SIBO Die Off Symptoms Explained (& How To Avoid Them)

SIBO Die Off

What Is SIBO?

In this post I’ll explain SIBO die off symptoms in detail, but first what is SIBO? SIBO stands for small intestine bacterial overgrowth and, as the name suggests, is when you have too many bacteria in your small intestine. It’s important to note that sometimes you might just have the wrong type of bacteria present – what I refer to as SID instead of SIBO – small intestine dysbiosis. 

What Causes SIBO?

There are numerous causes, and I have written extensively about this previously (check out the section of my blog on SIBO, which you can find to the right-hand side of this article). The main, well-accepted underlying causes include:

  • Poor motility through the small intestine – potentially caused by a bout of food poisoning. 
  • Low stomach acid.
  • Issues with the ileo-cecal valve – a valve that separates the small and large intestines that should prevent the migration of bacteria back up the intestine. 
  • Issues with bile production or flow – bile has antibacterial properties, and thus, issues with its production or flow may increase the risk of SIBO.
  • Compromised immunity in the small intestine.

How Do You Treat SIBO?

The conventional medicine approach to treating SIBO is with antibiotics. Research has shown that adding a prebiotic, PHGG, alongside the antibiotic actually increases efficacy, so this is something I recommend if you choose to go down this route. 

However, we have evidence showing us that herbal antimicrobial compounds such as oregano oil are as effective as antibiotics in treating SIBO. (source)

Other options include specific strains of probiotics that can be selected based on a client’s symptom profile and test results. For example, we may recommend a different probiotic if you have a positive methane result compared to if you have a positive hydrogen test when testing for SIBO

Supporting the digestive process can also be incredibly important; remember that low stomach acid and compromised bile production or flow are potential causes of SIBO. So, when appropriate, we can consider betaine hydrochloride, digestive enzymes, bile support alongside herbal antimicrobials and probiotics.

What Is SIBO Die Off?

SIBO die off is simply the term given when you feel a worsening of symptoms during your treatment for SIBO. 

The more technical term for it is the Jarisch–Herxheimer reaction, more commonly known as just Herxheimer reaction.

What Is The Herxheimer Reaction?

It’s named after European dermatologists who described patients with syphilis who developed exacerbations of their skin lesions after treatment with a mercury-based compound.

After penicillin became the drug of choice for syphilis in the 1940s, the Jarisch–Herxheimer reaction occurred during the first 24 hours of treatment in primary and secondary disease manifesting as fever, chills, headache, myalgias, and intensification of skin rashes.

In other infections, including Lyme disease, a similar reaction was reported after treatments with antibiotics. In addition, newer antimicrobials can provoke the Jarisch–Herxheimer reaction too!

What Causes SIBO Die Off?

It is thought that SIBO die off symptoms are caused when components of bacteria come into contact with your immune system, where it will mount an inflammatory response. The symptoms we experience are due to that immune-inflammatory response.

Is there anything we can learn from the research on the Herxheimer reaction?

Yes, there is!

In patients with rheumatic fever, plasma concentrations of cytokines (inflammatory immune signaling molecules) were measured and found to sharply increase 2–4 hours after antibiotic treatment when patients were experiencing a Jarisch–Herxheimer reaction. This returned toward baseline levels 12 hours after therapy. 

This confirms that the immune response leading to inflammation is involved in causing the symptoms.

What’s fascinating is that if you take anti-TNF antibodies (TNF being one of those inflammatory cytokines) before the antibiotic treatment, it prevents or reduces the Jarisch–Herxheimer reaction while also reducing levels of inflammatory cytokines call IL-6 and IL-8 during the reactions. 

But it’s not just inflammatory molecules called cytokines that might cause SIBO die off.

Histamine may also contribute!

Elevated blood levels of histamine were measured in patients with syphilis and rheumatic fever before and after the Jarisch–Herxheimer reaction. (source)

What Are The Symptoms Of SIBO Die Off?

