Are High-Fat Diets Bad for the Microbiome?

Are High-Fat Diets Bad for the Microbiome?

Written by Chris Kresser

Those in the Paleo and ancestral health communities have a tendency to follow high-fat, low-carb diets. After all, when you cut out grains, you naturally cut out a lot of carbs. But are there downsides? What happens to our microbiome on a high-fat diet? If you’ve been following my work for a while, you won’t be surprised when I say, “It depends.”

In this episode we discuss:

  • Questions to ask about these findings
  • High fiber and its impact on high-fat diets
  • Low-carb, low-fiber diets can be detrimental
  • Each person responds to high-fat diets differently

 Hi, Chris. Carrie Bennett from Carrie B Wellness. I have a question when it comes to a high-fat diet and the health of the gut microbiome when I’m coaching my nutrition clients. After reading the Sonnenburgs’ book about gut health and the gut microbiome, it seems to be that their recommendation is that fat can change the gut microbiota in a negative way. I’m just wondering how you view this in light of a Paleolithic, primal-style diet. I’m wondering if the studies that they’re referencing are utilizing poor fat sources as opposed to high-quality pastured or grass-fed animal fats, and just your take on, is high-fat healthy for the gut microbiota? Thanks.

Chris: Thanks so much for sending your question in, Carrie. This is a really good example of the complexity of modern research and where it often goes awry. Some studies do show an adverse effect of a high-fat diet on a microbiome, but there are many important questions that we have to ask about these findings.

Questions to ask about these findings

  1. The first question is whether these studies are in mice or in humans. They’re often in mice, rats, or other animals, and it’s just not clear how applicable those findings are to humans. Certainly some animals share common physiological mechanisms with humans, and we’ve learned a lot from animal research, but there are some important differences as well, and the microbiome and the gastrointestinal system is definitely one of those.
  2. Second, what is the quality of fats that’s being used in the study? Carrie alluded to this in the question. The assumption in much of the research out there is that fat is fat, so it doesn’t really matter what kind of fat you use. They often will use corn oil or soybean oil in these studies, particularly with the animal studies, and I don’t think that that’s actually a safe assumption that all fat affects us in the same way. We know there are already some studies that suggest that industrialized seed oils like soybean oil and corn oil have different effects on the microbiome than traditional fats do. I think if people embrace this question and there were more studies separating the different effects of different types of fats, we’d see even more support for that.
  3. Third question is: what is the context of the overall diet that the high-fat intake is occurring in? This is probably the most important question, in my opinion. It should be obvious that the effects of a high-fat diet that is occurring in the context of a Standard American Diet would be very different than a high-fat intake in the context of a nutrient-dense, whole-foods diet, but this is rarely acknowledged in any of these studies. Our hunter–gatherer ancestors, as you know, ate primarily meat and fish, wild fruits and vegetables, nuts and seeds, and some starchy plants. Those are the top sources of their calories, whereas the top six sources of calories today in the industrialized diet are bread, grain-based desserts, pizza, sugar-sweetened beverages, alcohol, and fried chicken dishes. Are we really supposed to believe that a high-fat diet for hunter–gatherers eating all real whole foods affects the microbiome in the same way as a high-fat diet in the context of an overall diet that’s rich in processed and refined foods? I think that there’s plenty of evidence to suggest that the answer to that question is no.

High fiber and its impact on high-fat diets

We have studies that have shown that high fiber intake blunts the possible adverse effects of a high fat intake, and I’m just going to read some titles from studies on the subject and then we’ll put the links in the show notes, but one is “Insoluble dietary fiber from pear pomace can prevent high-fat diet-induced obesity in rats mainly by improving the structure of the gut microbiota.” Essentially, they found that insoluble dietary fiber from pear protects against the effects of high-fat diet that could otherwise adversely affect the gut microbiota.

Here’s another one. “Long-term intake of a high prebiotic fiber diet but not high protein reduces metabolic risk after a high fat challenge and uniquely alters gut microbiota and hepatic gene expression.” They found that consuming probiotics, which of course are fermentable fibers, reduces any metabolic risk that would be confirmed by a high-fat diet and its effects on the gut microbiota and gene expression.

Here’s another one. “Effects of cereal fiber on leptin resistance and sensitivity in C57BL/6J mice fed a high-fat/cholesterol diet.” Cereal fibers probably wouldn’t be my preferred way of increasing the fiber intake, but it’s still fiber that would be expected to affect the gut microbiota, and in this occasion, mice that were fed a high-fat, high-cholesterol diet, the higher fiber intake protected against leptin resistance and improved overall metabolic health.

The last one is kind of a mouthful, but it’s “Dietary fiber prevents obesity-related liver lipotoxicity by modulating sterol-regulatory element binding protein pathway in C57BL/6J mice fed a high-fat/cholesterol diet.” So that’s pretty similar to the previous one that I just mentioned. Except that they were looking at dietary fiber in general and they were looking at its ability to protect against lipotoxicity that is obesity related.

Don’t worry if you didn’t get all that. There’s a lot of jargon there and in some of those study titles, but the gist of it is that fiber protects against the potential adverse effects of a high-fat diet on the gut microbiota.

Given all this, I think we can conclusively say that the effects of a high-fat diet will vary considerably depending on the overall quality of the diet. Context is king. That’s a good saying in this particular instance, and this is one of the huge problems with the way that modern nutritional research is done today because the goal is often to isolate a single variable, especially in a randomized controlled trial, and then to determine the effects of changing just that one variable. But that approach, while it can be helpful if you’re studying the effects of a drug versus placebo, is not really realistic or the way to go about studying the effects of nutritional changes because we don’t live in a metabolic ward where you can control every other aspect of the diet and then only change one variable.

Low-carb, low-fiber diets can be detrimental

Now, all of this said, I do think there are some important caveats that I like to point out here. I have argued previously that one of the risks of a very-low-carb, high-fat diet is a potentially negative effect on the gut flora. This might seem to contradict what I’ve said so far, but it really doesn’t. If you think about it, it supports it.

Imagine somebody goes on an Atkins type of diet and is eating very high intake fat and very low carb, but they’re still on a kind of Standard American Diet. They’re not eating a lot of high-fiber whole foods like non-starchy veggies. They’re probably not eating any fruits or very little and maybe not eating any starchy fiber-rich plants, not a lot of onions, garlic, juice, artichoke, or specific vegetables that are known to be high in fermentable fiber. They may be eating a lot of low-carb junk foods like low-carb tortillas and packaged and processed foods that Atkins sells. Maybe they’re eating a lot of cheese and dairy products, which I don’t necessarily have a problem with if the individual tolerates them well, but in this context where we’re talking about from fermentable fiber, dairy does not have any. This person on this sort of Atkins diet could definitely suffer some negative effects of a low-carb, high-fat diet, but that’s not due to the high fat intake per se; it’s due to the lack of fermentable fiber in this type of diet.

Jeff Leach, who is involved in the American Gut Project, an expert on the human microbiome, wrote an interesting article that alluded to this a while back called “Sorry low carbers, your microbiome is just not that into you.” In this article, which we’ll also provide a link to in the show notes, he talks about just some really informal research that they did at American Gut. I don’t believe it was ever published but they just looked at … American Gut Project is a microbiome sequencing project where people send in a stool sample and they sequence them with their gut microbiome. They have a lot of data from people following a lot of different kinds of diets because when you send in the sample to them, you have to indicate what kind of diet you’re eating; not everybody does that, but a lot of people did. What Jeff found was that people who were eating a very-low-carb diet did actually have a different microbiome profile than people that were eating more carbohydrates. But as he pointed out in the article, it mattered what type of low-carb diet they were eating. For example, if someone who was on a low-carb diet or even a ketogenic diet, but they were maximizing their intake of veggies that were in fermentable fiber and possibly even supplementing with resistant starch and other fibers, then their microbiome looked really different than somebody who was on that kind of Atkins low-carb diet that I mentioned that was really low in fermentable fiber.

Certainly if someone is on a very-low-carb diet and they’re not paying attention to fiber intake, then just by reducing or eliminating things like grains and legumes, which are very rich in fiber, and also starchy tubers, which are rich in fiber, it certainly is a concern. It’s something that somebody on a very-low-carb diet long term should be paying a lot of attention to. I have even argued that a lot of people who are on keto or low-carb diets should consider supplementing with prebiotic fibers that are non-caloric, so they don’t contribute to carb intake and won’t kick someone out of ketosis, but that could really help just shore up the fiber intake (which for us in the modern world is much lower than our Paleolithic ancestors and even contemporary hunter–gatherers).

That’s probably one of the biggest differences, in fact, between our modern diet, even our modern kind of Paleo, ketogenic-type of diet versus our ancestral diet, is the fiber intake. Americans on average get 15 or 20 grams of fiber. In some traditional cultures it was as high as 100. I don’t think all traditional cultures ate that much, but it was certainly anywhere from 40 to 60, I think, on average, which is three or four times higher than in the industrialized diet. Given what we know about how fiber feeds and supports the gut microbiome and the importance of the gut microbiome to overall health, I think that we could say that that’s a really, really significant difference that often is probably underemphasized in the discussion of these different types of diets.

This is, incidentally, one of the reasons I don’t just recommend a ketogenic or low-carb diet for the average person unless there is a specific therapeutic goal that they’re trying to achieve. And even then, with patients, I would work to try to get them to be able to start increasing whole-food carbohydrates in their diet if they can once they’ve achieved that therapeutic goal, unless that’s not possible. Because overall I think it’s easier to maintain a healthy gut microbiota and adequate levels of fiber intake when you’re not on a super-low-carb diet. It still is possible, as I mentioned, if you’re sticking with keto or low carb by adding fermentable fiber supplements or even just focusing on certain very fiber-rich foods like some artichokes, onions and garlic, and things like that, but it does require more attention and focus, and not everyone, unfortunately, is paying that attention.

Each person responds to high-fat diets differently

Another caveat here of course is that not everybody will respond to a high-fat diet in the same way. I say “of course” because I think that’s obvious to most of you at this point, but in the conventional world they’ve tended to approach these dietary questions as if humans are robots and all the same and all respond to foods and other environmental inputs in the same way. We know now that that’s just completely false. We not only have differences in our human genes and gene expression, for example, but we also have profound differences in our microbiome, and our microbiome has different genes and different gene expression, which we’re only beginning to understand. If you look at somebody who is from East Africa, for example, and compare them to our traditional Inuits, those two people could be expected to respond quite differently to the effects of dietary fat and carbohydrates.

I think we’re moving toward a place where we’re going to have a lot more sophistication in being able to answer these questions. We’re going to have all of the “omics” like transcriptomics, metabolomics, proteomics, kind of next-generation level of microbiome sequencing that’s beyond the 16S DNA sequencing that companies like uBiome and American Gut are offering that’s going to give us a more finely resolved view on the microbiome and even the expression of genes, proteins, and metabolic factors that will help us to answer perhaps a little bit more objectively than just experimenting what macronutrient ratios are right for each person. I don’t think we’re there yet, but I think we’re going to definitely get there and in the lifetime of everybody listening to this podcast and very possibly in the next five to 10 years.

The good news is that we don’t necessarily need that data to answer these questions. We can, I think, empirically answer many of them just by experimenting with different macronutrient ratios and watching how our digestion, elimination, and all of these things are influenced by the health of our microbiome respond.

Finally, I hope you’ll see that there are parallels here with a lot of similar questions. For example, you’ll often see this question: “Does a highsaturated-fat intake increase the risk of cardiovascular disease?” We’ve been trying to answer that question with a sort of blanket yes or no, but again we’re getting a lot more sophisticated in our approach here, and we now understand that the answer to that question depends on many factors including the overall context of the diet, which we just mentioned. Is high-saturated-fat intake occurring in a context of a Standard American Diet with a lot of processed refined foods? Or is it occurring in a context of a Paleo type of diet? That will affect the answer to the question but also the individual genes. Is the person’s APOE 34 or 44? Do they have an LDL receptor, a mutation that affects their ability to clear LDL particles? Now, those people might have a different response to saturated fat, and they may need to limit their saturated fat intake compared to someone who doesn’t have that genotype.

We’re moving toward a more nuanced approach. We’ve got a lot more to learn, but in the meantime we can look to traditional cultures to help resolve these questions because when we look at contemporary hunter–gatherers like the Tsimane, whom I have written about recently, in Bolivia, who have maintained their traditional diet and lifestyle; the Maasai in Africa; traditional Inuit; or other cultures around the world that have largely maintained their traditional ways. And some cases, like the Maasai, have a relatively high-fat intake, but no evidence of cardiovascular disease or other chronic diseases that plague us like diabetes and obesity. Then that tells us that higher fat intake within the context of a traditional diet and lifestyle does not necessarily have the same effects of higher fat intake in the context of our modern diet and lifestyle.

This, of course, is the core argument following a genetically aligned diet and lifestyle—a Paleo type of diet and lifestyle. It really tells us what we need to know, which is that context is king. We can’t extrapolate findings—isolated findings—about macronutrients like fat or carbohydrate in the context of an industrialized diet to a Paleo type of diet. If you see a study about high-saturated-fat intake and how it affects people, you have to assume that that study is being done on people who are following a Standard American Diet, and therefore those findings are not necessarily relevant to you if you’re following a Paleo type of diet. Again this is a nuance that often gets left out of not only the study itself, but also any kind of media discussion about that study.

Okay, so thanks, Carrie, for sending in your great question. Everybody else, please keep sending your questions in to, and I’ll talk to you next time.

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