You probably know by now that the health of your microbiome strongly influences the health of the rest of your body.  

Healthy gut bacteria promote digestive health, metabolic health, immune health, mental health and cardiovascular health. (1, 2, 3, 4) Unhealthy gut bacteria do the opposite, promoting a whole host of serious diseases, including anxiety, depression, obesity, infertility, polycystic ovary syndrome, autoimmune diseases, diabetes, heart disease, dementia, and cancer. (1, 2, 3, 4, 5, 6, 7) But what determines the health of your gut bacteria?

Factors That Lead to a Healthy Microbiome

There are many factors that play a role in a developing (and maintaining) a healthy microbiome. These include:  

  • Genetics (8)
  • Exposure to tobacco smoke (9)
  • Use of prescription, over-the-counter or recreational drugs (10, 11, 12)
  • Exposure to pesticides, detergents and industrial chemicals (13, 14)
  • Amount of daily physical activity (15)

One of the most important factors, however, is your daily diet.

Different types of diets promote different balances of gut bacteria — some are healthier, while others aren’t. (16, 17, 18, 19, 20, 21).   

And these changes in microbial balance can happen quickly — switching from diet to diet over a short period of time (from a day to a couple of weeks) is sufficient to significantly change the health of your gut bacteria. (22, 23, 24, 25)

It might seem odd that something as simple as food could have such a profound impact on the bacteria that play such a critical role in keeping you healthy. You’d hope that your bacteria would be pretty stable and keep working away to maintain your health, day-in, day-out, regardless of the food you eat.

But when you really think about it, it makes sense. After all, your gut bacteria come into direct contact with the food you eat, 3 times a day (or more!), every day. The food you eat (and its nutrients, contaminants, or toxins) can easily influence your bacteria’s normal biological and metabolic processes and, in turn, their overall health.

I’m often asked what the best macronutrient ratio is for gut health. Research has shown time and again that complex carbohydrates and fiber help to boost the health of your microbiome, while large amounts of sugar and fat have negative consequences on the health of your bacteria.

It’s easy to understand why carbohydrates and fiber are healthy for your gut bacteria since they are what your microbes feed on, but what causes a lot of confusion (and controversy) is the amount of fat that promotes a healthy microbiome.

So today, I’m going to focus on fat: how much is too much when it comes to gut health?

High-Fat Diets & Gut Bacteria

I’ll be the first to admit that I was a bit skeptical when I came across research that implicated high-fat diets as one of the causes of unhealthy gut bacteria. After all, I’m very much a “real foodie” and don’t shy away from recommending fats as a major component of a healthy diet.

But I kept seeing more and more research about fat and its negative impact on the health of the microbiome, and it became clear that I needed to investigate this further.

Truth is, there is a lot of research behind this idea and it’s pretty strong. Every type of study that’s been used — animal models, epidemiological studies, and human intervention studies — all show that your gut bacteria change in response to consumption of a high-fat diet. (16, 17, 22, 23, 26, 27, 28, 29) What’s more, the changes found by these diverse methodologies are, generally, very similar. (16, 17, 22, 23, 26, 27, 28, 29)

So what are those changes, exactly?

A high-fat diet appears to induce very specific changes in the ratios of the bacteria in the gut — high-fat diets are able to decrease the numbers of healthy gut bacteria while simultaneously increasing the numbers of less healthy gut bacteria. (16, 17, 22, 23, 26, 27, 28, 29)

This imbalance (a state referred to as dysbiosis), is an unhealthy situation for your gut bacteria, your gut, and you. It has been associated with gastrointestinal diseases, low-grade systemic inflammation and all of those serious conditions mentioned above. (1, 2, 3, 4, 5, 6, 7, 30)

Of course, this begs the question: Why? Why does a high-fat diet cause your gut bacteria to go so out of whack?

While we don’t know for sure yet (and there are many factors at play), there seem to be three main processes involved.

Let’s explore them one-by-one.

Increased Production of Bile Acids

Bile acids are molecules made by your liver to help your body digest and absorb fat. They work as a type of natural emulsifier, allowing fat from your food to mix into your water-based digestive fluids. This allows the fat you eat to come into contact with the necessary digestive enzymes to actually be broken down and absorbed.

Since bile acids are so important for being able to absorb fat efficiently, your body has an elegant system for making sure there are enough bile acids for all the fat from your food. When fat molecules, particularly big, bulky monounsaturated and polyunsaturated fat molecules, are detected by the cells lining the walls of your intestines, they begin producing a hormone called CCK. (31, 32, 33)

CCK is released in your bloodstream and is transported to your gallbladder, the small sack-like organ which stores bile acids from your liver until you need them. CCK tells your gallbladder to contract, causing the bile acids to be released out into your intestines. There, they can be used to help you absorb the fat you’ve eaten.

