Do Keto Diets Affect the Microbiome?

woman eating vegetablesJust how important is the gut microbiome — you know, the “critters” who live in your gut? Well, it plays a key role in digestion, metabolism, the immune and endocrine systems, and neurological functioning. Gut microbiota synthesize key nutrients like B vitamins and vitamin K, and neurochemicals like GABA and serotonin. Short-chain fatty acids (SCFAs) produced by gut microbes promote glucose regulation and insulin sensitivity.1 The microbiome “talks” to the brain via the gut-microbiome-brain axis, and the actions of gut microbes affect things the permeability of the blood-brain barrier and development of glial cells in the brain.2 The integrity of the gut lining also depends on a healthy microbiome. When that integrity is compromised and the gut becomes “leaky,” systemic inflammation, autoimmune illnesses, and central nervous system disorders ensue.3

This is only the short list, so basically, it’s impossible to overstate the importance of the microbiome for overall health. Arguably, you and I are just walking hosts, wholly dependent on the trillions of microbes inhabiting our guts for our ability to move through the world more or less functional and, ideally, disease-free.

No wonder people get alarmed when they hear the rumor that keto diets could be bad for the microbiome. If true, that would be a good reason for most of us to steer clear of these diets. 

At the same time, researchers and practitioners are keenly interested in keto diets’ potential to treat people with diseases including:

  • Inflammatory bowel diseases
  • Type 2 diabetes
  • Parkinson’s disease
  • Autism-spectrum disorder
  • Certain cancers
  • Alzheimer’s disease

One thing these diseases have in common is they are all associated with underlying gut dysbiosis (imbalances). Given that keto seems to be widely beneficial for these and other chronic health issues, is it likely that it would also pathologically “mess up” the microbiome? Not likely perhaps, but not impossible. Life-saving pharmaceuticals have undesirable side effects, too. When you dig into the evidence on keto’s effect on the microbiome, it is mixed, but it’s also quite limited at this point. The big question is: is there cause for concern?


What Constitutes a Healthy Versus Unhealthy Microbiome?

Let’s start by asking what constitutes a healthy or optimal microbial community so we know if keto helps, hurts, or has no systematic effect.

Broadly speaking, you want your microbiome to be diverse and “balanced.” Right now, you’re giving a ride to trillions of microbes, including 400+ species of bacteria, archaea, fungi, viruses, and other organisms. Scientists’ ability to analyze individuals’ microbiomes has advanced substantially in the past two decades, but there is still a lot to learn. Based on the available data, some types of microbes are generally considered to be helpful because of their role in metabolism and/or because they produce metabolites (byproducts of metabolism, essentially) that we need to function properly. Others are pathogenic, meaning they can cause disease and dysfunction if they become too prevalent. One of the good guys’ jobs is to keep the bad guys in check, but we’re always carrying around an array of both.

We have some idea about which microbes, and in what amounts, might predispose us to certain health problems like insulin resistance or cardiovascular disease. However, there is tremendous variability from person to person that makes it hard, maybe impossible, to characterize a “healthy microbiome.” Two equally healthy people could have considerably different microbial profiles based on their genes, diet, lifestyle, environment, and age.4 Moreover, most of the current research focuses on gut bacteria, which are only one piece of a complex system.

This is a roundabout way of saying that while we have some understanding of what’s good or bad on a population level, especially when it comes to major groups of gut bacteria, we don’t know what’s optimal for any given individual. Nor can we tailor dietary advice to a specific person based on their gut microbes.5 Remember, too, that our ideas of “normal” and “healthy” are based on the average population—i.e., mostly on people eating standard Western diets. What’s normal for them might not be optimum for someone eating a Primal, paleo, or “clean” keto diet. There will be similarities, surely. Overgrowth of pathogens is going to be bad for everyone. But in terms of specific effects or ideal balance between species, there may be important differences.

Do Keto Diets Affect the Microbiome?

Undoubtedly. There’s ample evidence that if you change your diet—from a typical Western diet to a carnivorous or vegan diet, for example—the composition of your microbiome will shift within a couple of days.6 Individuals with different habitual diets also have, on average, different bacterial profiles based on the relative amount of fat, protein, and carbohydrates they consume.7

Of course, different isn’t necessarily bad. We don’t just care if keto diets change the microbiome. We know they will.8 What we really want to know is whether keto diets reliably change the microbiome in consistent ways across individuals and whether those changes lead to positive, negative, or neutral effects when it comes to health. That data (mostly) doesn’t exist.

So why do people say that keto is bad for the microbiome?

