Continued Stomach Problems While on GAPS: Healing Journey Part 2

Continued Stomach Problems While on GAPS: Healing Journey Part 2

(READ my Healing Journey Part 1)


For over two weeks I have been taking

herbal antibiotics for a SIBO treatment protocol.

After 10 months on the GAPs gut healing protocol

I am still having stomach issues. Yeah, I know, not fair.

The reality of healing though is that

it is not EASY, nor QUICK, nor STRAIGHT-FORWARD.

No one wants to hear this, and no one wants to believe it.

But generally speaking it is definitely a foundation principle to healing.


How I came to this missing puzzle piece…..


A few months ago I decided I would read up on the ‘FODMAPS’ information I kept coming across, as I cannot stand when I continue to see something I know nothing about.


So as I read about what high FODMAPS foods are, things I was eating plenty of such as avocado, cauliflower, onions, garlic, honey…and what kinds of symptoms they cause….I started to wonder.


I decided that I had nothing to lose, and honestly with how nagging my stomach symptoms were continuing to be, I was willing to try something in addition to the GAPS protocol.

Change of Plans


So I started to eliminate high FODMAPS foods, and within 3-4 days of getting most of them out, there were NOTABLE changes in my symptoms. Now, I’m pretty aware of my body after 10 months of daily attention and a food journal, and I can usually tell when there are improvements or regression.


This had made a clear change in my IBS symptoms, and as much as I wanted to ignore it (because I didn’t want to eliminate ANY more foods!!) I just couldn’t ignore it.


So I realized that I now needed to reduce/eliminate these foods if my stomach symptoms were going to get any better.


But WHY??


After the initial shock of realization and acceptance, I went back to the obvious question of “why?!” Why were these foods (FODMAPS) causing IBS symptoms in me? There are several different reasons people may have a problem with FODMAPS (such as fast bowel transit time or less digestive enzyme output) but one of the common reasons one would not do well with these FODMAPS foods is a condition called SIBO.


SIBO stands for “small intestine bacterial overgrowth”….a chronic overgrowth of bacteria in the small intestines. Now the large intestine is teaming with bacteria, good, bad and neutral. But certain areas of the small intestine are close to sterile…it does not have near the numbers of bacteria the large intestines has. This is purposeful and has to be that way functionally.

When this is not the case, and the small intestine becomes overgrown with bacteria, the bacteria get to the food before it can be properly broken down and assimilated by the small intestine. The bacteria starts to rapidly ferment these FODMAPS substances in foods, and creates irritation and gases in the small bowel. This leads to bloating,pain, diarrhea and/or constipation (IBS).


“One thing is certainly clear, the symptoms of SIBO overlap with those of IBS and a large percentage of IBS sufferers test positive for SIBO.” Dr Allison Siebecker


I had assumed to have bacterial overgrowth in my bowel that is why we started GAPS in the first place, but recognizing the CLEAR response in my body when I removed high FODMAPS foods (the ones most easily fermented by bacteria) REMINDED me that even after 10 months of being on the GAPS diet, I definitely have an overgrowth of bacteria-  but maybe its not pathogenic (bad) bacteria that are causing my symptoms as I thought initially.


So what’s wrong with the GAPS diet?

The GAPS diet removes polysaccharides (starches) and any complex sugars, along with other hard to digest foods such as beans. The purpose in removing these foods are so that the small intestine can begin to rebuild itself appropriately, apart from the inflammation caused by the excessive bacteria (fed by the undigested sugars/grains!).


This is still very much the case with people with SIBO causing IBS.

The only problem is, in eating the traditional GAPS diet, you are consuming large amounts of high FODMAPS foods, which in certain people (possibly dependent on which bacteria is overgrown) can act in a similar manner that the SUGARS and STARCHES are acting.



These FODMAPS actually become food for these bacteria as well, continuing to promote the proliferation of bacteria in the small intestines.
This was the KEY that I was missing for my specific situation, and I believe it has hindered my healing, as these foods have been present in my diet all along, allowing far too much ‘food’ for the bacteria that is overgrown in my small intestines (whether its neutral or pathogenic bacteria, I do not know.)  It is not that the GAPS diet was not the right option for me, but I was missing a piece of the puzzle while on GAPS that has held me back more than I would have liked.  Many people on GAPS will not have these lingering symptoms related to SIBO, and for them GAPS diet alone will accomplish addressing the imbalance in their gut flora.  It is not about what interventions are ‘right’ or ‘wrong’, but about bio-individuality and what each persons body needs, which is ALWAYS a combination of many many things to 
re-create and support and ones health.




