SIBO is very tricksy kind of condition, so it’s common to try a treatment and then not feel better. Here are my reasons as an IBS & SIBO nutritionist why this might be the case. 


What is SIBO? 

Small Intestinal Bacterial Overgrowth (SIBO) is a complex digestive disorder. It occurs when there is an excessive accumulation of bacteria in the small intestine. 

SIBO can lead to a myriad of uncomfortable symptoms, ranging from bloating and gas to more severe digestive issues. It can even contribute to systemic symptoms like joint pain, brain fog or nutritional deficiencies. 

The post-treatment puzzle in SIBO

Even though you diligently followed a SIBO treatment, you might find yourself still grappling with persistent symptoms. This blog aims to explore the reasons behind what could be reducing your expected post-treatment improvements.

From incomplete bacterial eradication to lifestyle influences, each aspect will be examined to help you work out what’s next in your SIBO journey. 

There are eight main reasons why you might not feel better after treating your SIBO

Person with dark skin sitting on a bed wearing blue & white checked pajama bottoms and a grey t shirt. They are clutching their stomach as if in pain. The words 8 reasons your SIBO treatment didn't work.

1 Using the wrong type of treatment for the gas that you have

Your treatments for SIBO should be based on the type of microbes in your small intestine.

We can test this by measuring the gas that is being produced by your gut microbes. Your SIBO treatment also needs to take into account the amount of gas, and whether one or more gas is presentThis is why testing for SIBO is important, rather than guessing.

You can either treat it with antibiotics prescribed by a doctor, or with herbal supplements, or a combination of both. 

Using antibiotics for SIBO

The antibiotic with the most research for treating SIBO is called Rifaximin. Sometimes another antibiotic is taken at the same time.

The reason it’s so good is that Rifaximin is not absorbed into the blood, and is effective against bacteria in the digestive tract.

Rifaximin will kill off gram positive and gram negative bacteria, but doesn’t affect the rest of the body like other antibiotics. This means it’s less likely to lead to thrush, or upset stomachs like some antibiotics can. 

Antibiotics for SIBO – different types

Antibiotic treatment should selectively target those bacterial strains that cause SIBO. Your doctor will decide on the best treatment approach for you.

  • HydrogenRifaximin is commonly prescribed for hydrogen-dominant SIBO due to its effectiveness in the small intestine and minimal systemic absorption. This is typically 550mg, three times a day, for 14 days.
  • Methane dominant SIBO often requires a different approach. Rifaximin is still a consideration, but the addition of neomycin or metronidazole may be necessary.
  • Limited research exists on hydrogen sulphide SIBO, but rifaximin may still be considered. Neomycin and metronidazole are also potential options.

Some doctors will prescribe Rifaximin and another antibiotic at the same time, such as Metronidazole or Ciprofloxacin.

What if I can’t get Rifaximin? 

In cases where you can’t access Rifaximin other antibiotics that may be effective include Metronidazole, ciprofloxacin, tetracycline, amoxicillin-clavulanate, or neomycin. You can see a list of recommended dosages for SIBO in this paper online from 2014. 

Systemic antibiotics can be effective but they may disrupt the large intestine bacteria, and trigger digestive upset, or allow other microbes to overgrow (e.g. fungi)

The main issue in the UK is getting hold of Rifaximin. Many GPs, or even gastroenterologists can’t or won’t prescribe it. 

If you take antibiotics that aren’t the most suited to the type of SIBO that you have, it might not get better. 

Using herbal antimicrobial supplements for SIBO

Some studies have found herbal supplements are as effective for SIBO as antiobiotics,  even when compared against Rifaximin.

The most common treatments for SIBO using alternative supplements include:

Hydrogen – berberine, oregano, neem

Methane – allicin, oregano, 

Hydrogen sulphide – bismuth, berberine, oregano

Join my Group Gut Reset for IBS

2. You may have reduced the microbes but not reduced the symptoms, yet

Sometimes you will see a decrease in the SIBO gases on a retest, but the symptoms haven’t yet come down.

As long as the numbers are coming down that is a good sign. 

If you don’t see any improvement in your symptoms like bloating, diarrhoea, or abdominal pain, then it might be worth changing to another type of treatment.

For example, moving from antibiotics to herbals, or the other way round. 

Most of my clients can’t afford to keep retesting after each round, so typically we take a short break from the antimicrobial treatment to reassess what’s going on, and then start another round.

Using systemic antibiotics (e.g. not Rifaximin) multiple times may be associated with an increased risk of antibiotic resistance, diarrhoea, including Clostridioides infection, intolerance, and gut microbiota dysbiosis. 

3. False expectations – Most people need more than one treatment

The estimated reduction in gas ‘parts per million’ is about 30ppm per treatment round.

This means if your test showed gasses of around 140ppm, then you won’t get rid of the microbial overgrowth in one treatment round.

Successfully treating SIBO involves targeting and eliminating the overgrown bacteria in the small intestine.

However, achieving complete eradication is not at all easy. The antimicrobial treatments you choose plays a pivotal role in determining how effective the treatment will be. Things that get in the way of recovery: 

  • Duration of treatment: Incomplete treatment courses or premature discontinuation may contribute to bacterial regrowth.
  • Resistant strains: Some bacteria may develop resistance to certain antibiotics, necessitating careful consideration of alternative options. 
  • Biofilms: bacteria can clump together to create protective films over themselves and avoid action of the antibiotics. 
  • Underlying conditions: Concurrent health issues, such as motility disorders, may impede the effectiveness of antimicrobial treatments.

Relapse is common in SIBO

If you felt better for a short while, but now your SIBO is back, you’re not alone. Relapse is common in SIBO. Research has found 45% of patients will have recurrent SIBO following antibiotic therapy completion 43.7% showed recurrence at 9 months post antibiotics.

All patients in this study had a relapse rate of

  • 12.6% at 3 months,
  • 27.5% at 6 months, and
  • 43.7% at 9 months after successful treatment. 

This just shows how common it is to need further treatment, not just one treatment round. 

To help you get over SIBO you’ll need to address underlying factors such as motility issues and eating a balanced diet as well as killing off the microbes. Using a prokinetic after SIBO treatment, to help keep the migrating motor complex working helps to extend periods between relapses. 

Working closely with SIBO specialist to tailor the treatment to the specific type of SIBO is important. 

Woman's torso close up. She is wearing an amber cardigan and white T shirt, white trousers. She is clutching her stomach. The words Why you don't feel better after SIBO treatment.

4. It’s not actually SIBO causing your symptoms – underlying digestive issues

While SIBO treatment focuses on addressing bacterial overgrowth in the small intestine, there is a chance your symptoms are caused by other digestive disorders. 

Identifying and addressing these underlying issues is key for a comprehensive and successful approach to better digestion.

To do this it’s important other conditions have been ruled out, such as coeliac disease, IBD, and food intolerance. 

  • Irritable Bowel Syndrome (IBS):
    • SIBO and IBS often overlap, complicating the clinical picture. Individuals may continue to experience symptoms in the large intestine if is not adequately managed alongside SIBO.
  • Inflammatory Bowel Disease (IBD):
    • Conditions like Crohn’s disease or ulcerative colitis may coexist with SIBO. Managing inflammation is crucial for overall symptom relief.
  • Coeliac Disease:
    • SIBO is more prevalent in individuals with coeliac disease. 

Other things that make recurrence of SIBO more likely include older age, history of appendectomy, and chronic use of proton pump inhibitors.  

5.  You’re not addressing any of the factors that might contribute to SIBO

Whilst you’re working on SIBO treatment it’s also important to look at what could be allowing the overgrowth in the first place.

These might include SIBO causes such as

  1. Poor digestive defence – Poor breakdown of foods due to erratic eating patterns, rushing your meals, high stress levels. Bile acid is antimicrobial, so issues with bile flow may contribute to SIBO. Long-term proton pump inhibitor use, or gastric resection), pancreatic enzyme secretion. 
  2. Gastrointestinal motility. Slow transit time can allow microbes to grow in the small intestine. This can be down to other conditions such as diabetes, the effects of medication such as opioids or anticholinergic and antidiarrheal agents), or not eating enough food. 
  3. Gastrointestinal tract anatomy. Anatomical anomalies include small intestinal diverticuli, strictures, adhesions. 

One of the main issues I see is that people don’t use a prokinetic after their treatment, so they don’t maintain the gains in treatment. 

6. You’re deficient in certain nutrients

Unfortunately, SIBO can lead to nutrient deficiency.  This can happen due to

  1. following a very restrictive diet for a long time can lead to nutritional deficiencies. 
  2. bacterial can compete for some nutrients like B12 and iron. Deficiency in both of these may occur in SIBO as a result of bacteria using it. 
  3. Microbial overgrowth damaging the lining of the gut and reducing absorption of nutrients.

One common symptom of SIBIO is diarrhoea, often caused by bile acid deconjugation. This can affect the absorption of  fat soluble vitamins A, E, D and K. 

The way these deficiencies affect healing your SIBO include poor immune function, lack of energy, contributing to brain fog and general poor health.

You may be undereating or malnourished

If you’re on a very restricted diet you may find it hard to feel better. Expanding out your diet is the best way to regain strength and feel well again. You may need to be eating more than you think. 

7. The treatment was appropriate, but followed incorrectly

Sometimes I hear my clients say, ‘I tried XYZ but it didn’t do anything’.

And then during the discussion I’ll find out they only took it for a few weeks, or didn’t take a high enough amount to make a difference. 

Combination products are often not enough to get clinical effects. typically herbal supplements need around 6-8 weeks per treatment round. 

The most common issues I see are:

  • Not taking it for long enough
  • Not taking enough to be effective

8. Stress & anxiety

There is a strong connection between your mood and feelings, and your digestion. The vagus nerve is the main nerve connection between your brain and stomach, intestines and all organs in the torso. 

If you’re highly stressed or anxious it can lead to poorly absorbed food, stomach cramps, constipation, diarrhoea, nausea or bloating. 


Do you need help with SIBO and figuring out what to do next? Whether you’ve already done a treatment round, or you’re new to SIBO, I can help.

Read about my 3 month Gut Reset here. Book a free call if you want to ask me about working with me.

Work with me - IBS Nutritionist

Book a free call to talk about working with me

Hi I'm Anna Mapson, registered Nutritional Therapist.

I help people with IBS and SIBO get control of unpredictable gut symptoms to find long term relief from painful and embarrassing IBS without restrictive dieting.

I can help you to:

  • understand your digestion better, so you recognise your triggers
  • eat a well balanced diet, with tasty meals that are simple to prepare
  • develop better digestion and more energy

Find more about my 3 month 1:1 Gut Reset programme

How to use prokinetics in SIBO
How to use prokinetics in SIBO

This post will help explain the function, and benefits of using a prokinetic and how it can affect SIBO. What is a prokinetic The word means promoting (pro) and move (kinetic), so it's about promoting movement. Prokinetic supplements and medicines help to amplify and...

What is the Migrating Motor Complex & how to fix it
What is the Migrating Motor Complex & how to fix it

You might never have heard of it, but your Migrating Motor Complex (MMC) is super important. It's an impulse that moves through your small intestine keeping it clean and healthy. You really need to be aware of this little known biological process if you have IBS or...