You just finished your herbal or pharmaceutical antibiotics and you are confused why you still have bloating, GI upset and irregular bowel movements. What now?

I asked myself this same question following my 5 weeks on an herbal protocol. I discussed it with my practitioner at the time and he concluded that “if I still bloated, then I still had SIBO”. He advised me to jump on pharmaceutical antibiotics and “I would feel so much better”. With his advice, I made the biggest mistake of my SIBO journey and took CIPRO since Rifaximin was so hard to get ahold of back then. This antibiotic made everything much much worse.

Knowing what I know now, this decision to hop on more antibiotics, because I was still having bloating was very ill advised. I overtreated my SIBO and this made my battle back to health so much harder.

But, after immersing myself in the SIBO community, I realized that many others are making the exact same mistake. Just because you still feel bloated doesn’t necessarily mean that you still have SIBO. This belief can lead SIBO sufferers to get stuck in the kill mentality, which almost always leads to overtreatment.

As a SIBO patient, there tends to be way too much focus on the kill phase and not enough focus on the repair phase. To beat a dead horse, SIBO is a symptom of a bigger problem. It is going to take more than bombing your gut bugs with antibiotics and herbals to heal from SIBO.

I also believe that the kill phase is easier to address than the repair phase. We all have vastly different underlying root causes, which require individual treatment plans. It can be hard to pin down and address your root causes. The kill phase is more straight forward and doesn’t typically require tons of customization.

Just because you still have SIBO symptoms doesn’t necessarily mean that you still have SIBO. After my bloating persisted for awhile after treating my SIBO, I was convinced that my treatment was not effective and I still had bacteria in my small intestines. However, my breath test came back squeaky clean.

My bloating seemed to be a result of a problem further down stream. My stool tests showed many opportunistic pathogens and imbalances.

It can be easy to mistake large intestine imbalances with SIBO. And over treating the SIBO will exacerbate dysbiosis in the large intestines. There is a slim margin of error when you are treating SIBO with antimicrobials.

In the thick of my SIBO journey, I really had to change my strategy and figure out why I was still having symptoms even though my SIBO was gone.

I have compiled a list of reasons why you still might be bloated even after antibiotic treatment. Lets dive into it!


You have large intestinal dysbiosis

Like I said above, there seems to be this common belief in the SIBO world that if you are still bloating then you will still have SIBO. But, bloating after meals can just as easily be from large intestine fermentation as it can be from small intestine fermentation.

Everyone with SIBO usually has some level of imbalance in their large intestine bacteria. A diverse and robust large intestine microbiome can prevent SIBO from developing and becomes imperative to prevent relapse.

At some point in SIBO treatment, there needs to be a shift out of the kill phase and into the repair and grow phase. The timing of this shift will be different for each person, but you shouldn’t keep bombing the small intestine without a plan to rebuild a healthy microbiome when the time is right.

Reintroducing fermentable fibers, probiotics and even supplemental prebiotics are tools that can help grow a robust and diverse microbiome. Probiotics and a healthy dose of fermentable fibers in the large intestine will create an environment (lower pH) that becomes inhospitable to pathogenic bacteria. Restricting fibers can increase the pH of the colon, which leaves the door open for pathogens to thrive.

Choosing probiotics with out D-lactate producing bacteria is important. I really like MegaSpore. Prebiotics, especially GOS, should be started very low and slow to help turn the large intestines around without increasing GI symptoms.


You may have fungal issues like SIFO or fungal overgrowths in your large intestines

It can be easy to overlook fungal issues when you are overwhelmed trying to get rid of your SIBO. The sad truth is that many SIBO cases come with a side of candida.

To make matters even more difficult, it can be hard to determine if you have candida since the symptoms tend to mirror SIBO symptoms. More definitive signs that yeast may be present are thrush (a yellow/white coating on the tongue) or recurrent skin or vaginal yeast infections.

Antibiotic treatment for SIBO will create an environment for yeast to thrive and to overgrow. If you noticed a flair in symptoms or thrush developing during and following antibiotic treatment for SIBO, you may have a yeast issue that needs to be addressed. I had major flairs in yeast issues following my SIBO treatment that took pharmaceutical antifungals to clear up.

I believe yeast issues can be a huge reason why you may not be feeling well after clearing your SIBO.


You may have lingering nutrient deficiencies that make it hard to heal

If you have SIBO, you have nutrient deficiencies. When bacteria translocate into the small intestines, they disturb the absorption process and they steal the nutrients that we eat. Over time, this can lead to severe nutrient deficiencies across the board.

After you clear the SIBO, your intestines needs nutrients to heal locally like Vitamin A, zinc, glutamine, vitamin C and adequate protein. It also will take your body some time to start building up depleted nutrient stores.

A whole foods diverse diet is needed to jump start this repletion process and it becomes much harder to build up nutrient stores if you are on a highly restrictive diet. For this reason, I try to keep encourage my clients to keep their diets as broad as possible in the context of a nutrient rich whole foods diet.

