Are Probiotics Bad For You?

Are Probiotics Bad For You?

When Good Microorganisms Turn Bad

We are constantly bombarded with advertisements extolling the many virtues of consuming probiotics, whether in pill form, as a component of traditional fermented foods, and more recently in unlikely places as an additive to protein shakes, coffee, and, yes,..

Coffee protein shakes.

And while there is evidence suggesting there may be health benefits (something I’ve been exploring personally with the Genuine Health Probiotic, as have others) all this hype raises an alternative question:

Are probiotics bad for you?

The question itself rests on a false dichotomy.

Many of us (and I am very much among that “us”), are guilty of speaking of microorganisms as being either “good” or “bad,” as if they have moral agency.

They do not, at least not in any human sense of the concept.

Like pretty much every living thing on this planet (and I’ll leave it to you whether or not to include humans), they operate solely to their own benefit. Even when it appears as if they are working towards the benefit of another, it’s not a matter of bacterial benevolence or fungal philanthropy.

It’s a transaction.

You do something for me, and I’ll do something for you.

Probiotic microorganisms are no different.

To the extent they perform vital functions for us, whether it be synthesizing vitamins we cannot, warding off pathogens, or modulating the immune system, it’s an exchange, and they very much expect something of value in return.

That’s called “mutualism,” in which both parties benefit in some direct manner.

What happens if we violate that agreement? More on that in a bit, but by way of analogy, consider the consequences if you were to decide to stop feeding your beloved family Doberman for a week.

Let’s just say that you’re going to start bearing a striking resemblance to a T-bone.

Sometimes it’s not a mutually beneficial exchange. Some microbes are just along for the ride. They do neither harm nor good, like squirrels. They live in your trees and eat your nuts, but they are not really a bother, and so it is certainly not worth doing anything about.

It’s not like you’re going to eat the acorns.

That’s called “commensalism,” in which one party benefits, but not necessarily to the detriment of the other.

There is also the notion of there being “bad” microorganisms. This would be “parasitism,” in which one party benefits to the detriment of the other. Yes, there are pathogens that as far as we know do us nothing but harm, but there are many that are, to be anthropomorphic about it, more complicated characters.

Think, Loki.

But that is a topic for another time. (I’m looking at you H. pylori.)

For now, we’re focusing on “probiotics,” and those “good” bacteria living in our gut, making our lives better and helping to keep us healthy.

Except when they don’t.

For the purposes of this discussion I am also going to include the “squirrels,” or “commensals,” for reasons I will explain in a moment.

You Don’t Live Up To Your End of The Bargain

There are a number of mechanisms and circumstances under which once friendly microbes can turn on us, some perhaps obvious, some less so.

Let’s start with the obvious.

Many of the microbes inhabiting our gut are indeed helpful, essential really, if we are to maintain optimum health.

These “mutualistic” microorganisms provide direct benefits to their human hosts. Some produce butyrate and other short chain fatty acids (SFCAs) that are an energy source for the cells that make up our intestinal wall. Others produce vitamins K2 and B9 that the human genome is incapable of synthesizing and are poorly absorbed even when ingested.

Many aid in the regulation of the immune system helping to keep chronic inflammation at bay. It is believed that many of our modern chronic ailments involving a dysregulated immune system are connected in some way to an imbalanced microbiota.

Like your family Doberman, who provides companionship and protection in exchange for food and shelter, you provide your mutualistic microbes a comfortable living arrangement and nourishment.

Likewise, for your commensal microbes, the “squirrels” of your gut, the guys who hang around, set up shop, eat the food that passes through, but otherwise don’t cause any particular harm. I include them here because their mere presence in the human gut can help crowd out undesirable microbes, taking up space that might be otherwise occupied by pathogens.

Overall, it’s a great arrangement since you can’t directly use the food they prefer anyway (“acorns” if you will) as it is primarily in the form of various prebiotic soluble fibers. Sure, you still have to procure food that includes those nutrients, but it really doesn’t cost you anything extra necessarily, not if you are already consuming a healthy diet including a broad array of fruits, vegetables, and whole grains.

But you do need to consume that broad array of fruits, vegetables, and whole grains, because the only things the resident microbes that make up your microbiota, and any additional probiotics you may be consuming, have access to is what put in your mouth and swallow.

And that’s where the trouble can start.

Some quick background:

The inner surface of your intestinal walls is covered in a thick mucus. This mucus has a number of purposes, including serving as a protective barrier to the cells underneath and helping to keep pathogens (and other digestive contents) in the gut where they belong, and out of the rest of your body. It also provides shelter for the normally “good” microbes that inhabit it, but more than that, it is itself a source of food for them as well.

Some microorganisms prefer to rely on this mucus for sustenance, and that’s fine since the cells are constantly making more. The rest feed on the fiber you provide them through your diet. But even those microorganisms can munch on the mucus for in-between meal snacks if need be.

It’s a system that works fine, as long as you feed them regularly.

This is not unlike the deal you have with your Doberman. Give him his kibble, and he’s happy.

But if you don’t feed him, you find yourself with an increasingly less happy dog. (And I don’t mean to pick on Dobermans. You do not want to be standing between a cheese stick and a hungry Yorkshire Terrier either.)

If you don’t feed your microorganisms, like your Doberman, they will find other sources of food.

Also, like your Doberman, when push comes to shove, and there are no other alternatives, that source could be you.

In fact, for microorganisms, the only readily available source is you, or the mucus lining your gut. If these former mutualists (and let’s add the otherwise benign commensals while we’re at it) don’t get fed for very long periods of time, they will continue to eat away at that mucus lining, possibly overtaking its ability to regenerate.

