Why I keep relapsing with SIBO




I have been meaning to write this post for many weeks now but my gut instinct (no pun intended) was telling me to wait until I had treated SIBO again. I wanted to share the exact protocol I used to treat it so I can be of best help anyone going through it. 

I’ll start by going back to the beginning to give you some context of my journey and then go into the details about all the treatments, protocols, products and foods I’ve used. 

Why Gut Issues Can Be Complex

Over the years I have experienced a plethora of symptoms. Here is the full list and note that whilst some have subsided, I do still experience many as I continue to get to the root cause of my health (particularly relating to viruses in my body).



  • Low immunity: always picking up colds and bugs

  • Headaches/migraines, foggy head, lack of concentration

  • Hair loss, itchy scalp, dry skin

  • Lack of energy, fatigued, adrenal crashes

  • Lightheadedness, dizziness and hypoglycemic episodes (shakey)

  • Depression, anxiety, panic attacks, irrational moods, low moods

  • Acne including facial cysts and rosacea

  • Chronic sinus and mucus/phlegm congestion

  • Chronic sore throats, inflammation in the throat and regular mouth ulcers

  • Digestive disturbances: indigestion, heartburn, reflux, burping, gas, constipation, stomach pains, nausea, stitches

  • Hypothyroidism / underactive thyroid: slow metabolism, fatigued, sluggish digestion, cold hands and feet, lack of energy, constipation

  • Muscular and neurological pains throughout my body

  • Tingling, numbness and pains in my hands and feet

  • Hormonal issues and PMS: insomnia, ovary pain, breast tenderness, back pain, uncontrollable crying, mood swings, food cravings, low sex drive

  • Dehydration, excessive thirst, cravings for salt

Although many don’t obviously relate to the gut, surprisingly a lot are connected. For example, there are very strong correlations between the gut/mind and gut/immune system.

So what caused all these symptoms? Well, to this date, the following is my knowledge of the root causes…


Root causes

  • Gastrointestinal: Small Intestine Bacterial Overgrowth (SIBO), Candida, dysbiosis ->> Leaky Gut

  • Chronic infection: reactivated Epstein Barr Virus (EBV) and Human Herpesvirus 6 (HHV-6).

  • Stress: study, work, high paced lifestyle

  • Food intolerances: gluten, dairy, yeast, fungi

  • Toxic burden: moulds, heavy metals  

  • Genetics: Human Leukocyte Antigen (HLA), Lewis Non-Secretor and possible IgG 1 deficiency

So now that you have some context, let me zero in on the gastrointestinal issues. Specifically there was a timeline of events where I focussed on different root causes or should I more accurately say, discovered the varying underlying causes of my issues.


Gastrointestinal treatment

Here is the rough timeline of my diagnosis and treatment:

2013 - Diagnosed with Leaky Gut and Dysbiosis (and potential parasites)

2014 - Diagnosed with Candida

2015 - First round SIBO treatment with Rifaximin

2016 - Second round SIBO treatment with Bactrex and Allicin

2017 - Third round SIBO treatment with Atrantil and Allicin


I would like to bring your attention to a few key points throughout this timeline:

  • Leaky Gut is not the root cause of gastrointestinal issues. It is a symptom of some underlying problem within the gut or body.

  • Even if you treat for one root cause, if you don’t treat for EVERYTHING, then you won’t see the results you’re looking for.

  • SIBO keeps coming up. Yep thats right, it is a nasty, persistent little bugger and practitioners from all around the world are still trying to get to the bottom of WHY, yes WHY so many people keep relapsing with this condition. (Hint: have you ever wondered maybe this is why IBS seems to be a such a chronic problem for SO many people? Maybe it is in fact just relapsed SIBO ...when you think about it, greater than 70% of people with IBS have been shown to have SIBO! #justsayin)

OK, so I am going to try and break it all down for you so you know what worked for me and what didn’t work for me.

What caused my SIBO to relapse again



SIBO relapse #1

In 2016 when I relapsed from SIBO for the first time it was because I had taken a course of antibiotics, Rifaximin, that weren’t fully equipped to treat my Methane based SIBO. I believe the efficacy of Rifaximin when used alone to treat methane predominant patients is < 40%. This isn’t very reassuring now is it.