Most of the concern comes from two places. First, researchers point to individuals in traditional-living societies with virtually no incidence of modern diseases. Their microbiomes, which are much more diverse than the average person’s, are considered the gold standard of gut health. This diversity is due in part to the abundance of fibrous plants in their diets that provide microbiota-accessible carbohydrates, or MACs, to “feed” desirable gut microbes. Some scientists believe that the lack of MACs in high-sugar, high-fat modern diets directly contributes to the unchecked rise of diseases of civilization.9 Keto and other low-carb diets are also comparatively low in MACs, so they must be bad, right?

It goes without saying, though, that there is a world of differences in the diets, lifestyles, and environments of individuals living in traditional societies and the average modern adult, all of which affect health. It’s impossible to isolate the effects of one variable (fiber intake, in this case). Likewise, there are obvious and important differences between a Primal-aligned keto diet and high-sugar, high-(pro-inflammatory)-fat modern diets.

Second, some mouse studies suggest that high-fat diets lead to unfavorable changes in the microbiome.10 Mice fed higher-fat diets tend to harbor more bacteria associated with inflammation and disease in humans, and fewer bacteria that are generally regarded as “protective.” It’s not that these studies aren’t meaningful, but they only show associations between one aspect of diet and changes in a small subset of gut flora.. in mice. These findings are far from proving that well-formulated keto diets are bad for the human microbiome. Ultimately, we need human studies that show predictable diet-related changes in keto dieters’ microbiomes and that link those changes to specific health outcomes.

As long as I’m making requests, I have a few more:

Studies that use healthy human subjects

Human studies in this area have focused on people with preexisting health issues like drug-resistant epilepsy who are using a ketogenic diet therapeutically. Epilepsy is characterized by gut dysbiosis and reduced microbial diversity.11 It is also more common among people with other autoimmune disorders that are likewise associated with dysbiosis.12

Researchers believe that one reason keto diets help epileptic patients is that they alter the microbiome and the activity of gut microbes. Compared to kids who aren’t helped by the diet, children who experience fewer seizures on a keto diet also show distinct shifts in their microbiomes.13 In a quite remarkable series of studies, Olsen and colleagues demonstrated that keto-specific microbiome changes are directly responsible for the diet’s therapeutic effects.14 First, they showed that ketogenic diets raise seizure thresholds in mice, along with changing the levels of certain gut bacteria. Then they ran the same experiment again in mice without normal microbiomes, either because they were raised in sterile environments (“germ-free” mice) or given antibiotics. The keto diet did not protect against seizures in those mice, presumably because it couldn’t have the same effect on their guts. Finally, the researchers identified two bacteria that were increased in the original keto diet group (A. muciniphila and Parabacterioides) and transferred them to a new group of germ-free mice. The mice inoculated with these bacteria also became more resistant to seizures—but only when both types of microbes were administered.

Other studies suggest that microbiome changes mediate the beneficial effects of ketogenic diets for autism (in mice)15 and multiple sclerosis (in humans).16 We also know that keto diets can greatly improve quality of life for individuals with gut health and digestive disorders like IBS and Crohn’s Disease, providing dramatic improvement for their gastrointestinal symptoms.

On the surface, it seems unlikely that keto diets can help digestive health overall and reduce systemic inflammation17 but also be bad for the microbiome. However, we can’t rule out the possibility that keto is beneficial for people who start out with dysbiosis, but it causes unfavorable changes for people who start with a relatively healthy, diverse microbiome. That’s why we need studies of healthy human subjects.

Studies that examine ketogenic diets, not just “high-fat” or “low-carb” diets

Ketogenic diets aren’t just low carb and (relatively) high fat. Ketones themselves have all sorts of effects—providing energy for cells, reducing inflammation and oxidative stress, affecting mitochondrial function, epigenetic changes, hormone production, and more—that aren’t about carbs or fat per se.

One of the studies frequently offered as evidence that keto diets are bad is a 2019 study that compared the impact of high- and low-fat diets on the microbiome of 217 healthy young adults.18 The results showed supposed negative shifts in gut flora, as well as increased inflammatory markers, among people eating a high-fat diet. The thing is, though, that the high-fat diet was nowhere near ketogenic, with 40 percent of calories coming from fat and 46 percent from carbohydrate. In contrast, on a typical ketogenic diet, carbs only provide somewhere in the ballpark of 5 to 10 percent of daily energy. (Also, the increased fat in the high-fat diet all came from added soybean oil, yuck.)

