Small Intestinal Bacterial Overgrowth (SIBO) is a common but under-recognized cause of chronic gastrointestinal distress. It shares significant overlap with Irritable Bowel Syndrome (IBS), presenting symptoms such as poor appetite, nausea, bloating, diarrhea and constipation.
SIBO occurs when bacteria proliferate in the mostly sterile small intestine, disrupting digestion and nutrient absorption. Unlike the colon, the small intestine is a narrow, inelastic tube, and when fermentation occurs here, the resulting gas can cause significant discomfort.
Beyond digestive symptoms, SIBO is associated with histamine intolerance, allergies, rosacea, fibromyalgia, chronic fatigue, and in women, hormonal imbalances including PMS, perimenopause, PCOS and endometriosis.
Bacteria in SIBO typically arise from two primary routes: downward migration from the stomach due to low gastric acid (hypochlorhydria), or retrograde migration from the colon via a weakened ileocecal valve. Many factors can suppress stomach acid—stress, overeating and poor food combinations—but one of the most common modern culprits is chronic use of proton pump inhibitors (PPIs). These drugs, often prescribed for reflux, impair digestion by reducing acid, disrupting motility, enzyme output and bile flow—setting off a cascade of overgrowth and inflammation. Other medications such as antibiotics, analgesics and antidepressants also play a role.
Another important but often overlooked trigger is food poisoning, in which bacterial toxins can trigger an autoimmune reaction that impairs the migrating motor complex (MMC)—the system of wave-like contractions that cleanses the small intestine between meals.
SIBO is typically diagnosed with hydrogen/methane breath testing and often treated with antibiotics. These may reduce symptoms in the short term, but recurrence is common if the underlying dysfunction isn’t addressed.
Some practitioners turn to herbal antimicrobials like berberine, but treatments focused solely on killing microbes risk disrupting microbial diversity and tend to suffer from the same recurrence pattern. A truly holistic approach must address root causes and follow a structured, multi-phase protocol that may include:
Restore: Avoid cold, raw and dry foods. Emphasize warming, soupy meals and include digestive-stimulating herbs like ginger, black pepper and ajwain. Avoid overeating and keep heavy proteins separate from starches, and temporarily reduce fibre intake (i.e. low FODMAP diet). Support stomach and liver secretions with herbs like gentian, dandelion root and turmeric.
Clear: Use antimicrobial herbs—barberry, neem, black walnut hull—to inhibit bacterial overgrowth while preserving microbial balance.
Repair: Support gut healing with demulcent and vulnerary herbs such as calendula, licorice root and marshmallow root. Bone broth and nutrients like L-glutamine can also help restore the mucosal lining.
Reinoculate: Once symptoms subside, gradually introduce probiotic foods and supplements. Bifidobacterium strains are preferred for a constipation-dominant pattern, whereas Saccharomyces boulardii might be used for diarrhea symptoms. Live culture, fermented foods like pickles and sauerkraut, can also be used, but usually I recommend starting off with just small amounts of the brine.
Retrain: Regulate the nervous system to support digestive motility. Practices like breath work, meditation and vagal nerve stimulation can help shift the patient away from a fight or flight pattern. In some cases, using serotonin analogues such as psilocybin microdosing can help improve gut-brain signaling and resolve motility problems.
Recovery from SIBO is not simply about killing bacteria—it requires rebuilding the digestive system and promoting microbial balance. In some cases, fungal overgrowth (SIFO) coexists with SIBO, complicating the picture. This underscores the importance of personalized care that considers both microbial balance and the physiological mechanisms governing digestion.
Todd Caldecott is a medical herbalist and Ayurveda practitioner based in the qathet region who can be reached by email at [email protected] and via instagram.com/toddcaldecott. He contributes to the Peak's annual Live Well magazine, which comes out in late May.
Join the Peak's email list for the top headlines right in your inbox Monday to Friday.
