Why Reflux, Bloating, Constipation and Low Mood Might Be Coming from the Small Intestine

The Unexpected Party in Your Small Intestine

Picture your small intestine as a quiet cul-de-sac with only a few carefully chosen residents, cells that digest food and absorb nutrients. Now imagine a busload of uninvited guests (bacteria) moving in, throwing a fermentation party, eating all the food, and leaving behind a trail of gas, pressure and inflammation.

This is SIBO - Small Intestinal Bacterial Overgrowth. It is not a “bad bug” infection, and it is not a disease. In fact, SIBO is best described as a functional digestive disorder, a situation where bacteria from the large bowel migrate into the small intestine and disrupt the natural order. The good news is that it can be fixed.

What SIBO Feels Like

SIBO does not wear a name tag. It mimics other digestive issues and often goes overlooked. But there are some common telltale signs:

A belly that bloats like a balloon, especially as the day progresses
Belching, excessive gas, or a feeling of fullness after small meals
Reflux that does not improve with medication or returns once you stop
Diarrhoea, constipation, or a mix of both
Persistent fatigue, foggy thinking, and low mood
Feeling uncomfortable or heavy after eating even light meals

Up to 78% of people diagnosed with IBS test positive for SIBO using breath testing protocols [1].

What Causes SIBO?

Your digestive system is meant to operate like a conveyor belt, moving food and bacteria along smoothly. When that rhythm slows or stalls, bacteria can linger and multiply in areas where they should not.

Common causes include:

1. Slow Gut Motility (The Gut’s Cleaning Crew Goes Missing)
The small intestine relies on a cleansing wave called the Migrating Motor Complex (MMC) to sweep it clean between meals. If this wave becomes sluggish due to stress, infections or nerve dysfunction, bacteria can stay behind and multiply [2,12].

2. Low Stomach Acid (The Bouncer Leaves the Door)
Stomach acid helps sterilise food as it enters the small intestine. Long-term use of acid-blocking medications or low acid production with age reduces this protective barrier [3,9].

3. Structural or Functional Changes
Scarring, adhesions, abdominal surgery or gut conditions like coeliac disease, diabetes or hypothyroidism can reduce movement in the small intestine and lead to SIBO [4].

4. Antibiotic Disruption
Antibiotics may wipe out beneficial gut bacteria, allowing harmful or misplaced microbes to take over [5].

5. Chronic Stress and Vagal Nerve Suppression
Stress affects the Vagus nerve that communicates to the gut and slows digestion, contributing to poor gut movement and overgrowth [6].

Mood and the Gut: When Bacteria Influence the Brain

Your gut and brain are in constant conversation via the Vagus nerve, neurotransmitters, and immune signals. The gut even produces around 90% of the body's serotonin, the chemical responsible for our calm and relaxed state. When the wrong bacteria are in the wrong place, this gut-brain chat becomes distorted.

The result? Brain fog, low mood, poor sleep, or anxiety, or as I often see, all of these together.

Recent studies show people with SIBO are more likely to report symptoms of depression and anxiety [7]. Methane-producing bacteria have been linked to slower gut transit, constipation and fatigue [8].

Reflux That Doesn’t Respond to Antacids?

Sometimes reflux is not caused by too much acid, but by too much pressure. Gas produced by bacteria in the small intestine can push upward, forcing acid into the oesophagus.

Suppressing acid with proton pump inhibitors (reflux medications) may offer temporary relief and are often necessary, but can worsen the root issue by allowing more bacterial overgrowth [3,9].

How We Screen for SIBO: The Breath Test

The gold standard for diagnosing SIBO is the Hydrogen and Methane Breath Test, using a challenge sugar called lactulose.

Here’s how it works:

You follow a simple prep diet
Drink a measured lactulose sugar solution
Provide breath samples every 15 to 20 minutes for up to 3 hours
We measure hydrogen and methane; the gases bacteria produce when fermenting food

If these gases spike too early and too high, it suggests fermentation in the small intestine, not where it belongs (in the colon) [10].