  • If you have IBS, you probably have SIBO. (up to 84% of IBS patients have SIBO)
  • If you have SIBO, you probably have IBS (or other digestive symptoms) and could also have systemic symptoms.
  • If you have SIBO, you probably have FODMAPS intolerances, as well as problems with anything higher carb (even if you aren’t aware) (Source)
  • ‘Gut dysbiosis’ is an overgrowth of bad bacteria, while SIBO is typically overgrowth of neutral/good bacteria. They can exist together. (Source)


SIBO CAUSES: Many things can create this situation in the body. The most common ones are taking proton pump inhibitors-antibiotics-birth control, not enough stomach acid or bile, not enough pancreatic (digestive) enzymes, nutritional deficiencies, hormonal imbalances, an impaired migrating motor complex, and acute illness of gastroenteritis (which can ‘turn off’ the MMC) and consuming a diet high in carbohydrates and FODMAPS. In turn, these problems can be started by many different things. COM-PLI-CATED.


The red and purple squares not only cause SIBO, but are made WORSE by SIBO. It is truly a vicious cycle.


SIBO Experts and Treatment

As I began to dig into the work that Dr Allison Siebecker and Dr. Pimentel and their teams have done on SIBO and related diseases, I studied their “SIBO Treatment Protocol“. The diet (they recommend the GAPS diet or a diet similar to) is a major part of treatment, especially key to prevention of relapse. For acute overgrowth though, they do recommend herbal/pharmaceutical antibiotics. I am pretty hesitant to take any measures for my health apart from food if unnecessary, but seeing the positive responses they have seen treating the very resistant SIBO with antibiotics, was very encouraging to me. I don’t think it will prove necessary for everyone with SIBO, but since I have already been on the GAPS diet for 10 months, I thought this was a reasonable step in my treatment.


The pharmaceutical antibiotic most commonly studied in medical literature for SIBO is very expensive (Rifaximin over $1000). As this cost is prohibitive for us, and according to the physicians mentioned above and their experience, they were seeing similar recovery responses from the pharmaceutical antibiotic vs. the herbal antibiotics.


Herbs it is! So I am taking garlic, goldenseal, enteric coated peppermint and oregano oil at varying strengths and times a day for approximately 1 month.


A Naturopathic doctor who was able to talk with me briefly said that she thinks the herbal antibiotics will help, almost diagnostically proving my theory of having SIBO to be true, but then that I may require the actual pharmaceutical antibiotics to really deal aggressively with the overgrowth. I hope her thoughts are accurate about the herbs helping a lot, but really hope that I don’t require the pharmaceuticals.


I am hopeful that this herbal antibiotic protocol, along with a low FODMAPS/GAPS diet will help reduce the load of bacteria to a more manageable level, so that in turn my IBS symptoms reduce in intensity and frequency. (Lots of hope here!)


I will check back in after the treatment is complete and inform you with where I am with symptoms and future eating plan.


                                                                ♥ Mindful Mama


(Quick update on my husband:  He also has had IBS for years that improved greatly, almost gone, until for whatever reason lingering stomach issues reappeared.  He does not have as many of the risk factors for developing SIBO that I do, but his symptoms are so classic IBS, so the likelihood of SIBO being present in his GI tract was high. He is choosing to do this herbal antibiotic treatment hoping that it will help his IBS symptoms related to possible SIBO. )




IBS–free at last! FODMAP Elimination Diet, Patsy Catsos MS RD LD
Aglaee MS, RD
Aglaee MS, RD
Dr Allison Siebecker
Allison Siebecker, ND, MSOM, LAc, and Steven Sandberg-Lewis, ND, DHANP


Shared with Real Food Wednesdays, Mostly Homemade Mondays, Fat Tuesday, Natural Family Fridays and Foodie Friday

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About Mindful Mama

Real food lover. Follower of Jesus Christ. Passionate about helping to heal and maintain family's health. Sister. Daughter. Nurse. Avid reader. Emotional. Being part of a birth experience exhilarates. Thrives off of genuine relationships. Verbal processor. Learner of cultures. Bearing the scars of motherhood. Disorganized, messy cook. Drawn to bold colors. Forgiven and loved. Music speaks the words the heart. Radical. Lacking boundaries. Moved by "the least of these". Advocate for orphans. Devoted to friends. Basking in GRACE. Mindful Mama.