A targeted supplementation strategy may be necessary if your diet is limited or if you are very depleted in certain nutrients.  I recommend working with a Dietitian or nutritionist if you are planning on supplementing to replete your nutrient status.

Until your gut has enough nutrients to heal and your body’s nutrient stores are replete, you are not going to feel your best. This repletion process can take a considerable amount of time, but be patient and you will get there.


Your diet may be too low in carbs

A diet that is low in carbs can be problematic in a couple different ways. First, carbs are needed to stimulate insulin, which activates thyroid hormones. When you eat too low carb, your thyroid hormones will be suppressed leading to symptoms like slow motility, bloating, constipation and feeling sluggish.

It can be easy to skimp on carbs since many SIBO diets restrict carbs as a way to starve the bacteria. But, like I have said before, SIBO can’t be starved. And by trying to do so, you will end up just starving yourself.

Increasing carbs may be necessary to boost your thyroid function. For clients with low thyroid hormones, I like to see them eating at least 30% of calories from carbs.

The second reason why low carb could be problematic is that is stimulates cortisol release. Our brains require glucose to function. If you go too low carb, your body has to make glucose by breaking down protein in a process called gluconeogenesis. Cortisol is released when blood sugar is low to promote the process of gluconeogenesis.

The rise in cortisol to increase blood glucose will have negative effects on the gut. High cortisol levels will decrease MMC activity, blood flow, enzyme release and immune function in the gut. Eating enough carbs to avoid surges in cortisol can improve not just gut health, but overall health.

The third and final reason why too low carb is problematic is simply that it is hard to consume enough fermentable fibers when you are limiting carbohydrates in your diet. I love this post by Dr. Jeff Leach, a prominent microbiome researcher, who discusses how low carb diets don’t provide the gut microbiota with enough fuel to thrive. He also points out that the gut pH shifts that happen when you are too low carb can lead to dysbiosis and opportunistic pathogens.

If you suspect that you may be a little too low carb, I would suggest experimenting with more carbs and seeing how your gut and body respond. There may be an adjustment period as your body needs to adapt to an increase in carbohydrates. But, I usually find that many people feel much better when they up their carb intake.


You may have cortisol dysregulation from high levels of physical or emotional stress

Chronic stress will prevent you from healing from SIBO and will exacerbate symptoms. Stress comes in many forms. It can be emotional like feeling pressure at work or feeling stuck in a toxic relationship. Or stress can be physical such as undereating or over exercising. Both physical and emotional stressors will raise cortisol levels, which can wreak havoc on the gut.

As I mentioned above, high cortisol levels will reduce MMC activity, digestive enzyme release, stomach acid release and immune function in the gut. To make matters worse, high cortisol will also increase intestinal permeability. Basically, stress shuts down digestion.

Some stress is unavoidable. Raising your stress tolerance to emotional stressors by employing stress management techniques into your daily routine can help you with unavoidable stressors that are often positive like starting a new job or having a baby.

Physical stressors can be a little bit harder to pinpoint, but are very common in SIBO patients. Undereating due to restrictive diets is a HUGE physical stressor that I see all the time in SIBO clients. It is easy to unintentional under eat when you are restricting so many foods.

Lack of sleep, sunshine and physical affection are other really common physical stressors in the SIBO world.

Wrangling stress is not always easy, but it is imperative for good gut health.


You may still have brain-gut axis issues

Majority of SIBO patients have reduced motility and MMC function. Unless this is corrected, relapse is inevitable following antibiotics.

Strengthening the vagus nerve and supporting MMC function with prokinetics will help repair and support the brain-gut axis and prevent relapse. Brain-gut axis exercises are often an after thought in SIBO treatment, but these need to be top priority in treating SIBO.


You may need some time for inflammation to settle down

SIBO causes lots inflammation in your small intestine. It can take a hot second for that inflammation to calm down and our gut barrier to become strong again. You may have some lingering symptoms that are a result of this lingering high level of inflammation.

Probiotics and glutamine can be great tools to help reduce inflammation and intestinal permeability following antibiotic treatment for SIBO. Good bacteria are essential for strengthening the gut barrier and glutamine is the fuel source for the cells lining the gut.


You may still have SIBO

There are cases of SIBO that might require a couple rounds of treatment. I believe that these are more of the exception and not the rule. One round of antimicrobials might not be enough.

If you feel like you still have SIBO even after antimicrobials, then it is best to re-test and not guess. Because like I said before, SIBO symptoms can often mirror large intestinal issues.


Bottom Line:

Lingering symptoms following antibiotics doesn’t always mean that you still have SIBO. There are many reasons why you may still be having symptoms other than the SIBO still being present. Address any other possible explanations for your symptoms and if you still feel symptomatic, test don’t guess.


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