A recent article titled “Brain fogginess, gas and bloating: a link between SIBO, probiotics, and metabolic acidosis” published in Clinical and Translational Gastroenterology has the whole SIBO world buzzing. I want to take a moment to dissect this article and discuss what it does and doesn’t tell us.

I use probiotics all the time with my SIBO patients and I get great results doing so. For that matter, there was a meta analysis published in 2017 showing that probiotics are capable of ‘decontaminating SIBO, decreasing H2 concentration, and relieving abdominal pain.’ So what gives? Are we all supposed to throw away our probiotics and run for the hills? Not so fast. Let’s take a good, hard look at this new study before we throw the baby out with the bath water.

SIBO Probiotics D-Lactic Acidosis and Brain Fog

Limitations noted by the authors (page 8, last two paragraphs):

  • “Whether the brain fog group had SIBO prior to using probiotics is unclear”

  • They only cultured fluid from the duodenum, the part of the intestine that is closest to the stomach. This means that they could have missed SIBO patients who’s overgrowths were not as bad/high up.

  • They did not re-test for SIBO (I can live with this, personally) or d-lactic acidosis (bigger deal, see below) after treatment was completed

  • There is no medical definition of “brain fog,” though they did their best to properly assess for it (not a deal breaker, in my opinion)

Other Limitations noted by Dr. D:

  • The researchers didn’t re-test patients for d-lactic acidosis after treatment. It would have been great to see them retest the brain-fog cohort, comparing changes in d-lactate in the people who reported a resolution of brain fog (85%) with those who did not (15%).

  • It would have been a clearer study if they treated things one at a time. Rather than doing antibiotics, dietary advice, and discontinuing probiotics all at once, they could have done one at a time and re-tested and re-assessed between phases.

Falsely stated, over-stepping, or confusing statements:

  1. Page 5, under “Breath Test”: “The patient’s typical brain fog symptoms experienced at home was reproduced during the breath test in 20/30 and all of them had evidence of SIBO either with the breath test or with culture.”

    1. According to Table 1A, the following patients experienced brain fog while doing the breath test but showed no evidence of SIBO on either test. Granted, they may have been false negatives and had SIBO.

      1. Patients 1, 3, 7, 9, 12, 16, 18, 21

  2. Page 6, under “Testing Summary”: “19 (63.3%) patients were diagnosed with SIBO and all of them had d-lactic acidosis.”

    1. According to table 1A, the following patients tested positive for SIBO but did not have d-lactic acidosis.

      1. Patients 2, 5, 6, 10, 20, 29

  3. Page 6, under “Follow up”: “All patients with evidence of lactic acidosis and/or SIBO were treated with various antibiotics… and were asked to discontinue probiotics (N=23).”

    1. This is unclear. In the BF group, 23 had d-lactic acidosis but another 6 patients had SIBO without d-lactic acidosis. It sounds like they are saying that only those with d-lactic acidosis were treated with antibiotics, but that can’t possibly be right..? If they really did treat both groups, that only left 1 patient (3.3%) who was not given antibiotics.

  4. Page 7, first few lines on the right: “The use of prolonged or excessive probiotics and/or cultured yogurt further contributed to the small intestinal colonization by lactobacilli and other bacteria.”

    1. This needs a citation. If this is being concluded from this study I think it’s over-stepping it’s reach in a big way.

  5. Page 7, last paragraph: “These measures led to significant improvement of symptoms in 70% of our patients and complete resolution of brain fogginess in 85% of patients, reaffirming that the symptoms were related to d-lactic acidosis and SIBO.”

    1. “and/or” would have been more appropriate. Re-testing d-lactate levels afterward would have proven or disproven this claim.

Other notes:

  • 11 patients in the brain fog group were consuming cultured yogurt daily. Two patients were consuming astronomically high amounts (20 oz per day!). Considering how common casein sensitivity and lactose intolerance are, this is definitely relevant. My concern would be less about the probiotics and more about the inflammatory food (dairy), though.

  • One patient in the non-brain fogged group used probiotics. It is unclear which patients that was and if they were one of the people with SIBO or d-lactic acidosis.

  • 21 patients had SIBO

    • 14 of which had d-lactic acidosis(67%), 7 of which did not have d-lactic acidosis

  • 25 patients had d-lactic acidosis

    • 14 of which had SIBO (56%), 11 of which did not have SIBO

  • 15 patients used PPIs

    • 10 PPI users had SIBO (67%), 5 PPI users did not have SIBO

    • 11 PPI users had d-lactic acidosis (73%), 4 did not have d-lactic acidosis

  • Assuming that the two testing methods they used identified all of the people with SIBO (assuming no false negatives)(see above), the two tests have the following error rates:

    • Glucose breath test: missed 7/18 patients, 38.9% false negative rate

    • Duodenal culture: missed 4/18 patients, 22.2% false negative rate


In the brain fog group, all patients with acidosis and/or SIBO were treated with antibiotics and were asked to discontinue probiotics. This group of 23 patients make up 76.67% of the brain-fog group (also, see bullet number 3 above). The remaining 7 people were asked to discontinue probiotic and yogurt use and given individual dietary advice. Dietary advice included diets for fructose, lactose, or fructan intolerance (per email with the lead author, Dr. Rao).

  • After treatment 70% reported significant improvement in gut symptoms

  • After treatment 85% reported complete resolution of their brain fog

  • In the non-brain fog group, four people were treated with antibiotics and reported significant symptom improvement. This sounds like they treated everyone with either SIBO or d-lactic acidosis (see bullet #3 above).

Assuming that only 23 patients were treated with antibiotics (see #3 above), that still makes up 76% of the brain-fog cohort. I can tell you with a great deal of certainty that infected patients feel a lot better when you kill their infection (SIBO). This includes brain-fog and inflammation symptoms. Likewise, people who are eating foods that they cannot digest (fructose, lactose, fructan) feel better when they stop doing so. I would have expected similar results even without the probiotic changes, and I am unsure how much cessation of probiotics played a role in this study. Worse still, none of us can be clear, because everything was treated and evaluated together. I understand that this helps people feel better quicker (good doctor-ing!), but it makes for less clear research.

Does this mean we shouldn’t use (d-lactate forming) probiotics?!

No, it does not tell us that:

  • The authors note that they were not able to conclude which came first, the chicken or the egg. We can’t tell which came first: d-lactic acidosis, SIBO, brain fog, or something else (inflammation, leaky gut, food sensitivities).

  • There was no clear association with discontinuing probiotics and symptom resolution. Discontinuing probiotics was one of three things used to treat patients (along with antibiotics and diet), and we cannot tell which helped and which may not have.

What this does tell us:

  • Brain fog is common among SIBO patients

  • d-lactic acidosis is common among SIBO patients

  • Many people with gut and cognitive issues (brain fog) use probiotics

  • Testing for SIBO is imperfect (false negatives)

  • Treating SIBO makes people feel a lot better

How to find the right probiotic for YOU:

It’s worth saying that not all SIBO patients are ready to handle probiotics right off the get-go. I rarely start SIBO patients on probiotics on day one, but I almost always work them in within a month or two. Still, determining the “best” probiotics for you is tricky at best and costly at worst. This is why I’ve devised a way to do this on the cheap! Check out this video below to hear the method to my madness.

Wishing you the best of poops,

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