Then I did a lot of research and discovered that including allicin in the mix was a critical component when treating methane based SIBO. I didn’t want to go back on antibiotics so I decided to treat my relapsed SIBO with natural herbs. I chose to take Bactrex and Allicin in combination.

This seemed to work and by end 2016 and for the first few months of 2017 I felt like 95% of my gut issues had disappeared. I no longer suffered from any of the following symptoms:

  • Constipation

  • Gas

  • Bloating

  • Abdominal pains

  • Nausea

  • Stitches

  • Food reactions

  • Restless legs (not feet, they are separate issue)


SIBO relapse #2

So what happened? Well a few months into 2017 I started getting some symptoms again including:

  • Nausea

  • Stitches

  • Constipation

  • Abdominal pains

In addition to this I got my leaky gut results back and it had over doubled to 1.5. I was really disappointed because I had worked so hard to get my gut in check and had felt so much improvement just a few months earlier.

On the same day I got these leaky gut results that night, around 2am, I got severe abdominal cramps. My GI tract and tummy were spasming causing very severe pains. It was gas trapped which was causing the spasms and essentially I didn’t feel better until it came out either end!

In the moment I 100% knew what these pains were because it all made sense. I had been eating fodmaps, specifically ½ apple that afternoon (apple for me is the worst, raw that is) and I had been getting nausea for about 2 weeks prior. At the time I was trying to figure out what was causing the nausea, whether it was gut related or toxicity or liver burdened. Then getting my leaky gut result back that day showing that it had worsened proved that there was an underlying problem. So in a way, I was very thankful that all the dots connected and I started the SIBO protocol that next day. 

I believe this second relapse was caused by three main factors:

  1. Food

  2. Probiotics

  3. Prokinetics (or lack there of)


  1. Foods


Well during this same time I was doing treatment to target the Epstein Barr Virus (EBV) and Human Herpes Virus 6 (HHV-6) in my body. This led me to have a  lot of die off which hurt my liver and caused me to lose my appetite a bit. Also, I had read about all the healing benefits of fruits, vegetables and herbs in overcoming illness. Specifically if you read Medical Medium or Life Changing Foods by Anthony William you too will be inspired to cut out a lot of foods from your diet! Now don’t get me wrong, I’m the biggest fan of Medical Medium, however, by limiting my consumption of animal products significantly and without consuming legumes, grains or processed foods, I was starting to lose weight. I was also doing some intermittent fasting (15:9 type) which felt amazing on my gut and also surprisingly my energy levels. It just made me feel great, however, as you can imagine this wasn’t helping me to maintain the weight.

So, at this point I’d lost a couple of kilos and also lost my period. This is usually the first sign to me that one of two things is wrong: (i) thyroid has slowed down again; and (ii) I’m underweight. (Note: it can also happen for many other reasons, another major one being training too hard, however, I only really walk and do yoga so knew this wasn’t the problem).

Although it was a catch 22, because eating more foods, especially loosening the diet, wasn’t necessarily making me feel better - in terms of my digestion/gut and liver. Regardless, I knew I had no choice but to put on the weight, because your body can be in stress when it is underweight.

So off I went broadening my diet, but lesson be learnt, you can do it the right way and you can do it the wrong way. Unfortunately, some of the choices I made weren’t the best foods and I think this contributed to my second relapse of SIBO.

I was eating:

  • More grains - rice, buckwheat, quinoa

  • Corn (maize) and egg in gluten free breads

  • Canola oil and natural flavourings in chips (I became obsessed with these chips)

  • Having some non-organic meat when out or if my boyfriend cooks

  • Occasional sugars contained in gluten free cereals

  • Peanut butter (the salt and sugar free one)

  • Having some bhuja mix (well, picking out the fried peas and rice crisps)

  • Having some onion and garlic in spice mixes

  • Pureed cauliflower in gluten free lasagne

  • Having some of my family’s takeaway thai dishes e.g. pad thai, massaman curry

  • Having avocado in my morning smoothies and salad

  • Having fermented protein powders in my smoothies, bliss balls + mixed with yoghurt

  • Eating coconut yoghurt which contained live strains of probiotic

As you can tell there I was eating a much higher amount of fodmap veggies and carbs (especially grains). However, this alone wasn’t the cause of my SIBO relapse ...


