Presumed Safety of Probiotics Questioned

In certain medical conditions, probiotic supplements may actually make things worse.

If you’ve ever made sauerkraut at home, you know you don’t have to add any kind of starter bacteria to get it to ferment, because the lactic acid-producing bacteria are already present on the cabbage leaves themselves out in the field. This suggests that raw fruits and vegetables may not only be a source of prebiotics—that is, fiber—but also a source of “novel” probiotics. 

As I discuss in my video Culture Shock: Questioning the Efficacy and Safety of Probiotics, researchers have since worked on characterizing these bacterial communities and found two interesting results. First, “the communities on each produce type were significantly distinct from one another.” Indeed, the tree fruits harbor different bacteria than veggies on the ground, and grapes and mushrooms seem to be off in their own little world. So, if these bugs do indeed turn out to be good for us, this would underscore the importance of eating not just a greater quantity but also a greater variety of fruits and veggies every day. And, second, the researchers found that there were “significant differences in [microbial] community composition between conventional and organic” produce. “This highlights the potential for differences in the microbiota [or bacteria] between conventionally and organically farmed produce items to impact human health”—but we don’t know in what direction. They certainly found different bacteria on organic versus conventional produce, but we don’t know enough about fruit and veggie bugs to make a determination as to which bacterial communities are healthier.

What about probiotic supplements? I’ve talked before about their potential benefits in my videos Preventing and Treating Diarrhea with Probiotics and Gut Feelings: Probiotics and Mental Health, but there appears to be publication bias in the scientific literature about probiotics. This is something we see a lot with drug companies, where the sponsor, such as the supplement company paying for its own probiotic research, may not report negative results. It won’t publish it, as if the study never happened. In that case then, doctors just see the positive studies.  

As you can see at 2:00 in my Culture Shock: Questioning the Efficacy and Safety of Probiotics video, using fancy statistical techniques, researchers estimated that as many as 20 unflattering studies “with smaller or deleterious results” were simply MIA. They just weren’t published. What’s more, even in the studies that were published, even when the authors were directly sponsored by a yogurt company, for example, “very commonly conflicts of interest are not reported…”

There’s also been concerns about safety. A review for the government’s Agency for Healthcare Research and Quality concluded that there’s “a lack of assessment and systematic reporting of adverse events in probiotic intervention studies,” so while “the available evidence in RCTs [randomized controlled trials] does not indicate an increased risk [for the general public]…the current literature is not well equipped to answer questions on the safety of probiotic interventions with confidence.”

Let’s talk about the study that freaked people out a bit. Acute pancreatitis, sudden inflammation of the pancreas, is on the rise and can become life-threatening in some cases, as bacteria break through our gut barrier and infect our internal organs. Antibiotics don’t seem to work, so how about probiotics? They seemed to work on rats. If you cause inflammation by cutting the rats open and “mechanically damaging” their pancreas, not only do probiotics show “strong evidence for efficacy,” but there were “no indications for harmful effects…” So, half the people with pancreatitis got probiotics, and the other half got sugar pills. As you can see at 3:37 in my video, the mortality rates shot up in the probiotics group compared to placebo within ten days. More than twice as many people died on the probiotics. Thus, probiotics for acute pancreatitis probably aren’t a good idea, and, even further, probiotics “can no longer be considered to be harmless”…

The researchers were criticized for not cautioning patients about the risk before they signed up for the study. (The study subjects were told probiotics had a long history of safe use with no known side effects.) In response to the criticism, the researchers replied that there were no known side effects—until their study.

At the start of this blog, I alluded to my Preventing the Common Cold with Probiotics? video.


Perhaps it would be safer and more effective to focus on fostering the growth of good bacteria by feeding them prebiotics (fiber and resistant starch). Learn more:

In health, 

Michael Greger, M.D.

PS: If you haven’t yet, you can subscribe to my free videos here and watch my live presentations:

How to Reduce Your TMAO Levels

Should we be concerned about high-choline plant foods such as broccoli producing the same toxic TMAO that results from eating high-choline animal foods such as eggs?

Choline- and carnitine-rich foods—meat, eggs, and dairy—can be converted by our gut flora into trimethylamine, which in our livers is then turned into TMAO, a toxic compound that may increase our risk of heart failure, kidney failure, and atherosclerosis, or heart attacks and strokes. The good news, though, is that this “opens up exciting new nutritional and interventional prospects” for prevention, as I discuss this in my video How to Reduce Your TMAO Levels.

Okay, so how do we do it? Well, if our gut bacteria can take meat, dairy, and eggs and turn them into TMAO, all we have to do is…destroy our gut flora! We could give people antibiotics to eliminate the production of TMAO. However, that could also kill our good bacteria and “facilitate the emergence of antibiotic-resistant bacterial strains.”

