By Stacey Raffety ND

SIBO is defined as an abnormally large amount of bacteria growing in the small intestine, a dysbiosis (as opposed to a symbiosis) of the normal flora. This is not unlike C. difficile or candida overgrowth in that it can interfere with well-designed treatment for Lyme and other infections, but SIBO can be more insidious: its symptoms can be acute and dramatic, but more often are mild and chronic.  Over time, it can quietly lead to malabsorption, malnutrition and toxic burden. Once thought to be relatively rare, SIBO is now known to be more prevalent than original estimates. New interest of late has led to a better understanding of the process that creates this bacterial overgrowth, how to test for it and how to treat it.



Normally the small intestine contains about half the amount of bacteria found in the large intestine (1).  There are several systems that maintain this ‘terrain’: gastric secretions inhibit the growth of invading organisms, and normal intestinal motility clean out excess bacteria before it can attach itself in the small intestine. There is also a barrier provided by the healthy bacteria – the probiotics – that prevents invading organisms from attaching. Other defensive mechanisms involve mucosal immunity, intestinal, pancreatic and biliary secretions, and the ileocecal valve.

Anything that disrupts these systems – the natural aging process, anatomical changes, changes in pH, neurotransmitter excess or deficiency, or any number of diseases as well as side effects of the necessary antimicrobial treatment – allows an overgrowth of bacteria. Not only are there increased numbers of intraluminal bacteria, but the composition of the flora also changes to a predominantly anaerobic one, resembling that of the colon.

The consequences of SIBO occur because of a cascade of events that result in maldigestion and malabsorption of nutrients: (2)

  • Bacteria damage the small intestine mucosa, decreasing brush border enzymes, and disaccharides (sugars) can no longer be broken down and absorbed. Bacteria feed on the undigested sugars, proliferate and release gas and toxins as waste. (3)
  • Peptidases are another group of brush border enzymes that erode and protein malabsorption results. (4)
  • Digestion and absorption of the fat soluble vitamins (A, D, E, and K) are disturbed due to bacterial deconjugation of bile acids; symptoms from these deficiencies are only seen in extreme cases. (5)
  • Cobalamin (vitamin B12) deficiency is common due to malabsorption and bacterial uptake of the vitamin. (6, 7)
  • Folate levels are often elevated because the bacteria produce folate on their own. (8, 9)


Depending on the degree and duration of the events described above, some or all of these symptoms will be present:

  • constipation, diarrhea, or both (IBS)
  • bloating
  • flatulence, belching
  • abdominal cramps, abdominal pain
  • nausea
  • leaky gut
  • anemia
  • malnutrition
  • weakness, fatigue
  • steatorrhea, weight loss


Treatment for TBD can cause and/or exacerbate existing SIBO. Use of oral antimicrobials can cause the loss of protective flora and changes in motility that enables bacterial overgrowth, causing slow onset GI distress. Or mild and undiagnosed SIBO may be present before treatment for TBD and oral antimicrobials clear up their gastric symptoms, but only temporarily. This pattern may be 1/ a relapse of TBD symptoms or 2/ diagnostic of a pre-existing SIBO.

Tick-borne disease, itself, may cause and/or exacerbate SIBO. Gastrointestinal symptoms, while not usually the only symptoms, are common complaints in Lyme disease. (10)  If Lyme is disrupting gastric motility, causing intestinal inflammation or lack of appetite, SIBO may follow.

SIBO decreases the absorption of antibiotics. Once the mucosal lining of the small intestine is damaged, the malabsorption of medication and food can cause treatment for TBDs to stall.

SIBO can mimic TBD, gluten enteropathy, intestinal candidiasis, and C. difficile, and should be added to the list of potential ‘obstacles to cure’ to be addressed during treatment for tick-borne disease.

Certain oral antibiotics may be effective for TBD and SIBO at the same time (see Treatment section below). Identifying the presence of or tendency to SIBO can affect choice of antibiotic treatment.



