Does the Use of Whey Protein Supplements Negatively Affect Gut Health?

fitness-conceptIf you’re a regular reader of, you’ve undoubtedly picked up on the fact that I’m not a fan of protein supplements. In previous articles I’ve pointed out that protein supplements are evolutionarily novel food products with an abnormal nutrient composition and that the consumption of the most popular type of protein supplement on the market today – whey protein powder – causes a surge in insulin and has been linked with various health issues.

In the past I’ve briefly mentioned that I strongly suspect that the use of whey protein supplements negatively affects gut health. Actually, I would go as far as to say that I’m as good as convinced that whey protein supplementation is detrimental in the context of gut health. In today’s article, I thought I’d try to explain why I hold this belief…

The 5 primary reasons why I believe the use of whey protein supplements adversely affects gut health

1. Anecdotal reports indicate that a lot of people have experienced gut problems as a result of whey protein supplementation

A lot of gym goers and fitness enthusiasts I’ve talked to over the years have told me that they feel the use of whey protein supplements, in particular whey protein powders, destabilizes their gut. I’ve gotten so used to hearing this type of testimonial that an alarm bell now always goes off in my head when a client or another person I’m in contact with about health/fitness-related stuff tells me that he/she uses whey protein supplements. The ring of this bell is especially loud if the person in question complains about poor gut health. Anecdotal reports obviously don’t classify as solid science; however, they shouldn’t be brushed off as insignificant.

2. Whey protein supplements are evolutionarily novel additions to the human diet and have a nutrient composition that looks nothing like that of any of the foods that were a part of ancestral human diets

It’s important not to forget that it’s only very, very recently that protein supplements became a part of humans’ nutritional milieu. Our ancestors obviously did not use protein supplements of any kind. This is important to acknowledge, because it implies that protein supplements probably don’t agree well with our biology.

As you know if you’re a regular reader of this site, foods and nutritional products that have only recently become a part of the human diet typically induce some adverse health effects when they are consumed, which isn’t surprising, seeing as natural selection hasn’t gotten around to fully adapting the human body to its novel nutritional environment. One of the things “modern foods” such as bread, chocolate, and very fatty meats have in common is that they, when consumed, produce a microbiota that is a suboptimal match for the human biology. For example, regular consumption of refined grains and highly processed foods produces an inflammatory oral microbiota (1, 2, 3). This isn’t surprising, seeing as the human body evolved in the presence of the type of microbiota that is produced by real, whole foods; not by modern, processed food products.

I see no reason to think that whey protein supplements differ from other evolutionarily novel, processed food products in this regard. Actually, as I’ll talk more about in the next section, I suspect that whey protein supplements may be even less gut-friendly than many other modern food products. It’s important to note though that proteins are primarily absorbed in the small intestine, and hence, don’t reach the microbial reactor that is the human colon.

3. Milk, including the whey proteins it contains, was designed to support the growth and development of young mammals

The dairy industry has long promoted the consumption of cow’s milk and frequently points out in their commercials and ads that milk is packed with high-quality protein, vitamins, and calcium. I won’t dispute this claim. Milk is indeed high in protein, vitamins, and calcium. What’s often forgotten though, is that milk is a very special type of food. It was specifically designed, via natural selection, to support the growth and development of young mammals. The milk of each mammalian species on Earth is unique. Not only that, but its composition is affected by maternal genetics and nutritional status, the needs of the offspring, and other factors. Cow’s milk is not just this innocuous white liquid rich in calcium and protein. It also contains a variety of other compounds, including various hormones, which together with the nutrients, have been specifically selected because they produce strong, fit, and healthy cows.

The milk of the human female contains a range of factors that are known to support the development of the infant gut microbiota, rich in bifidobacteria (4) and other critters that are known to be important for the development of the immune system of human infants. Whey protein, which is an essential component of both cow’s milk and human milk (5), was until very recently not a part of the adult human diet. Its effects on the gut microbiota are probably not as potent as those induced by the complex carbohydrates found in milk. With that said, I find it very likely that the consumption of whey protein does significantly alter the gut microbiota. This idea is supported by studies showing that whey protein is bifidogenic (6, 7, 8, 9). Infants greatly benefit from being breastfed, in part because the consumption of milk enforces the development of a gut microbiota dominated by bifidobacteria and lactobacillus and low in pathogen. However, it’s a very unnatural behavior for an adult mammal to consume milk – and even more so large quantities of a specific compound (e.g., whey protein) found in milk.

4. My own gut wasn’t, and probably still isn’t, fond of whey protein supplements

In my teens, I drank whey protein shakes. I did so to support my heavy strength training regime. I can clearly remember that I felt that this practice did not agree with my body and gut; however, it took quite some time before I gave it up nonetheless, in large part because I’d been led to believe from reading fitness blogs and talking to people at the gym that whey protein powder should be a part of the nutritional arsenal of all strength training enthusiasts. It took me quite some time to recognize the fallacy of this notion.

I don’t dispute that it’s important for athletes, and in particular bodybuilders, to take in moderate-large quantities of protein or that its very convenient to use whey protein supplements; however, I very much question the idea that it’s healthy to supplement with protein. If the choice is between taking in insufficient amounts of protein and using a protein supplement, I would probably choose the latter; however, if possible, I would get all of my protein from real food.

