Causes Of SIBO Recurrences

SIB0-Small Intestine Bacterial Overgrowth

Adopted from Dr. Allison Siebecker (


Cause of recurrences in SIBO:


SIBO is a disorder that relapses because bacterial eradication itself does not always correct the underlying cause(s).  Two of the main physiologic underlying causes are deficiency of the migrating motor complex (MMC) and anatomical/structural alteration affecting the small intestine.

The MMC moves bacteria down into the large intestine during fasting at night and between meals, clearing them from the small intestine (SI) on a daily basis.  Structural issues can also block the clearance of bacteria (i.e., adhesions), allow them to get trapped (blind loops, diverticulosis), or allow backflow from the large intestine (surgical removal of the ileocecal valve).

Bacteria can repopulate the SI within 2 weeks of finishing antibiotics, herbal antibiotics, or elemental diet, without prevention, though it may take longer.  If diet alone is used as treatment, the underlying causes must still be addressed for optimal improvement.  

In 2006 Dr. Pimentel shared his prevention protocol which includes a prokinetic drug (small intestine motility agent) and a lower carbohydrate diet.  The combined use of these two (#'s 1 & 2 below) is of key importance for the prevention of relapse.

The main strategies for prevention are:

  • Stimulate the migrating motor complex (MMC), the bacterial cleansing wave of the SI, with a prokinetic agent (see below).
  • Follow a SIBO diet ongoing.  More restricted SIBO diets are usually expanded to include more carbohydrates as tolerated during the prevention phase.  
  • Support Hydrochloric Acid (HCl), the antibacterial acid of the stomach, if deficient with Betaine HCl, herbal bitters, or apple cider vinegar (1tsp in 1 cup water) before meals.
  • Remove proton pump inhibiting drugs (PPI's), and antacids, a cause of reduced HCl and a risk factor for SIBO.
  • Get Visceral Manipulation which can help with motility and structural issues and/or other bodywork.  Visceral manipulation practitioner directory (international). (I Dr. Marks practice visceral manipulation as well.)
  • Correct Ileocecal Valve Syndrome (IVC) if present; is the physical barrier to bacterial backflow from the large intestine (LI). See Functional Gastroenterology by Dr. Sandberg-Lewis, chapter 15.
  • Correct neurological deficits and dysfunctions, including sympathetic dominance (chronic stress).
  • Treat any concomitant diseases that contribute to SIBO.
  • Prokinetic Options and Dosing

The following information is provided for physicians.  A trial removal of the prokinetic after at least 3 months is suggested, but continued long-term use may be needed.  Prokinetics studied for SIBO include:

Pharmaceutical Options

Low-dose Naltrexone (LDN)- 2.5 mg for diarrhea types or 5 mg for constipation types, at bedtime (Ploesser et al)

Low-dose Erythromycin- 50 mg at bedtime (Pimentel et al).  Compounding is necessary for this low dose, or quarter a 250mg pill to get 62.5 mg, at bedtime.

Prucalopride (Motegrity/Resolor/Resotran) 0.5-1 mg at bedtime.   Original studies were done on Tegaserod (Zelnorm 2-6mg hs, Pimentel et al) which showed greater success than erythromycin at prolonging SIBO remission.  Prucalopride has not been studied for SIBO but has the same mechanism of action, higher receptor selectivity, excellent safety (Manabe et al) and effectiveness and has therefore been used in place of Tegaserod while it was absent from the US market (which is available again as of 2019).

Natural Options

None of the natural prokinetics have been studied for SIBO but Iberogast (an herbal combination without ginger) and Ginger Root (an ingredient of all the other options listed) have both been studied as prokinetics in other conditions and shown efficacy.

Iberogast 30-60 drops at bedtime

Ginger Root 1,000mg at bedtime

Ginger containing Prokinetic Formulas:

Prokine (Vita Aid) 1-3 caps at bedtime

Motil Pro (Pure Encapsulations) 2-3 caps at bedtime

Motility Activator (Integrative Therapeutics) 2 caps at bedtime

GI Motility Complex (Enzyme Science) 1 cap at bedtime

SIBO-MMC (Priority One) 3 caps at bedtime

Bio. Me.Kinetic (Invivo) [the UK only] 2-3 caps at bedtime


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