2. Probiotics


The second cause I believe is probiotics. Over the months of December 2016 and January 2017, a new doctor I had seen put me on the Michael Ash stewed apple protocol. It is a protocol which involves mixing probiotics with stewed apple and other optional additions like yoghurt, berries, almonds with the purpose of repopulating the gut microbiota.

You see my immune killer cells kept showing up as being deficient. To be honest they have done so for many years and the doctors have never quite understood why. It really is one of two things;

  1. They are temporarily suppressed maybe because they are continually fighting pathogens; or

  2. It is a genetic.

The stewed apple and probiotic protocol is often used to repopulate your gut microbiome which is where majority of your immune system lives. So we would hope to see some improved immunity whilst taking the probiotics.


So how did I go?

Well I only ever managed to stay on the mixed Bifidobacteria (I took Bioceuticals Ultra Biotic 500, which is the same as VSL 3 for those in the US) and not the Saccharomyces Boulardii. The first few weeks or so I had gas which was my main symptom however then it improved whilst on the mixed Bifidobacteria. The Saccharomyces Boulardii symptoms never improved and because of my HLA genetic disposition I had to be very carefully with yeast products, that being one, so I removed this component of the protocol. I continued on the stewed apple, mixed Bifidobacteria and coconut yoghurt for close to 8 weeks.

I think i overdid it. After the 8 weeks, I started to experience some nausea, stitches and abdominal pains again. Although I initially felt better taking the probiotic, I think the quantity and possibly even the type really was too much for me. Although I really think this was the MAJOR cause of my SIBO relapse, there was one more factor...


3. Prokinetics


The final factor I believe is the prokinetics. Prokinetics are herbs or drugs that enhances gastrointestinal motility. Research has shown that impaired gut motility i.e. migrating motor complex is a large cause of SIBO. This can be particularly evidenced in cases of SIBO relapsing because you treat the SIBO, you feel temporarily better and then don’t prevent the bacteria overgrowing again.

I wasn’t taking a prokinetic consistently with a good month or so without one. In hindsight, I should've kept it up to ensure prevention of recurrence. My favourite prokinetics are:

Overall cause of SIBO relapsing

So overall I think it started with the very strong probiotics. Then the lack of daily prokinetics meant that my migrating motor complex wasn’t “sweeping” the small intestine properly allowing an overgrowth to take effect. Then lastly, the poor diet added fuel to the bacteria in the small intestine even more allowing it to perpetuate into a full on relapse of SIBO.

An after thought as well is the role of herbals on a regular basis may play. For example, taking allicin on a regular basis - which would be killing two birds with one stone for me, gut and virus treatment. 

On this note, don't forget all those other issues I mentioned up top. The reason I want you keep the whole body in mind is that I don't know how much for example the viruses are impacting the progress with my gut. 


My 3-5 week SIBO treatment protocol

This time around I tweaked my SIBO treatment protocol. I wanted to use only natural herbs and so knew I didn’t need to go on any antibiotics. I knew the 3 step formula that worked for me previously and I wanted to prove that it worked again. And it 100% worked to get rid of my SIBO in the short term. The reason I say short term is because there is a missing link - whether that is continual use of prokinetics, vagus nerve stimulation or other reasons causing my migrating motor complex to be impaired and thus make me more prone to relapsing compared with others.

You can read my blog article - 3 steps to treating SIBO.

So what did I change this time? Well I added a new herbal antimicrobial into the mix.




Ok, so if you haven’t heard of this tablet you should go look into it. So what it is?

Atrantil has 3 core ingredients which work together to remove unwanted methane from the small intestine and hence help to relieve SIBO and IBS symptoms. It was developed by a board-certified gastroenterologist Kenneth Brown, MD who had a mission to develop a natural alternative to treat IBS and SIBO. 

  1. Peppermint Leaf (M. balsamea Willd extract) calms the small bowel. This gives Atrantíl’s two other botanicals the right amount of time to work most effectively.