Hydrogen gas overproduction (SIBO) is often linked with diarrhoea
Methane gas overproduction (IMO) with constipation and sluggishness
A mixed pattern is also possible and can cause a lot of confusion in the bowel – sometimes constipated and sometimes diarrhea.

Our Functional Medicine Treatment Approach

SIBO is stubborn but manageable when addressed holistically and sequentially.

1. Manage the Overgrowth
Using targeted antimicrobials such as herbal blends (e.g. berberine, allicin, oregano oil) or specific antibiotics where indicated [11].

2. Improve Gut Motility (Movement and Rhythm)
We support the MMC with natural prokinetics like ginger, bitters or botanicals to restore gut rhythm [12].

3. Adjust the Diet (Short-Term Supervised)
A low-fermentation or Bi-Phasic diet can help reduce symptoms. Long-term, we reintroduce foods to support microbiome diversity.

4. Heal and Rebuild
We repair the gut lining with key nutrients and support healthy microbial balance with prebiotics and probiotics.

5. Prevent Relapse by Addressing Root Causes
Including stress, hypothyroidism, low stomach acid, past infections, or structural issues.

SIBO Is a Functional Imbalance, not a Disease

It is essential to clarify that SIBO is not a disease like coeliac or Crohn’s. Rather, it is a ‘Situation’ we refer to as a ‘functional digestive disorder’, and it can be corrected with the right testing, treatment, and support.

Your Next Step

If you have been feeling bloated, gassy, foggy, or just “off,” you do not need to guess. We offer Professional SIBO testing, interpretation, and personalised functional support plans.

Book a Visit today to get started.

References

Pimentel M, Chow EJ, Lin HC. Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome: a double-blind, randomized, placebo-controlled study. Am J Gastroenterol. 2000;95(12):3503–3510.
Vantrappen G, Janssens J, Hellemans J, Ghoos Y. The interdigestive motor complex of normal subjects and patients with bacterial overgrowth of the small intestine. Gastroenterology. 1979;77(3):468–475.
Lombardo L, Foti M, Ruggia O, Chiecchio A. Increased incidence of small intestinal bacterial overgrowth during proton pump inhibitor therapy. Clin Gastroenterol Hepatol. 2010;8(6):504–508.
Ghoshal UC, Shukla R, Ghoshal U. Small intestinal bacterial overgrowth and other intestinal disorders in hypothyroidism: An underrecognized association. World J Gastroenterol. 2011;17(38):4220–4225.
Khanna S, Tosh PK. A clinician’s primer on the role of the microbiome in human health and disease. Mayo Clin Proc. 2014;89(1):107–114.
Breit S, Kupferberg A, Rogler G, Hasler G. Vagus nerve as modulator of the brain–gut axis in psychiatric and inflammatory disorders. Front Psychiatry. 2018;9:44.
Rezaie A, Pimentel M, Rao SS, Safdi A, et al. Alteration of the gut microbiome in functional bowel disorders and its role in the pathophysiology and management. Neurogastroenterol Motil. 2017;29(5):e12918.
Pimentel M, Lin HC, Enayati P, Van den Burg B, et al. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity. Am J Physiol Gastrointest Liver Physiol. 2006;290(6):G1089–G1095.
Niebauer K, Gill RK. Proton pump inhibitors: Are they contributing to the pathogenesis of small intestinal bacterial overgrowth? Clin Transl Gastroenterol. 2020;11(12):e00276.
Rezaie A, Buresi M, Lembo A, Lin H, et al. Hydrogen and methane-based breath testing in gastrointestinal disorders: The North American Consensus. Am J Gastroenterol. 2017;112(5):775–784.
Chedid V, Dhalla S, Clarke JO, et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med. 2014;3(3):16–24.
Tack J, Janssen P. Prokinetics and fundic relaxants for the treatment of functional dyspepsia. Nat Rev Gastroenterol Hepatol. 2011;8(5):252–261.

By Kylie Cloney | BHS. Complementary Medicine/Functional Medicine Practitioner | Clinical Naturopath/Wellness for Life

Disclaimer:

This post is for general education only and is not medical advice. Please consult your healthcare professional. See our Medical Disclaimer.

Understanding SIBO: When Your Gut Has Too Many Guests.