  • dramatic but transient improvement in gastrointestinal symptoms with antibiotic treatment
  • gluten-free diet doesn’t improve symptoms when Celiac is suspected
  • probiotic containing prebiotics (inulin or FOS) worsens gastrointestinal symptoms
  • fiber worsens constipation and/or other gastrointestinal symptoms
  • carbohydrates worsens gastrointestinal symptoms
  • inability to tolerate even small doses of any antibiotic therapy
  • antifungals don’t relieve symptoms of what appears to be intestinal yeast


The gold standard for testing for SIBO has been aspiration and direct culture of contents from the middle of the small intestine (jejunum).(11) This test is invasive, and has only has a 38% accuracy (12)

Breath tests are replacing aspiration in popularity. The breath tests measure hydrogen and methane, gasses produced by bacteria ingesting unabsorbed carbohydrates. If the small intestinal mucosa was intact and able to absorb the carbohydrates, none of these gasses would be present.

Sensitivities for breath tests range from 70-90% and specificities from 40-100%. Currently it’s believed that the glucose hydrogen breath test has a higher sensitivity than the lactulose because glucose is more readily absorbed. With lactulose, changes in transit time confuse the interpretation. (12)

Other drawbacks include disagreement on interpretation of breath tests results, though if there’s any increase in hydrogen or methane, it is there because of bacterial fermentation of undigested carbohydrates. Preparation for the breath test – elimination of carbohydrates for 12 hours and then fasting for 12 hours before doing the test – is rigorous, but necessary, and shorter or longer than normal transit time can still alter the interpretation of the results. Alterations in flora (antibiotics or diarrhea) and motility disorders can also confuse results.



The human gastrointestinal microflora is a complex ecosystem of approximately 300–500 bacterial species. (12) Clearly treatment with oral probiotics alone isn’t going to reestablish what was there before infection or treatment with antibiotics. For this reason and because of the length of time it takes to restore the absorptive surface of the small intestine, treatment is protracted and must accomplish a sequence of goals rather than just eliminating pathogenic bacteria.


Treatment Goals

  1. Avoid further damage.

Eat whole foods, 3-4 low-carb (avoid feeding the overgrowth), gluten-free (avoid irritation and inflammation) meals a day. Avoid known allergens. Meals should be on average 4 hours apart (eating without breaks inhibits ‘fasting phase’ motility in the small intestine, which is responsible for sweeping toxins, die off, undigested food, and pathogenic bacteria out of the small bowel and into the large bowel for elimination). Taking a break from antimicrobials might be necessary till the gut is healed.

  1. Remove the pathogens and the toxins.

Recent studies have shown efficacy with a 10-day course of Xifaxan (or the generic, Rifaximin), 400 mg, tid.(13) Xifaxan is originally intended for treatment of traveler’s diarrhea, at a lower dose of 200 mg tid for 3 days. The risk of side effects is very low, in part due to the fact that the drug is not absorbed into the blood stream and remains 100% in the digestive tract. Other antibiotic treatments that are potentially effective are Neomycin (especially with constipation when prescribed with Xifaxan), Tetracycline and Sulfamethoxazole. Nutraceuticals that are potentially effective are grapefruit seed extract, Berberine aquafolia, and enteric-coated peppermint oil.

  1. Replace what was lost.

Supplement any nutrient deficiencies (give the body what it needs till it can fully absorb nutrients again from food).

  1. Reinoculate with healthy flora.

Remember, we originally utilized 300-500 strains of beneficial flora. So switch brands with every new bottle to get as many different strains as possible. Choose dairy free brands to lower the amount of sugar till the absorptive surface is repaired. Avoid prebiotics of inulin and FOS (they feed bacteria).

  1. Repair the cause.

Repair motility, balance acidity and pH, restore digestive enzymes, restore gall bladder contractility, increase secretory IgA, heal villous atrophy, restore mucosal integrity and absorptive surface, and establish regularity of elimination.


The dramatic changes in the bacterial flora of the small bowel that occur in SIBO have a multitude of effects that if left untreated will only get worse over time. The medications necessary for treatment of TBD can cause or exacerbate SIBO. Recognizing and treating SIBO during treatment for tick-borne disease can improve treatment outcomes by removing the toxins of bacterial overgrowth, eliminating GI distress, and improving absorption of nutrients and medications.



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