  2. Flavonoids from Quebracho extract (a South American hardwood tree) soak up hydrogen and create an unfriendly environment for the archaebacteria. They weaken the cell walls—setting the stage for Atrantíl’s third botanical.

  3. Saponin/flavonoid, a natural antibacterial from Horse Chestnut (Conker Tree extract), reducing methane production. It binds to the reductase enzyme in the weakened archaebacteria—stopping methane production.


My dose

I did 3 weeks of 6 tablets a day. I then dropped it back to 2 tablets a day when I felt I had made significant improvements. I now usually take a maintenance dose of 2 per day and find that it is serving me well. I’m not sure how long I will be on it for, but I’m glad I have it, especially when I go out on the weekends or travel, just to know I have an easy solution to keep it in check.



I can only speak for myself and I have had great success with it and the 3 main reasons why I have been enjoying this product is it:

  • Is 100% natural ingredients which I have found can be taken over longer time frames compared to some other herbal antimicrobials (e.g. berberine);

  • Effectively treats methane predominant SIBO by removing methane from small bowel;

  • Protects good bacteria.

I have heard others who it didn’t work for. My only advice to you is to give it is a try. It is really affordable compared to the cost of some supplements and I’ve found the customer support team at Atrantil to be incredible so if you don’t see results just let them know.


The whole protocol

  • Prokinetics: ginger daily

  • Diet: low fodmap, low carb foods

  • Other antimicrobial herbs: Atrantil 6 tablets a day for 3 weeks. I also did 2 weeks of Bactrex (which contains berberine /phellodendron, clove oil, thyme oil and oregano oil) and Canxida. I didn’t feel I actually needed to do this, it was more for caution and to ensure that I removed any overgrowth of yeast or parasites etc if there was anything hiding in there. I am also taking allicin daily moving forward. 


After SIBO Treatment

So what now after I’ve finished the 5 week protocol? Well I don’t know the right solution. It is all trial and error. So all I can do is learn from my past mistakes and try a new approach.

Here is my approach:

  • Largely stick to a low fodmap, low carb/grain diet midweek and then allow myself small liberations on the weekend;

  • Take prokinetics daily

  • Take allicin daily;

  • Ensure I eliminate every day;

  • Take enzymes with my food - I select from either Betaine/HCL, Super Enzymes or Ox Bile;

  • SLOWLY, yes very slowly trial probiotics. This time I’m starting with a tablet three times a week and only starting with one strain instead of multiple.

I will provide an update in 3-6 months to let you know of my success!


Don’t give up

Finally, I would like to remind you that if you have SIBO and are frustrated by relapsing or the speed of recovery ...don’t be too hard on yourself. After approx 7 years of studying SIBO, Dr Allison Siebecker admits to not having “cured” herself of SIBO. For some people it is a simple fix and for others (usually those who have methane type and other health issues) it is a journey. Much of it is trial and error with foods, herbal supplements and lifestyle management.

I know it is frustrating, especially if you have been dealing with it for many years however if you do your homework and the hard yards - find foods that make you feel good (and if you are reintroducing foods do it VERY slowly and listen to your body) and take a prokinetic, I’m sure you will start to see improvement.


In conclusion my SIBO journey has been a long and somewhat frustrating one, however, I now feel more confident than ever before about knowing how to treat it. I have successfully treated it twice now using the 3 step approach:

  1. Diet

  2. Herbal supplements

  3. Prokinetics

My next step is to figure out the last step to the equation which is how to reintroduce foods in a healthy way and what, if any probiotics should be used.

If you are currently dealing with SIBO and you aren’t having any success, I encourage you to give the 3 step 3-5 week protocol a go and let me know how you go! 


Let me know in the comments below what your SIBO story is? What has worked or not worked for you? I read and reply to every comment. 


If you liked this article, please help me spread the healing information by sharing it on Facebook, Twitter or Pinterest. 





Amy is based in Sydney, Australia. She has suffered many health problems in her late teens and 20s. Throughout her journey she learnt a great deal from health influencers and discovered the value in sharing her own insights to help people on a similar journey. She founded The Routine Fix as a hub for influencers to spread their message and inspire others to up level their health, business and life.


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