If it looks like a….


Today I woke up to a comment from a long-time reader by the name of Sam, and thought my reply would be better served by a short post. Here is Sam’s comment:


Recently Chris Kresser did a podcast with a question about probiotics. The link is:


Here is an excerpt:

** Most people with SIBO do have gut symptoms, but some patients, I’ve seen them just come in complaining of primarily mental health problems, perhaps a skin disorder or something like that, and I test them for SIBO and find that they have SIBO and they have an overgrowth specifically of D-lactate-forming species of bacteria, like Lactobacillus acidophilus, which is otherwise a good guy, a good bacteria. But the problem is when it’s overgrown or there’s too much of it in the wrong place, it can cause these kinds of issues.

So for people who have SIBO, they probably want to avoid probiotics and fermented foods that have high amounts of D-lactate-forming species like Lactobacillus acidophilus **

Reading this, it appears that one of the most prevalent probiotic in supplements and foods may be bad for some people – what are your thoughts.”

Before I respond, let me also quote what Mr. Kresser said before this:

“So when D-lactate accumulates in the gut, it then can bet [sic] absorbed into the bloodstream, and other factors can enhance D-lactate absorption into the bloodstream, like if you have a leaky gut or if you’re under chronic stress or if there’s a lot of lipopolysaccharide, which is an endotoxin that’s produced by some gram-negative bacteria in the gut, hanging around that can increase the rate of D-lactate absorption into your blood. And there are a lot of studies that actually suggest that too much D-lactate in the blood can be problematic.  For example, there were two species of bacteria that produce D-lactate in higher amounts found in greater concentrations in patients with chronic fatigue syndrome, and in an animal study, animals that had excessive D-lactate in their gut exhibited anxiety, aggression, and impaired memory.  D-lactate can cross the blood-brain barrier, and it interferes with the energy supply of neurons, or brain cells.  These studies involve relatively low grade of D-lactate increases.  They weren’t huge, ridiculous doses of D-lactate that you would never get in real life, and the problem is that conventional medicine doesn’t really test for D-lactate, although it can be tested for with one of the tests I use frequently in my practice, an organic acids urine panel.

Some bells might be ringing for some of you because we’ve talked a lot about the gut-brain axis before and the connection between things like SIBO, small intestine bacterial overgrowth, and mental health problems, like anxiety, depression, insomnia, things like that, and this is one of the mechanisms here.  Overgrowth of lactate-producing bacteria, like acidophilus in the small intestine, the D-lactate gets across the gut barrier because it’s permeable often in people with SIBO and gets into the blood, goes up, crosses the blood-brain barrier, starts interfering with the energy supply of neurons, and then that can cause all kinds of different problems in the brain.  And it’s worth pointing out that this can happen even without any gut symptoms.  Most people with SIBO do have gut symptoms, but some patients, I’ve seen them just come in complaining of primarily mental health problems, perhaps a skin disorder or something like that, and I test them for SIBO and find that they have SIBO and they have an overgrowth specifically of D-lactate-forming species of bacteria, like Lactobacillus acidophilus, which is otherwise a good guy, a good bacteria.  But the problem is when it’s overgrown or there’s too much of it in the wrong place, it can cause these kinds of issues.”

First off, while it is true that elevated D-lactate levels can cause mental health issues, claiming that D-lactate producing bacteria are the reasons for this is a hypothesis that needs to be proven. Of course, by Mr Kresser’s own admission, this entire process also requires a “leaky gut” and gram-negative gut pathogens.

Nevertheless, the overwhelming majority of the published research on gut-brain interactions has very little to say about lactate-induced mental issues. As I’ve written repeatedly over the past year, it’s gram-negative endotoxins, and the immune responses they provoke, that are mainly implicated in mental and energy disturbances like anxiety, depression and chronic fatigue syndrome.

The fact of the matter is that a major way beneficial gut flora guard against gut pathogens is precisely by reducing the pH of the gut wall via lactic acid production. To quote Wikipedia:

“The lactic acid bacteria (LAB) are rod-shaped bacilli or cocci characterized by an increased tolerance to a lower pH range. This aspect partially enables LAB to outcompete other bacteria in a natural fermentation, as they can withstand the increased acidity from organic acid production (e.g., lactic acid).”

Raise gut pH by eradicating these bacteria, and I can guarantee you intestinal hell on earth.

