healing is just one step in my process. I’m grateful for this experience, for the fact that I do have the time and resources to commit to such an intense protocol, and for all the things I learned and re-learned along the way.

My doctor and I decided NOT to re-test for SIBO at the end of Phase 2, mainly because I am still experiencing symptoms and I did start with a negative test. We’ll be exploring other avenues, including a stool test and a food intolerance test, after a few weeks of re-introducing foods.

I know that this isn’t a quick fix. That my gut issues run deeper than that, and that it’s going to take time and patience to feel REALLY better.

But I’m #hereforit. Ultimately our guts are our guides, and if something isn’t right down there, there’s often more than just food that needs to change.

I’m doing what I can now, taking the steps I can with my body, my work and my life. Bigger change is coming, and deep in my heart I know that these changes are going to be so good for my gut.

When life gives you a challenging diet, make  MUFFINS !

When life gives you a challenging diet, make MUFFINS!

As always, THANK YOU for reading, for being a part of this journey and for cheering me on all along the way! If SIBO is something you’re dealing with or you’re curious in learning more about this condition, I suggest checking out the articles and resources I’ve linked below.

And finally, a HUGE thank you to my team of healers and support over the last few months. I definitely wouldn’t have made it this far without you!

Dr. Cicerone and the Spark Health team (SIBO and gut specialist!)

Delia Ahouandjinou (Manual Therapy NYC)

Christine Nichols (Alchemical Acupuncture)

The Studio NYC

Megan Bruneau