A study published in 2020 in the prestigious journal Cell shows why this distinction is so important.19 First, the researchers had overweight or obese non-diabetic men follow either a ketogenic or high-fat (but not keto) diet for four weeks. When they analyzed their microbiomes, the researchers identified key differences, notably a reduction in Bifidobacterium, in the keto diet group. Next, they conducted a series of experiments in mice, which showed that the ketone body beta-hydroxybutyrate (BHB) inhibits Bifidobacterium. Finally, they used an elegant series of experiments to demonstrate that the reduction in Bifidobacterium, especially B. adolescentis, lowers pro-inflammatory Th17 cells in the intestine.

Studies that compare different types of ketogenic diets

As always, it’s important to remember that all keto diets are not created equal. We wouldn’t expect a keto diet comprising mostly gas station jerky and processed “cheez” products to have that same impact on the gut—or any marker of health—as a Primal-aligned keto diet.

Keto diets can vary not only in terms of food quality but also in relative macronutrient composition, fiber content, the types of fat one consumes, meal timing, total energy intake,20 and other variables that probably affect the gut.

Long-term studies

Long-term dietary studies are difficult to conduct for lots of reasons, but at least one study shows why they’re so important. In this experiment, researchers had 10 people with multiple sclerosis follow a ketogenic diet for six months and compared their levels of 35 important gut bacteria to healthy controls.21 At the beginning of the study, the folks with MS had less microbial diversity than the healthy controls, although there was a lot of variability between individuals. In the first two weeks, the MS group’s diversity decreased even more—a strike against keto. However, when the researchers checked again at 12 weeks, diversity was on its way up. By the end of the study, the two groups’ microbiomes were indistinguishable. If the study had been shorter, as most studies are, it would have looked as though the ketogenic diet had been harmful; but after six months, it proved quite beneficial.

So Where Does This Leave Us?

As far as I’m concerned, it’s a “wait and see” situation. Many researchers are still cautious about ketogenic diets, particularly because of studies that show that keto diets inhibit Bifidobacterium, which are generally counted among the “good guys.”22 Ultimately, the Olsen et al. study 23 showed that it is important to consider the big picture rather than focus on any specific bacteria (or even several bacteria). As the authors of the aforementioned Cell paper remind us, “[T]he short- and long-term impact of KDs (keto diets) on host health and disease likely depends upon a complex series of beneficial, neutral, and detrimental shifts in microbial ecology.” This will be a huge challenge for researchers moving forward, both because of the practical limitations of modeling something as complex as the human microbiome and the logistics of running all the necessary studies.24

The good news is, thousands of microbiome studies are published every year. There is massive interest in understanding the bidirectional links between gut health and disease and, importantly, how interventions that affect the microbiome can be used to treat disease.25 Diet is one such intervention that could potentially be used cheaply and easily with a better understanding of the effects.

Unfortunately, for those of us who want to know now how keto our diets might be impacting our guts, we simply don’t have the answer yet. We’re hampered by a lack of long-term (or any) studies in healthy human subjects.

In the meantime…

Whether you’re eating a strict keto diet or something else, you should still do the same things to promote gut health:

  • Eat a variety of foods, including plant foods, that “feed” your microbiome. Low-carb options include avocados, alliums (onions, garlic, leeks, shallots), mushrooms, nuts, even dark chocolate. Carnivores, consider a carniflex approach that nets you some fiber and other beneficial plant compounds.
  • Include fermented foods in your diet.
  • Consider adding resistant starch occasionally.
  • Sleep.
  • Manage stress.
  • Don’t smoke.

Always watch for signs that your gut is unhappy and adjust accordingly. Otherwise, pick a way of eating that allows you to feel great, achieve your health and fitness goals, and enjoy your food.

About the Author

Lindsay Taylor headshot

Lindsay Taylor, Ph.D., is a senior writer and community manager for Primal Nutrition, a certified Primal Health Coach, and the co-author of three keto cookbooks.

As a writer for Mark’s Daily Apple and the leader of the thriving Keto Reset and Primal Endurance communities, Lindsay’s job is to help people learn the whats, whys, and hows of leading a health-focused life. Before joining the Primal team, she earned her master’s and Ph.D. in Social and Personality Psychology from the University of California, Berkeley, where she also worked as a researcher and instructor.

Lindsay lives in Northern California with her husband and two sports-obsessed sons. In her free time, she enjoys ultra running, triathlon, camping, and game nights. Follow along on Instagram @theusefuldish as Lindsay attempts to juggle work, family, and endurance training, all while maintaining a healthy balance and, most of all, having fun in life.

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