The greater the amount of dietary fat, the more CCK made, and the more bile acids released.

Okay, but what does any of this have to do with your gut bacteria?

Well, it turns out that some species of gut bacteria use bile acids to make antibiotics that kill off their neighbors. (22, 34, 35, 36) It’s a useful little trick for them, helping them make sure no one invades their patch of intestinal wall.

When produced in normal amounts in response to a moderate fat diet, these antibiotics help to ensure that the ratios between different species of bacteria in your stay balanced by preventing certain species from growing out of control.

However, high-fat diets produce high concentrations of these antibiotics, which can cause imbalances in bacteria to develop. When too many of these crafty bacteria’s neighbors are killed off, their populations may drop to unhealthy levels.

Researchers suspect that this might be exactly what happens in those eating a high-fat diet, and it may be one of the main reasons for the high-fat-diet-associated unhealthy changes in gut bacteria. (22)

Increased Absorption of LPS

Another mechanism strongly suspected of underpinning the relationship between high-fat diets and poor gut bacterial health is an increased absorption of a toxic molecule called lipopolysaccharide (LPS).

While “leaky gut” or intestinal permeability is the main way large amounts of toxic LPS get into your body, it turns out that small amounts of LPS are regularly transported through an entirely healthy gut wall by little transport vehicles called chylomicrons. (37, 38, 39)

Chylomicrons are small, round packages made by your body to hold digested long-chained dietary fats. They are responsible for transporting these fats through your intestinal wall and taking them to your liver for proper processing and re-packaging for transport to the rest of your body.

If you consume greater amounts of dietary fat, your body has to produce more chylomicrons to transport them all. The more chylomicrons, the more LPS can be accidentally packaged up with the dietary fat and absorbed into your body.

When LPS gets into your body, your immune system immediately (and accurately) recognizes it as dangerous and mounts an attack. (40, 41, 42) Your immune cells begin producing all kinds of inflammatory chemicals intended to help fight off any intruder and begin pumping them into your bloodstream.

These inflammatory chemicals signal to your gut that there danger is present, which in turn leads to changes in the walls of your intestine that affect how well your gut bacteria survive. (43, 44) Eventually, this leads to the development of dysbiosis, or the imbalance of good and bad bacteria in the gut.

Decreased Intake of Complex Carbohydrates

The final mechanism currently believed to play an important role in linking high-fat diets to changes in gut bacterial health is very indirect, but may ultimately prove to be one of the most important.

By definition, a high-fat diet must contain a lower percentage of calories from carbohydrates and protein. Researchers think that the drop off in the intake of these macronutrients, particularly complex carbohydrates, may be responsible for the development of dysbiosis. (45)

See, many gut bacteria use dietary fiber — sugar complexes made by plants that your body cannot digest — as their primary (or only) food source. (46) Without enough fiber, these species may fail to thrive. And in fact, we see significant improvements in gut health when bacteria have plenty of fiber to consume. (26, 45, 46, 47)

Problem is, nearly all high-fiber foods are also carbohydrate-rich (with the exception of foods like coconuts, avocados, and nuts). So those who follow a high-fat diet are mostly missing out on these high-fiber choices, especially if they are eating a Standard American Diet that consists of lots of processed junk food. Without the healthy fiber found in carbohydrate-rich foods, your gut bacteria suffer. (45, 48)

Are All Fats Bad for Gut Health?

When we dive into the research, there are clear hints that the type of fat, not just the amount, plays a key role.

For example, omega-3 fatty acids (found in fish) have been found to induce positive changes in the microbiome, while omega-6 fatty acids (found in industrial seed oils like canola oil) have a damaging effect. (49, 50)

As discussed earlier, the production of CCK stimulates the release of bacteria-harming bile acids. But CCK is produced much more efficiently in the presence of unsaturated fatty acids. This suggests that replacing some of these unsaturated fats with saturated fats may protect your gut bacteria. Since omega-6 fatty acids (a type of unsaturated fat) have proven harmful to microbial health, it makes sense to take some of these out and swap them for saturated fats.

Compared to omega-6 fatty acids, saturated fats do not cause nearly as much damage to the gut. (51)

But you also don’t want to overdo it. Switching to a diet containing primarily saturated fatty acids may end up harming your gut bacteria too.

There are a couple of reasons for this.

