SIBO Die Off Symptoms: What You Should Know

by Dr. Nick Zyrowski April 13, 2021

Occasional stomach cramps or nausea are normal symptoms that can crop up from time to time. But lots of people find that, over time, their stomach just doesn’t feel right.

Maybe they see a little bloating where they’d never had a problem like that before. Or maybe they’ve noticed that they suffer from constipation or diarrhea more frequently than normal. Still others might occasionally get bouts of deep discomfort or abdominal pain.

Narrowing down the source of all these symptoms can be tricky. But in many cases, the culprit is a condition called SIBO. SIBO can be uncomfortable and lead to long-term health complications if it isn’t taken care of.

Unfortunately, treating SIBO also leads to a host of ancillary symptoms. Let’s take a closer look at SIBO die-off and its symptoms so you know how to manage your SIBO with success. 

What is SIBO?

“SIBO” is an acronym that stands for small intestinal bacterial overgrowth. To understand this, you must understand your gut microbiome.

In a nutshell, our intestinal tracts are home to a microbiome of probiotics or positive bacteria. These helpful microorganisms, yeast, and fungal organisms provide a number of health benefits. They:

•    Help us digest and absorb nutrients from food

•    Prevent harmful bacteria from taking up space in our intestinal tract

•    Influence bodily hormones and the kinds of foods we are interested in eating

•    And more

The healthier your gut microbiome is, the healthier you will be as well.

However, our digestive systems function the best whenever the microorganisms of the microbiome are in the colon and intestines. Whenever the microbiome is unbalanced, either due to antibiotics or other factors, digestive issues can arise and we might notice a number of negative side effects.

Furthermore, if unhelpful bacteria set up shop in other spots in our digestive systems, such as the small intestine, you might also experience illness and other symptoms.

SIBO is technically a type of dysbiosis, characterized by imbalanced bacteria in your gut. This occurs, as its name suggests, when bacteria collect primarily in your small intestine when they should be in the colon or large intestine instead.

Symptoms of SIBO

If your body experiences bacterial overgrowth, you might also feel SIBO symptoms like:

•    Loss of appetite

•    Nausea and possible vomiting

•    Abdominal pain

•    Acid reflux

•    Bloating

•    Diarrhea

•    Weight loss

•    Malnutrition

•    An uncomfortable feeling of fullness after you eat

Leaky Gut

In the worst-case scenarios, SIBO can actually break down the walls of your intestines. This can cause a condition called leaky gut, leading to bacteria spreading throughout the other tissues of your body and your bloodstream.

If this is left unchecked, bacterial infections can plague your entire body, setting up colonies in your skin, respiratory tract, thyroid, and more. This, in turn, can lead to more severe symptoms like:

•    Brain fog

•    Skin or tissue irritation

•    Severe mood swings

•    Seasonal or severe allergies

•    Autoimmune disorders

  • IBS or irritable bowel syndrome

•    And more

All in all, SIBO is always bad news, so it’s a good idea to get rid of your SIBO as quickly as possible.

Is It SIBO or Candida?

Candida is a similar condition that's caused by yeast overgrowth, whereas SIBO is caused by bacterial overgrowth. Your doctor can help you identify which condition you might be experiencing. Symptoms are similar between both.

How to Treat SIBO

Fortunately, there are a number of effective SIBO treatments you can pursue. Once your doctor diagnoses you with SIBO, or if you personally suspect that SIBO is the primary cause of any symptoms you’re experiencing, you can start looking into solutions.

For example, many people suffering from SIBO follow a so-called SIBO diet, which reduces how many fermentable carbohydrates you consume. It's similar to a low fodmap diet and gluten-free diet, although a low fodmap diet is used primarily to treat IBS. Both diets involve limiting the carbs you eat, as fewer carbs starves bacteria and leads to better gut health.

When you do this, the bacteria in your small intestine have less fuel they can use to reproduce and cause damage. Following a SIBO diet is a tried-and-true way to show any harmful bacteria that they are unwelcome in your intestinal tract.

Furthermore, you can pursue treatments like antibiotics or herbal treatments with antimicrobial effects. Various herbs and antimicrobial solutions can create an inhospitable environment in your small intestine, either killing off the bacteria there or starving them so they can’t reproduce.

Antibiotic treatments are more intense and focus on killing bacteria in your digestive tract. However, this treatment can also have a big impact on your digestive health since it also kills good bacteria, along with healthy digestive enzymes. Therefore, it's worthwhile to look into more functional medicine before using antibiotics in most cases.

Regardless, any type of SIBO necessarily causes SIBO die-off: a period where the bacteria in your small intestine start to die off en masse, which can lead to a number of uncomfortable symptoms before they’re all gone.

What is SIBO Die-Off (or the Herxheimer Reaction)?

SIBO die-off, also called the Herxheimer Reaction, is a condition characterized by side effects as a result of killing rogue organisms and bacteria in your small intestine. As you starve the bacteria or kill them through antibiotics and herbal treatments, the bacteria will release toxins as they fight back.

As the bacteria are made to be uncomfortable, they may make you feel even worse in order to pressure you into eating fermentable carbohydrates and other food that they can use for fuel. If you or someone you know is currently under the effects of a Herx Reaction or SIBO die-off, it’s important to recognize that treating SIBO will not be a smooth ride.

You’ll need to whether several uncomfortable SIBO die-off symptoms before the condition is fully eliminated.

Symptoms of SIBO Die-Off

As mentioned, SIBO-causing organisms release a variety of toxins and cause other uncomfortable side effects as they begin to die off in large numbers and as the intestinal environment becomes less hospitable for their species.

Although SIBO die-off is relatively short-lived and should not take too long to complete, expect to see the following symptoms. They are fairly similar to the regular symptoms you would experience in the throes of SIBO.

•    Anxiety – this can be either moderate or severe depending on if you have anxiety is a precondition. For example, if you are already anxious, then SIBO die-off can make your anxiety much worse

•    Bloating – this is one of the most common SIBO die-off symptoms overall

•    Fatigue or exhaustion – this may kick in toward the end of the SIBO die-off cycle. At this stage, your intestinal tract may need to rebuild the gut microbiome, so it may not be absorbing as many nutrients as it would normally

•    Nausea and vomiting – both of these symptoms can be caused as toxins are released into the small intestine, triggering a sickening feeling in the stomach and leading to vomiting

•    Diarrhea – alternatively, the toxins released by SIBO bacteria may cause diarrhea, leading to severe discomfort and difficulty digesting food. Be sure to drink plenty of fluids if you experience this symptom

•    Flu-like symptoms including aches and fever – your body may induce a fever as a reaction to detecting a bacterial infection at this point

•    Muscle and joint pain overall – it’s not known why exactly this occurs, but this symptom is reported by many people who experience SIBO die-off 

How Long Do SIBO Die-Off Symptoms Last?

Although the above symptoms can be tough to deal with, the good news is that SIBO die-off usually doesn’t take more than a few days. It depends largely on the type of treatment you pursue. Some types of SIBO treatments are more effective and may cleanse your intestinal tract more quickly, while others may need more time to get the job done.

Those individuals who can improve their digestive function before treating their SIBO typically have fewer symptoms or spend less time with SIBO die-off symptoms overall. Overall, SIBO die-off symptoms usually last between 2-7 days, with plenty of variation based on individual factors or circumstances. 

How to Tell if SIBO Die-Off Symptoms Aren’t Normal

Some people are unfortunate enough to have more severe or exacerbated SIBO die-off symptoms. This is not normal, and if you experience exacerbated symptoms, there may be something wrong with your treatment plan or there may be an additional underlying condition affecting the situation.

If your SIBO die-off or other symptoms persist for multiple days, you should contact your healthcare practitioner or doctor. Remember, regular SIBO die-off symptoms should only ever last a few days or up to a week or so at most.

Symptoms like hives, allergic reactions, intense nausea, inability to focus or think, and other serious issues are not common to the SIBO die-off process. If these symptoms begin only after you started treating your SIBO problem, stop the treatment immediately and contact your healthcare practitioner.

Some SIBO treatments just don’t agree with certain bodily symptoms. Fortunately, there are multiple ways to treat SIBO if a specific solution doesn’t seem to be doing the trick.

Can You Avoid or Mitigate SIBO Die-Off Symptoms?

You cannot avoid SIBO die-off symptoms directly, nor should you necessarily want to. The symptoms are a sign that your SIBO treatment is succeeding.

However, you can mitigate how uncomfortable the symptoms are, and potentially prevent some symptoms that typically show up later in the process, by practicing some healthy strategies.

Focus on Bowel Movement Regularity

For one, be sure to pass bowel movements frequently. If you are constipated or can’t pass bowel movements during your SIBO treatment, you need to take care of that problem by taking constipation medicine or eating laxatives.

The faster you pass bowel movements, the faster you’ll pass unhelpful bacteria and toxins out of your intestinal tract. It literally flushes your intestines of the bacteria that are giving you such a hard time. For the best results, focus on reducing constipation before you begin SIBO treatment and make sure you are eating a bowel-movement-friendly diet.

The longer your bowels stay in your intestines, the longer bacteria have to fester and make you uncomfortable.

Stay Hydrated

Similarly, you’ll want to stay hydrated with as many fluids as possible, particularly if one of your SIBO die-off symptoms is diarrhea. The more hydrated your body is, the easier it can flush out toxins in both urine and diarrhea.

Furthermore, if you are well hydrated, you will be able to prevent constipation, have more energy, and be less likely to feel anxious. In other words, being hydrated can help to mitigate the effects of many common SIBO die-off symptoms.

If you are taking an herbal tea treatment for your SIBO, chances are you are already well-hydrated due to the tea. But drinking regular water or chamomile tea is still a great idea regardless.

Get Plenty of Sleep

SIBO can be exacerbated if you don’t get enough or high-quality sleep. Sleep can actually affect your digestive system and cause problems if you don’t get enough of it.

That’s because sleep is the prime time for your body to rest and repair daily damage, as well as create new cells and regulate bacterial growth in the gut. The more well-rested you are, the more energy your body will have to fight off SIBO and to recover from its uncomfortable symptoms.

Even better, more sleep means a better functioning immune system. If any SIBO bacteria try to give you a hard time, your immune system will be able to fight back more effectively if you got eight hours of zees the night before.

How to Manage SIBO Die-Off

SIBO die-off is frequently quite uncomfortable for many people going through it. If you find that the symptoms are too much to bear, you can practice several strategies to wear down the harmful bacteria in your small intestine over time.

Go Slowly

When you purge your small intestine of harmful bacteria, they release a lot of toxins. If you try to kill them all too quickly, you may induce more severe symptoms.

If you and your healthcare practitioner try several methods with the intention of getting rid of SIBO in a couple of days, but nothing seems to work, go more slowly and work with your practitioner to cleanse your intestine over a period of weeks.

Reduce Other Toxins

While you get rid of toxins in your intestines, it’ll help to get rid of toxins in other parts of your body as well. If you smoke or drink lots of alcohol, for instance, you can make things easier on your body by quitting those habits at least temporarily.

The less your body has to deal with, the better. It can devote more of its attention to the bacteria in your intestines and get rid of them more efficiently.

Similarly, make dietary changes and try to avoid overly sugary or toxic foods. Eat lots of healthy vegetables and make sure that you’re getting plenty of vitamins, either through dietary sources or through a supplement you can take with a major meal.

Sweat Up a Storm

You might be able to accelerate the detoxification process by sweating! Start exercising or have a relaxing session in an infrared sauna so you can sweat out toxins through your pores. This may be particularly effective for SIBO conditions that have progressed to the leaky gut phase.

Afterward, clean your pores by taking a relaxing soak in Epsom salt baths. These can clear away the toxins to prevent reabsorption and soothe your body as it recovers from SIBO.

Wrap Up

All in all, SIBO die-off can be an uncomfortable experience for anyone who is unfortunate enough to get SIBO in the first place. But even though the symptoms can be difficult to manage or sit through, it’s important to treat SIBO as quickly and efficiently as possible by coordinating with your doctor and by following some of the treatment strategies described above.

Left unchecked, SIBO can lead to a host of serious side effects. Cleansing your intestines and eliminating excessive bacteria in places where they shouldn’t exist will go a long way toward maintaining long-term, holistic health.

Disclaimer: this is not intended to take the place of full medical advice. Contact a medical professional if you have questions.

Dr. Nick Zyrowski
Dr. Nick Zyrowski



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