This can expose the inner wall of your large intestine to pathogenic organisms possibly creating an inflammatory response making it ever more difficult to produce that protective mucus.

These are “good,” microbes, yes, good under normal circumstances, but they will do good for you only so long as you do good for them.

Basically, they are less a spouse who is with you in sickness and in health, and more like a roommate who is with you as long as you keep up with the utilities.

But here’s the thing to understand. When that happens, in this specific case, it’s basically your fault.

Starve these friendly microbes, and you’ve violated the agreement settled upon eons ago through the co-evolution of humans and our microbial populations.

If you keep your part of the deal, they’ll stay good. Well, mostly…


Another way normally “good” microbes can cause you trouble is when they venture out from their normal environs into others where they do not belong, or don’t belong in great numbers.

Think of your Doberman getting up on your bed and the squirrels running around in your attic.

This is called SIBO, or Small Intestinal Bacterial Overgrowth, and as the name implies, occurs when you have bacteria growing in your small intestine that either don’t belong there at all, or belong there only in small numbers.

A couple of squirrels on your deck is cute. 1000 is an infestation.

And even one squirrel sitting on your kitchen counter is one too many. (BTDT.)

By way of background, the vast majority of your gut microbiota resides in your large intestine. By the time your food gets there, all the nutrients that you can absorb on your own have been (employing only your human genome and the relatively paltry number of enzymes it can produce), leaving primarily the fiber content of your food. These are the nutrients the microorganisms of your microbiota feed on.

There, these microorganisms number in the billions, their combined mass weighing between two and six pounds.

By contrast, the microbes that usually reside in your small intestines, including the probiotic genera Lactobacilli and Bifidobacteria, number in the thousands at the beginning (the duodenum, just after the stomach) and finally in the millions towards the end (the ileum), just before your large intestine.

When a large portion of the billions of microbes from your large intestine migrate to your small intestine, or the microbes in your small intestine begin multiplying excessively, that’s when you are said to have SIBO, the symptoms of which can include bloating, pain, gas, and overall intestinal misery.

The causes of SIBO are poorly understood, but risk factors include prior injury or scarring to the small intestine, extensive antibiotic use, low stomach acid (often a consequence of chronic proton pump inhibitor use), slow intestinal motility (movement of food) and physical abnormalities of the small intestine.

Treatment for SIBO traditionally involves the use of antibiotics to wipe out the bacteria, although that can have unfortunate consequences regarding your overall microbiota. Regardless, if the underlying causes are not addressed the malady and symptoms will likely return.

Regarding the use of probiotics, this is a matter of some controversy. There are those who make the seemingly obvious argument that adding more probiotics to a system that has too many already (at least in the small intestine) is like throwing gasoline on a fire.

Similarly, the use of prebiotics, the food for these microorganisms, seems counter intuitive. The gas and pain individuals suffering from SIBO experience is a direct byproduct of this excessive fermentation (the manner in which microbes consume prebiotic fiber) occurring in the small intestine where it doesn’t belong. (In fact a common diagnostic test for SIBO is to check for methane or hydrogen on the breath.)

There are others who argue that it is more complicated than that.

I do not take a hard position either way at this point, and am frankly not qualified to do so, but this is a real problem, one best addressed with your healthcare practitioner.

And there’s still more


And then there are the far more complex mechanisms through which normally helpful or harmless microbes start doing you real damage.

Think dogs and squirrels, only with rabies.

A recent study found that Lactobacillus reuteri can, in the presence of Lupus (an autoimmune disease) turn very “bad” indeed.

While the L. reuteri is identified as a commensal in the report, it is in fact a mutualist, and a component of many probiotic formulations (including one I take).

And for good reason. It has been associated with the inhibition of pathogens, the reduction of pro-inflammatory substances, and, ironically (we’ll see how in a moment), the prevention of “leaky gut,” in which contents of the gut leak into the rest of the body causing all manner of havoc.

However, in lupus patients, L. reuteri appears to do the exact opposite. It presents itself in higher-than-normal numbers, and actually increases “gut leakiness” worsening autoimmune symptoms.

It was further found that the consumption of resistant starch (RS), a specific type of prebiotic fiber, suppressed the L. reuteri (by favoring microbes that produce butyrate, an SFCA to which L. reuteri is intolerant) thereby relieving symptoms.

The mechanisms through which this all takes place are not fully understood, but nevertheless reinforces the notion that when it comes to microorganisms being “good” or “bad,” it is almost wholly a matter of context.

One person can be seeking out the very same probiotic another is desperately trying to eradicate.

And both courses of action are perfectly sound, again, depending on the context.

So, Are Probiotics Bad For You?

To get back to the original question, the short answer is “it depends.”

They are not generally believed to be bad for you under normal circumstances. They are considered to be GRAS (Generally Recognized As Safe) by the United States Food and Drug Administration (FDA) and for the most part have been a component of the human diet (in the form of fermented foods) for millennia.

So, unless you have some specific allergy or other preexisting condition, popping a probiotic should not cause you harm beyond the occasional bloating and gas.

But it’s useful to keep in mind that these are living creatures with their own biological agenda, and depending on the circumstances, some of which you can control such as diet (feed your probiotics!) and some that maybe you can’t, such as succumbing to SIBO or lupus, they can be good.

Or they can be bad. Very bad.

Thank You!

That said, I will surely continue to use the shorthand of “good” and “bad” and other synonyms when discussing probiotics, commensals, and parasites (or pathogens), depending on the context, In fact, I did it more than once in this very piece.  But I will also keep in mind that it’s not that simple, and point that out when it is relevant.

Thank you so much for reading. Any thoughts you’d like to share, personal experiences, or question are more than welcome in the comments section below.

Take care!