Symptoms could be a simple deterioration in your current symptoms, but common symptoms of SIBO die off include bloating, abdominal pain, changes to bowel movements, headaches/migraines, brain fog, nausea, skin symptoms such as spots and generalised inflammatory symptoms such as body aches or moodiness and irritability. (source)

How To Avoid SIBO Die Off?

Go slow: The most common cause of SIBO die off, in my experience, is when someone either starts with too high a dose of antimicrobials or increases their dose too quickly. So, if you are concerned about SIBO die off, you may like to slowly work up to the therapeutic dose of antimicrobial you’ve been recommended. I always remember one client who was particularly unwell with chronic fatigue who had to start with 1 capsule of oregano oil twice per week and slowly build up to the recommended dose (4-6 capsules per day). While progress was obviously slow, she was able to successfully treat her SIBO and regain her health. It’s so important to be patient and to be gentle with the healing process. One of the problems I’ve seen over the years is people trying to rush the healing process, and you simply can’t do this. Healing is not something that you can push or force. It has a life of its own. We need more compassion, more gentleness, more nurturing. Things that often get conditioned out of us by the modern, fast-paced, competitive world.

Heal The Gut: Although controversial, some suggest doing a bit of gut healing work first. The idea here is that if you have leaky gut, there will be an increase in the amount of bacterial components interacting with your immune system, resulting in more inflammation and, thus, a bigger die off reaction. While I feel there is truth to this, I don’t think it is that black and white (i.e., if you have a leaky gut, you are destined to experience SIBO die off). Also, you definitely can’t heal leaky gut if you have imbalances in your microbiome in the first place. 

Reduce your toxic burden: I am not aware of any evidence on this, but it is thought in the naturopathic space that if you already have compromised detoxification pathways, then you may be more susceptible to die off. In my clinical experience, there is something to this, as it is often those who have known toxin exposure (mycotoxins, heavy metals, etc.) and are the most compromised who experience SIBO die off. We can reduce our toxic burden in so many ways, but the two main considerations are reducing your exposure to toxins and improving your body’s capacity to eliminate toxins. We can reduce exposure to toxins by changing our toiletries to natural organic products, our kitchenware to non-toxic products, and improving our indoor air quality by using an air purifier and ventilating the house by opening the windows for a few minutes each day (if we don’t live in a city!).

Support your detox pathways: Now that we have reduced our burden, we can clean up the rest! We can support the body’s capacity to eliminate toxins by ensuring we are pooing at least once or twice per day, and ensuring we have good nutrient status. Yes, these are simple considerations, but they are by far the most important – I have various resources that dive deeper into these and other considerations on my podcast and website. Don’t get fooled into thinking you need an overly complex protocol when it comes to detoxification.

What Can You Do When You’re Experiencing SIBO Die Off?

Take a binder: In animal studies, binders such as bentonites are used to help bind endotoxins from bacteria, as well as mycotoxins from mold (mycotoxins are a huge problem in animal feed). Options include bentonite clay, activated charcoal, or chlorella.

Reduce your dose of antimicrobials: This should be an obvious one! You may need to reduce the amount of antimicrobial herb you are taking and slow down the process of eradicating the overgrowth.

Support detoxification: Some recommend taking things like NAC or liposomal glutathione to support detoxification during this time.

How Long Does Die Off Last?

Unfortunately, there is no generic accurate answer as it depends on so many variables ranging from specific details around detox capacity to what you have done to reduce the symptoms. I’ve seen clients improve within a day or two of reducing the dose of supplements, while others are still not feeling quite right several days afterwards. It also depends on the extent of the Herxheimer reaction – has it led to any significant change in the gut microbiome or in gut function (inflammation can shift the composition of the gut microbiome, can impact the integrity of the gut lining, and influence activity of other organisms). 


In summary, SIBO die off is when you experience a flare-up in symptoms due to the treatment that’s been prescribed. It is the result of immane activation and an inflammatory response and should settle by either stopping or reducing the dose of antimicrobial you are using. Additional tools can be considered, such as supporting detoxification with products such as NAC or glutathione. 


Share this post