5. Whey protein supplementation has been linked with certain health disorders that are closely associated with gut dysbiosis

Most of the research on whey protein supplementation has historically focused on how the use of whey protein supplements affect muscle growth and athletic performance. Not a lot of studies have looked into the negative aspects of whey protein supplementation. With that said, we do have some research to go on. For example, studies have shown that whey protein supplementation promotes the development of acne vulgaris in some individuals (10, 11, 12, 13). This potential of whey protein to cause and aggravate acne is often attributed to its insulinogenic and growth-promoting properties. Personally, I strongly suspect that one of the main reasons why the use of whey protein products has been shown to cause acne in some individuals has to do with its effects on the gut, and in particular, the microbiota of the gut. As I’ve pointed out on the site in the past, dysbiosis of the skin and gut seem to be a fundamental cause of acne vulgaris.

What about the studies that seem to show that whey protein supplementation positively affects gut health?

As I’ve pointed out in some of my previous articles on science and the human microbiome (e.g., this one, this one), PubMed is a minefield. Unless one possesses knowledge about evolution and statistics and knows a thing or two about how the scientific process works, one may quickly end up atop of an explosive object if one decides to head into the realm of science. What I mean by that is that it’s easy to misinterpret studies, jump to the wrong conclusions, and make decisions that unfavorably affect one’s health or the health of others.

For example, let’s say that we do a study to investigate how the use of a whey protein supplement affects muscular development in hard-training bodybuilders. We split 60 bodybuilders into two groups and instruct the participants in one of the groups to consume 60 grams of whey protein each day, whereas we tell those in the other group not to use any protein supplements. We also instruct all of the participants to adhere to the same strength training program. At the end of the intervention, as we collect our final data and assess the outcome of the study, we find that the whey-consuming group came “out on top” with respects to hypertrophy.

Some people may look at this type of study and jump to the conclusion that it’s unequivocally beneficial to use whey protein supplements. I’d argue that that is a big mistake. First of all, we can’t exclude the possibility that the participants in the whey-consuming group took in more total protein every day than the participants in the other group. In many, if not most, studies on whey protein supplementation and athletic performance, protein intake is not the same in the different study groups, which is obviously problematic. Second, the hypothetical study above only looked into the effects of protein supplementation on muscular development. It tells us nothing about its effects on other aspects of human health or physiology. One can’t exclude the possibility that the whey-consuming participants fared worse than the other participants with respect to various health outcomes that were not assessed in the study.


Mother’s milk contains a long list of compounds, including whey proteins, that are known to stimulate the growth, immune maturation, and development of young infants. These compounds are a natural and important part of the diet of babies; however, they are not an evolutionarily normal part of the diet of adult humans.

The point I’m trying to make here is not that we can’t learn anything from the scientific literature, but rather that it’s very important to be cautious when one interprets the findings of scientific experiments. As I pointed out under point 3 in the list above, studies have shown that the use of whey protein products promotes the growth of bifidobacteria and enhances intestinal barrier integrity. Many of the researchers who’ve made these observations have concluded that it’s benefical, gut health wise, to use whey protein supplements. I’d argue that this is probably an erroneous conclusion.

One doesn’t have to be a genius to figure out why there is a link between whey protein supplementation, the growth of bifidobacteria, and intestinal permeability. It makes complete sense that certain types of bifidobacteria are fond of whey proteins, as well as certain other compounds found in mammalian milk, seeing as bifidobacteria are a dominant part of the gut microbiota of infants. Moreover, it makes complete sense that researchers who’ve looked into how the use of whey protein supplements affect gut barrier integrity in patients with gut disease have found that whey protein supplementation improves intestinal barrier function (6, 14) seeing as mammalian milk, with all its whey proteins, hormones, and nutrients, was specifically designed to support the development of the gut and immune system of young mammals and protect them against harm.

What’s important to point out is that the fact that some studies seem to show that whey protein supplementation decreases intestinal permeability, lowers the pathogen load of the gut, and promotes the growth of bifidobacteria does not mean that whey protein supplementation is beneficial in the context of building a healthy, adult human. It merely reveals the obvious, namely that milk-derived compounds such as whey protein possess potent immunomodulatory properties.

Key takeaways

It’s obviously highly beneficial for a baby to consume mother’s milk, seeing as the compounds found in milk, such as whey protein, promote the growth of certain types of bifidobacteria in the gut of the infant, keep pathogens at bay, and enhance the integrity of the infant’s intestinal barrier. Basically, they support the growth and immune development of the child.

These types of processes are a natural and essential part of the developmental phase of mammals. They are not, however, a natural part of the adult phase of the human life cycle. I very much question the idea that it’s healthy for an adult person to consume large quantities of one or a few compounds derived from milk. Doing so may nudge the gut microbiota of the person in question towards a configuration that is characteristic of the infant gut microbiota, thereby undermining the development and maintenance of a healthy adult gut microbiota, and adversely affect immunity, intestinal health, and digestion over the long-term.

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  1. Hi Eirik. I’m sure you’ll get a lot of arguments from fans of whey protein, but I agree with you a hundred percent.

    I, too, am one of those people who got sick from consuming whey protein in my younger and dumber days. I’m talking about nausea, cramps, and diarrhea, not just slight discomfort. I thought it was because I’m somewhat lactose intolerant, but whey protein isolate, which I was assured contains little to no lactose, made me just as sick.

    I’m always amazed that proponents will carefully limit the amount of protein they consume from real food, the thinking being that too much protein activates the mTOR pathway and can cause cancer (a theory I find debatable). But then those same persons will ingest copious amounts of highly processed, totally unnatural whey protein instead, having bought into the hype that a lab product is somehow better than real food. This makes no sense at all to me.

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