In the case of SIBO caused by gastric-barrier dysfunction, the typical kinds of bacteria that colonize the small intestine are of the gram-positive variety:

“When the gastric acid barrier fails, contaminating bacteria are mainly composed of upper respiratory tract (URT) flora, such as viridans Streptococci, coagulase-negative Staphilococci, Haemophilus sp., Diphtheroids, Moraxella sp., Lactobacilli and other streptococci, most of which are Gram-positive bacteria. (1)

As you see, Lactobacilli can be part of the mix, but far from the only bacteria found in this variety of SIBO. I’ll explain in a minute why this finding is likely irrelevant.

That said, the overwhelming cause of SIBO is due not to impaired gastric-barrier function, but instead to impaired intestinal peristalsis. And in these cases, the predominant pathogens that colonize the small intestine are gram-negative bacteria. L. acidophilus has never been, is not now nor will ever be a gram-negative bacteria.

But a bigger question I have is how does Mr. Kresser know that there is an overgrowth of L. acidophilus in the small intestine of the clients he’s seeing? According to accepted medical practice, the only way to know with any certainty what microorganisms are overgrowing in the small intestine is by endoscopic aspiration. But even with this method, there are serious limitations that I’ll get to shortly.

This procedure involves sticking a flexible tube down a patient’s throat, through the stomach, into the small intestine and retrieving one or more samples from the gut wall. These samples are then sent to a lab to determine what bacteria are colonizing the small intestine.

Although considered the “gold” standard of SIBO diagnoses, there are, as I mentioned, limitations to this test. The first, of course, is how intrusive it is. Apart from cost, not everyone is clamoring to have a tube shoved down their gullet.

Another limitation is that it may miss an overgrowth of bacteria. It’s quite conceivable that the test misses a bio-film of pathogens because they are localized in an area not sampled.

A third huge limitation is that over 50% of the bacteria that are brought up cannot be cultured in a lab. They just do not survive when exposed to oxygen. Therefore, this test can only give an approximation of what is actually growing in the small bowel. This is one reason why eradicating small intestinal infections can be so vexing.

A fourth limitation to this test is contamination. Lactobacillus species are often found in endoscopic aspirate. However, that isn’t too surprising as these are the predominant beneficial bacteria found in the small intestine.

I had a very short back and forth once with Mr. Kresser because he erroneously claimed that the small intestine was sterile. While it does indeed contain far fewer commensal organisms than the colon, it is most definitely not sterile. Nor, by the way, are the stomach or lungs, two organs that until fairly recently were also considered sterile.

So the fact that labs often find Lactobacillus species in aspirate fluid proves only that the poor individual who underwent the procedure had not totally screwed up their small intestinal gut flora. As far as I’m concerned, this is good news, not bad.

Now, unless Mr. Kresser, who is a California-based acupuncturist, has somehow convinced the California Medical Board to allow him to perform endoscopic aspirations in his office in-between pin pricks, how exactly is his diagnosis being made?.

Anyone who tells you that a stool test can determine what bacteria is overgrowing in the small bowel is, to put it as charitably as I can, grossly mistaken. As SIBO typically involves bio-films that would not be affected by the passage of chyme, the chances of any stool test accurately detecting the type of bacteria colonizing the small intestine is exactly zero. Gastroenterologists would be using these tests on a daily basis if this were the case.

Another issue is how exactly would Mr. Kresser’s preferred method of testing have any way of knowing where in the digestive track the L. acidophilus was coming from? Does the L. acidophilus come tagged with a small intestinal zip code that localizes it to this part of the digestive tract and not the colon? I assume Mr. Kresser is aware that L. acidophilus also inhabits the colon, but given what I’ve read so far I’m having my doubts.

Finally, regardless of which probiotic you use, the reality is that there is conflicting evidence as to whether probiotics alone can cure SIBO without resort to antibiotics, pharmaceutical or otherwise. As I wrote in my post on SIBO treatment options, the jury is still out on this issue.

They certainly were insufficient to clear up my SIBO, and I suspect I’m not atypical. That is why I spent most of that post talking about rifaximin (brand name Xifaxan) and garlic.

Anyone on antibiotics for SIBO needs to be on probiotics and prebiotics to mitigate the damage to beneficial gut flora caused by these medications. If you choose to take a probiotic without L. acidophilus while on antibiotic treatment for SIBO, don’t blame me if you end up with another case of gut dysbiosis caused by devasted L. acidophilus populations. As I wrote in this post, L. acidophilus is not something you want to lack, especially if you’re a women.

And that, Sam, is what I think of that.

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