What about probiotic supplements? Maybe if we add good bacteria, they will crowd out the ones that take the meat, egg, and dairy compounds and turn them into the TMA that our liver turns into TMAO. But, that doesn’t work. Adding good bacteria doesn’t seem to get rid of the bad. What if we added new bacteria that could somehow siphon off the TMA made by the bad bacteria? Well, there’s a bacterium inside the guts of cows and sheep that turns trimethylamine into methane. Could we use that bacterium to get rid of some of the trimethylamine from our gut, like a cow fecal transplant? There’s a problem with that. If it didn’t take, you’d have to keep giving it to people: “Continuous administrations may be necessary if subjects do not become colonized.” So, might the fact that Consumer Reports found fecal contamination in every sample of beef it tested be a good thing? No. Methane-producing bacteria may be able to eat up our TMAO, but, unfortunately, these bacteria may be associated with a variety of diseases, from gum disease down to colorectal cancer, as you can see at 2:15 in my video.

If antibiotics and probiotics aren’t going to work to prevent gut bacteria from taking meat, dairy, and eggs and turning them into the trimethylamine, which our liver makes TMAO out of, I guess we have no choice but to cut down on…our liver function!

That was the billion-dollar answer to cholesterol. The same foods—meat, dairy, and eggs—raise our cholesterol, but dietary change isn’t very profitable. So, the drug industry developed statin drugs that cripple the liver’s enzyme that makes cholesterol. Could “pharmacologic inhibition” of the enzymes in our liver that make TMAO “potentially serve as a therapy for CVD [cardiovascular disease] risk reduction”? Trimethylaminuria is a genetic condition in which this enzyme is naturally impaired, in which there is a build-up of trimethylamine in the bloodstream. The problem is that trimethylamine is so stinky it makes you smell like “dead fish.” So, “given the known adverse effects…from sufferers of fish odor syndrome, the untoward odorous side effects of inhibiting this enzyme make it a less attractive [drug] target.”

Do we have to choose between smelling like dead fish or suffering from heart and kidney disease? If only there were some other way we could stop this process from happening. Well, what do those with trimethylaminuria often do to cut down trimethylamine levels? They stop eating animal products.

About a third of those who complain of bad body odor despite good personal hygiene test positive for the condition, but reducing or eliminating meat, egg, and dairy intake can be a real lifesaver. But, given what we now know about how toxic the end product TMAO can be for normal people, cutting down on animal products may not just save the social lives of people with a rare genetic disorder, but help save everyone else’s actual lives.

The “simplest point of intervention” is to simply limit the consumption of foods rich in choline and L-carnitine, which “can be an effective strategy to limit circulating TMAO.” But, wait! We could always try to genetically engineer a bacterium that eats up trimethylamine, but “the simplest and safest recommendation” may just be to eat more healthfully. You can completely eliminate carnitine from the diet, since our body makes all we need, but choline is an essential nutrient so we do need some. Thankfully, we can get all we need in fruits, vegetables, beans, and nuts. “However excess choline, such as that found in eggs, may be worth avoiding.”

Need we worry about high-choline plant foods, like broccoli? Consumption of cruciferous vegetables is associated with a significantly longer life and less cardiovascular disease mortality, as you can see at 5:34 in my video. To see what was going on, researchers took the vegetable highest in choline, brussels sprouts, and had people eat two cups a day for three weeks. What happened? Their TMAO levels actually went down. It turns out that brussels sprouts appear to naturally downregulate that TMAO liver enzyme—not enough to make you stinky, but just enough to drop TMAO.

And, people who eat completely plant-based may not make any TMAO at all—even if you try. You can give a vegan a steak, which contains both choline and carnitine, and there will not even be a bump in TMAO because vegetarians and vegans have different gut microbial communities. If we don’t eat steak, then we don’t foster the growth of steak-eating bacteria in our gut. So forget the cow—how about getting a fecal transplant from a vegan? From a TMAO standpoint, we may not have to eat like a vegan as long as we poop like one.


Can you sense my frustration as I read paper after paper proposing those ridiculous (but profitable!) answers when the safe, simple, side-effect-free solution was staring them in the face the whole time? It makes me think of so many parallels, not the least of which are:

For more on TMAO, the “smoking gun” of diet-microbiome-disease interactions, see:

In health,

Michael Greger, M.D.

PS: If you haven’t yet, you can subscribe to my free videos here and watch my live presentations:

Is Candida Syndrome Real?

Does the presence of Candida in stool correlate with “Candida-hypersensitivity” symptoms, such as headaches and tiredness? And what happens when people are placed on a high-sugar diet?

Despite its extensive use in the brewing and baking industries, only about 5 percent of healthy people—1 in 20—have anti-yeast antibodies in their bloodstream, whereas that percentage is more like 60 or 70 percent in people with Crohn’s disease. Most people with Crohn’s have antibodies that react to regular baker’s, brewer’s, or nutritional yeast, which are all just different forms of a yeast known as Saccharomyces cerevisiae.