First, CCK produced from unsaturated fatty acids is also responsible for transmitting a key “I’m full” signal to your brain. (33) Without it, it becomes a lot easier to overeat. And overeating –regardless of macronutrient content– can harm your gut bacteria. (52)

Additionally, saturated fat may be less easily absorbed in your small intestine (perhaps as a result of less CCK and bile acid release). Studies indicate that if a diet contains too much saturated fat, the small intestine may not be able to absorb it all and some of the fat can make it into your colon and disrupt the delicate balance between the species of healthy gut bacteria. (53)

Finally, at higher concentrations, saturated fatty acids have been shown to be able to trigger an immune response by binding to a receptor on some of your white blood cells called TLR-4.

Similar to the effect seen when LPS triggers an immune response, immune cells activated by saturated fats release inflammatory chemicals that change how the walls of your intestines function, altering how well your gut bacteria survive. (54)

A happy medium may be to reduce your intake of omega-6 fatty acids from industrial seed oils and include some monounsaturated fats in your diet so that you have a healthy amount of CCK production, while still reducing the overall amount of omega-6 fatty acids that you consume.

Monounsaturated fat (like that found in olive oil), has been shown to mitigate the damage done by high-fat diets. (55) Scientists believe that some of the beneficial effects of olive oil may actually come from its polyphenols, as research indicates that virgin olive oil has a much more protective effect than refined olive oil. (56)

Given everything we know about how different types of fats affect the microbiome, it makes sense to avoid industrial seed oils (omega-6 fatty acids) and eat a mix of monounsaturated and saturated fats, with small amounts of omega-3 fatty acids coming from foods like fish and nuts. In this sense, the real food movement strikes a great balance when it comes to consuming the proper balance of fatty acids for gut health.

Do I Need to Eat a Low-Fat Diet to Have Healthy Gut Bacteria?

Interestingly, the negative consequences of a “high-fat” diet only happen when you start eating approximately 42% to a whopping 70% of your calories as fat

Moderately high-fat diets (35% or less calories from fat) do not show these same effects. (39)

That means that if you’re eating a 2000-calorie diet, you can have up to 78 grams of fat per day with no negative consequences to your microbiome.

Eating a calorically-appropriate diet is vital since overeating harms gut bacterial health as well.

On top of that, it’s important to eat the right types of fats. As I discussed previously, I believe consuming mostly monounsaturated and saturated fats with small amounts of polyunsaturated fats from fish and nuts is the right approach here. The key is to avoid high amounts of omega-6 fatty acids.

To review, here is what we currently know about the best diet to support your microbiome:

  • Eat a moderate fat diet (<35% of calories from fat)
  • Eat an appropriate amount of calories overall
  • Avoid industrial seed oils (like vegetable oil) and aim for a mix of monounsaturated and saturated fats, with small amounts of polyunsaturated fats from fish and nuts
  • Choose high-fiber carbohydrate foods

What If I Want to Eat a High-Fat Diet?

There are probably some of you reading this article who know you do best with a high-fat diet. You might have diabetes and a low-carb diet keeps your glucose levels normal, or perhaps you’re using a ketogenic diet to help manage a condition like epilepsy.

If this is you, don’t worry! There are ways to mitigate the negative microbial effects of a high-fat diet.

Here’s what the research says:

  • Eat enough fiber from the foods you can eat. If you’re following a high-fat diet, this means making sure you’re eating tons of fibrous veggies, berries, avocados, nuts and seeds that fit within you plan. Eating lots of plant matter also helps you consume plenty of polyphenols which have a protective effect on your gut bacteria as well. (57, 58)
  • Take prebiotics. Prebiotics have been shown to protect gut bacteria from the negative effects of a high fat diet. (59, 60)
  • Take probiotics. Much like prebiotics, probiotic supplementation can attenuate the negative impact of a high fat diet. (61, 62, 63)

Just as you should when following a moderate-fat diet, you should also consume an appropriate amount of calories and eat the right types of fats to promote microbial balance in the gut.

And even if you aren’t eating a high-fat diet, eating high fiber foods and taking probiotics and prebiotics is a great idea to ensure a healthy gut.

The Bottom Line:

Clearly, the relationship between the fat you eat and your gut bacteria is complex.

However, research indicates that a moderate fat diet (<35% of calories) is best, especially when you’re eating fats that are protective of your microbiome (like olive oil and omega-3 fatty acids).

If you want to consume a higher fat diet, choosing these types of fats may keep your gut healthier than if you ate a high omega-6 fatty acid diet. You can also consume prebiotics and probiotics to protect your gut bacteria while on a high-fat diet.

Now I’d like to hear from you: will you be changing your macronutrient intake as a result of the evidence presented in this article?

4 replies
  1. Jake3_14
    Jake3_14 says:


  2. Marisa De More
    Marisa De More says:

    Excellent research. Thanks so much for taking the time to put things into perspective. Incidentally, This ‘leave a reply’ box seems set to capital letters only! Is that how you set it? Thanks. Best wishes.


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