11 Responses

  1. You may want to check out the post on about GAPS. Matt Stone explains why sometimes GAPS patients don’t improve or get worse. Lots of good info on that site. Good luck! Never stop learning!

  2. I’m always looking for my missing link. Right now I’m suspicious of candida, however this post made me wonder about SIBO. I eat a lot of food on the FODMAPS list of “sometimes” like avocado, coconut milk, and almonds. Like you, I hate to cut out anything more. I’m already pretty much down to chicken and veggies, with a little fruit here and there. But like you, if I could fix my IBS, I’d do whatever it takes.

    • Alison- this was my missing link. I totally get what you mean! It seemed so unlikely and bizarre, but def. has showed HUGE improvements for me. You can do even a 2 week trial run of eliminating high FODMAPS and see how you feel….I noticed a big change in pain, bloating and stool change within 1 week. If its not you, you weren’t hurt any, but if it is, the knowledge you will have on your body will be well worth it! I am eating the biggest variety I can at this point, and I feel okay most of the time….I am even doing small amounts of FODMAPS and not having symptoms which is HUGE for me!! Feel free to write me if you have any more thoughts on this or questions. I kind of felt like I was in the dark with this because its not that commonly talked about, but the reality is A LOT of people that do paleo/primal/GAPS and other grain-free diets still continue to have A LOT of stomach issues….i’m sure you’ve seen that with your clients. Anyways…..blessings Alison!

  3. Hi, I was just wondering how far along you are on your herbal antibiotics. Is it helping. I am also wondring what your dosages are on these herbal antibiotics. Did you get help in deciding which ones to use? Thank you in advance for any response.

    • The herbal antibiotics were very helpful for my situation and symptoms. My symptoms are not completely gone, unfortunately. This is one of the main resources I used: I decided to use peppermint, garlic, oregano and goldenseal. I would recommend finding a natural health practitioner who could assist you if at all possible. Ask them if they have any experience working with people with bacterial overgrowth of the small intestines (as i’m assuming that is what you believe you have). Check to see if there are any NTP/NTC who are near you- they are fantastic natural health practitioners (I am training to become one right now, and am super impressed with the program).

  4. Enjoyed this Lauren. I have just started a natural treatment for a bad bacterial overgrowth, including garlic, thyme oil and oregano oil among others. I will let you know how it goes.

    • How do you feel it helped Ginger?? My treatment was def. effective. I think sometimes the course needs to be done more than once though.

  5. Do you have any recipes that are okay for gaps as well as low/no fodmaps? I’ve been on a gaps/scd/autoimmune paleo diet for over 6 months now and have removed all fodmaps as well as anti candida for 4 months. I’m also taking herbs to combat yeast, bacteria and parasites as well as HCl, digestive enzymes, probiotics, adrenal supplements etc. Unfortunately, I’m still having digestive issues and I’m so bored with what little foods I can eat. So, I’m just wondering if you have any ideas for yummy meals that are gaps and low fodmap. Thanks so much!

  6. Another reason why GAPS, SCD, Low carb, FODMAP is not the only solution, is the new information provided in Dr. Robillard’s book: Fast Track Digestion:IBS. Aside from the use of splenda in his book, which you can obviously avoid, nothing I have read about SIBO, IBS, or gut health makes more sense than this book. It is one of the KEY factors missing from many of the gut healing diets. Dr. Robillard has REALLY stumbled onto something. Measuring the fermentation potential of each foods to keep the amount of food that is digested by the bad microbes much lower. Read his forum and his blog and his book. It may also allow you to re-incorporate FODMAPS and is one of the least restrictive gut healing diets for microbial overgrowth (SIBO) that I have read. It has really given my healing a huge leap!

    • Thank you so much for passing this onto me!! I’m checking out his info now and its quite intriguing. I’m so thrilled this has pushed your healing forward!!! Have you ever done anti-microbials for your SIBO?