But baker’s/brewer’s/nutritional yeast has never been directly implicated in Crohn’s. Maybe the antibodies are a direct reaction to it, or maybe they are a reaction to another yeast altogether and just mistakenly cross-react with regular yeast. Indeed, it was discovered that antibodies against Candida, a totally different kind of yeast (the yeast that causes thrush and vaginal yeast infections), can cross-react with Saccharomyces. Is it possible that baker’s/brewer’s/nutritional yeast was just an innocent bystander all along? I investigate this in my video Is Candida Syndrome Real?.

For nearly 30 years, we’ve known that antibodies to Saccharomyces are linked to Crohn’s disease, but instead of bread, beer, and nutritional yeast leading to Crohn’s disease, perhaps Candida is causing the Crohn’s disease and the antibodies. Or maybe Candida is the innocent bystander, and exposure to food and beverage yeast is the real culprit. You don’t know until you put it to the test: Remove yeast from the diet of Crohn’s patients, and see if they get better. If they do, then yeast was indeed the culprit. If they don’t? Then maybe Candida is the real cause.

Before I get to the study, let me first bust some Candida myths. Candida is a normal constituent of our gut flora. Get some Candida in your bloodstream, though, and it can cause a life-threatening infection. But it is normal to have some Candida in your mouth or colon—what’s important is location! location! location! It’s similar to how having stool bacteria in our colon is normal, but stool bacteria in our blood or a wound would be bad. Because of the ability of Candida to cause problems in the wrong location or in people who are immunocompromised, a Candida-syndrome theory arose, linking the presence of Candida to all sorts of health problems. This led to “mycophobia”—or fungalphobia—“spreading due to the false interpretation” that the finding of Candida in your mouth or stool is evidence of some kind of infection, rather than just being totally normal. (If you think the authors of that paper were being a little overdramatic with their phobia talk, just google “Candida” and you’ll see.)

Not only is it normal to have Candida in your gut, you apparently can’t get rid of it even if you wanted to. Give people powerful antifungal drugs, and you can drop levels down, but they pop right back up again as soon as you stop the antifungals. What about the concept that sugar feeds yeast, so you should go on a low sugar diet? It doesn’t make much sense because sugars should get absorbed high up in the small intestine and never even make it down into the colon unless you’re lactose intolerant. Indeed, there appears to be no correlation between Candida counts and sugar consumption. You can put people on a high-sugar diet by adding an additional 14 spoonfuls of sugar to their diets and still not see an effect. Of course, there are lots of science-based reasons to cut sugar from your diet, but Candida does not appear to be one of them.

There does not appear to be good “evidence for the existence of the so-called “Candida-syndrome” at all. But those are fighting words! “Few illnesses have sparked as much hostility between the medical community and a segment of the lay public as the chronic candidiasis syndrome.” The medical community has dismissed purported sufferers as emotionally disturbed and they’ve also been dubbed just plain crazy. Of course, you can’t just come out and call people crazy. “Psychiatric diagnoses need to be presented gently…” Some patients, for example, prefer to believe their mental illness is caused by the Candida, in which case doctors may just pat them on the head so they’ll take their pills. “However, patients self-diagnosed as having the yeast connection will only infrequently relinquish their illness”—some even to the extent they attempt to use their yeast as a drunk driving defense: I wasn’t drinking, your Honor. My yeast was just self-brewing beer in my gut!

The whole concept of Candida syndrome is officially derided by the American Academy of Allergy and Immunology as “speculative and unproven,” without any proof that it exists. The presumption that “the ubiquitous C. albicans [Candida] has some toxic effect on the human immune system…[is] without a trace of clinical evidence or scientific proof.” If you want proof, argued a response to the study, what about the millions of unnecessary tonsillectomy surgeries and all the radical mastectomies? At least putting people on low-sugar diets doesn’t disfigure them. Though some anti-Candida therapies can be “potentially dangerous,” antifungal drugs might breed resistance and can have side effects. Nystatin isn’t so bad, but ketoconazole can damage your liver. And, indeed, there are reports of people being treated for what may be a fake diagnosis and ending up in quite dire straits because of it. So, it’s important to know if the syndrome actually exists. Researchers decided to put it to the test in a super simple study: Give subjects stool-tubes to take samples, and ask them questions about their symptoms—headaches, stomachaches, tiredness, and all the other typical Candida syndrome symptoms. The result? The researchers found no relationship to whether or not the subjects had Candida growing in their guts. No hints of Candida syndrome could be found.


This was a bit of a tangent from the topic of my video Does Nutritional Yeast Trigger Crohn’s Disease?. I return to that topic in my video Is Nutritional Yeast Healthy for Everyone? and then offer hope for sufferers of another inflammatory condition in Dietary Cure for Hidradenitis Suppurativa.

In health,

Michael Greger, M.D.

PS: If you haven’t yet, you can subscribe to my free videos here and watch my live presentations: