SIBO relapse and recurrence

SIBO rarely returns for just one reason. In most cases, recurrence reflects an unresolved underlying issue. Below are the most common contributors.

1. Inadequate treatment the first time

If the initial treatment did not fully reduce the bacterial load, relapse is likely. This may occur when:

• The antimicrobial or antibiotic dose was too low

• Treatment duration was too short

• Biofilms were not adequately addressed

Partial improvement does not always mean eradication. Residual bacteria can quickly repopulate the small intestine.

2. Incorrect identification of SIBO type

There are three main types of SIBO, classified by gas production:

• Hydrogen-dominant

• Methane-dominant

• Hydrogen sulphide–dominant

Your breath test gas pattern reflects how different microbes behave in your gut. Each type responds best to different treatment strategies, including different antimicrobials and post-treatment support.

For example, methane-dominant SIBO is strongly associated with slowed gut transit, so ongoing motility support after treatment is often essential to prevent recurrence.

3. Failure to restore a healthy microbiome after treatment

Think of your gut like a garden:

• The intestinal lining is the soil

• Beneficial microbes are the plants

Antibiotics and antimicrobials reduce bacterial overgrowth—which is necessary—but they also reduce microbial diversity. Without proper repopulation and ecosystem rebuilding, the gut becomes unstable and vulnerable to relapse.

A diverse, balanced microbiome is far more resistant to overgrowth returning.

4. An unresolved condition slowing gut motility

Normal gut motility is one of the body’s primary defenses against SIBO. Conditions that impair motility—such as post-infectious nerve damage, hypothyroidism, connective tissue disorders, or medication effects—must be identified and managed.

If motility remains impaired, recurrence is far more likely regardless of how effective treatment was initially.

5. Co-existing or emerging SIFO (fungal overgrowth)

SIBO and SIFO (Small Intestinal Fungal Overgrowth) are distinct conditions but can coexist.

When bacterial populations are reduced, fungal organisms may expand to fill the gap—particularly in susceptible individuals. This phenomenon is well recognised elsewhere in the body (for example, thrush following antibiotics).

SIFO does not respond to antibacterial treatments and requires a different therapeutic approach. Candida albicans is often involved, but it is not always the sole organism.

6. Excessive snacking between meals

Snacking is not inherently harmful, but frequent eating can suppress the Migrating Motor Complex (MMC)—a wave-like cleansing mechanism that clears bacteria from the small intestine every 90–120 minutes.

Each time you eat, the MMC pauses. In people prone to SIBO, constant grazing may prevent the small intestine from adequately clearing bacteria.

7. Prolonged sitting and low physical movement

Extended sitting reduces blood flow to the digestive tract and slows intestinal motility. Sluggish movement allows food to remain in the small intestine longer, creating an environment where bacteria can thrive and overgrow.

Regular movement supports both motility and microbial balance.

8. Post-infectious gut damage after food poisoning

Food poisoning is a well-established trigger for both initial SIBO and recurrence.

Certain pathogens—such as E. coli, Campylobacter jejuni, Shigella, and Salmonella—produce cytolethal distending toxin (CDT). This toxin can damage intestinal nerves and impair MMC function long-term.[2]

In these cases, the gut may need extended time and targeted support to fully recover.