How to Feed Your Gut Bacteria

root-vegetablesDo you take the trillions of microbes in your gut – which have a profound impact on your immune function, metabolism, mood, and behaviour – into account when you plan what you’re going to eat? If the answer is yes, then you are in the minority.

The average intake of dietary fiber – the primary substrate our colonic bacteria feed on – in the U.S. is about 16 g/day (1), which is much less than what you need to take good care of your friendly gut bacteria and many times lower than the levels consumed by hunter-gatherers and traditional, non-westernized people. Also, of particular importance to the health conscious people who follow this blog, due to recent changes in food production and processing practises, even those people who eat a nutrient-dense, ancestral diet often take in lower than optimal amounts of dietary fiber every day.

The importance of the indigestible (to the human host) component of our diet

There are few components of the human diet that have gotten as much attention as dietary fiber. Fiber, which is plant material that resists human digestive enzymes, is usually spoken of in warm words, and even those people with little to no knowledge about nutrition have typically heard about the supposed benefits of eating enough indigestible (to the human host) carbohydrates, perhaps from a commercial promoting the consumption of whole grain crackers or from a health & fitness website.

However, there are also people out there who have either neglected the importance of fibrous plant foods or dismissed dietary fiber as nothing more than a substance that bulks up the stool and “irritates” the intestine. Some Paleo dieters and people who praise the benefits of following a high-fat, very-low carbohydrate diet fall into this group, typically because what led them to a diet that goes against conventional wisdom in the first place was that they never got a feeling of good health and well-being from eating a diet high in grains, the food group that is often most strongly associated with fiber. However, as we know, grains aren’t the only source of dietary fiber in the human diet, and as we’ll see later, a true hunter-gatherer diet actually tends to be very high in roughage.

Food for microbes

Dietary fiber has typically been categorized into soluble and insoluble fiber, but what has become increasingly clear over the last couple of years is that it might be better to categorize indigestible (to the human host) carbohydrates based on whether or not they can be accessed by the microbial hitchhikers that reside in the human gut.

While we’ve known for some time that we’re not the only organism dining on the food we eat, it’s only recently that we’ve started to understand the complexity and importance of the microbial community deep in our gut, a community that is responsible for breaking down complex polysaccharides, producing neurotransmitters (which affect our brain), and regulating our immune system, among many other things.

Given the vital importance of the gut microbiome in human health and disease, it probably doesn’t come as a surprise that it’s the types of fibers that can be broken down by our gut symbionts that we should be most concerned with, as opposed to the types of carbohydrates that aren’t broken down by neither man nor microbe, but simply pass all the way through undigested.

The carbohydrates that are fermented by gut bacteria in the large intestine primarily consist of complex polysaccharides found in plants and are often referred to as fermentable fibers or Microbiota-Accessible Carbohydrates (MACs). The term “prebiotic” is more specific and is used to refer to chemicals that induce the growth or activity of microorganisms (e.g., bacteria and fungi) that contribute to the well-being of their host.

The fermentable fibers found in real, whole foods help improve glycemic control, increase satiety, elevate the production of short-chain fatty acids in the colon, improve intestinal barrier function, and promote a healthy gut microbiota (2, 3, 4). A Western diet, which is very low in fiber, is primarily digested and absorbed in the small intestine, leaving few nutrients for the microbes deep in the colon. This sets the stage for colonic dysbiosis, chronic low-grade inflammation, dysregulation of the gut-brain axis, and eventually, chronic diseases of civilization such as colon cancer, type-2 diabetes, and acne vulgaris (3, 5, 6).

How much dietary fiber should we really consume?

In the U.S., the recommended Adequate Intake (AI) for dietary fiber for adults is 25 to 38 g/day (14 g/1,000 kcal/day) (1). This intake level is much higher than what the average American actually gets through his diet (1), something that is especially concerning as the recommendation isn’t especially high to begin with. It’s difficult to estimate an “adequate” or “optimal” intake of fiber for humans, but it could be argued that the recommended AI level is on the low side of what we should actually be consuming if we’re looking to achieve great health.

When we’re looking to answer nutrition-related questions, a good first step is always to look back at diet and health through the lens of evolution. This can give us a good picture of what is “normal” for our species, an understanding that lays the basis for deciphering modern nutritional science.

There is a great spectrum of fiber intake levels among hunter-gatherer communities, with forager populations who eat plenty of fibrous plant foods on the one end, and peoples inhabiting the Arctic regions who largely subside on animal source food on the other end. However, in general, it’s safe to say that the amounts of dietary fiber consumed by hunter-gatherers far exceed the average intake in industrialized nations today (5, 6, 7, 8). Also, the ratio of soluble/insoluble fiber in hunter-gatherer diets is higher than in modernized nations, since much of the fiber in cereal grains is of the insoluble type.

A 2010 paper by Boyd Eaton and colleagues suggests that most hunter-gatherer diets contain at least 70 g dietary fiber/per day, which is many times higher than what most contemporary, westernized people take in (7).

There’s some controversy regarding this number, largely because fiber intake varies greatly between different tribes, and because there’s a limited amount of good data on the subject. However, there’s little doubt that in general, hunter-gatherers got a lot more fiber through their diet than what we consider “normal” today. This is something that can be inferred since we know that the wild plant foods eaten by forager populations are markedly higher in fiber than domesticated plants, a knowledge we can use to roughly calculate total fiber intake by looking at studies of plant-animal subsistence ratios in hunter-gatherer diets (9).

Since it’s difficult to draw firm conclusions about diet from looking at coprolites and fossil records, we don’t have precise information about fiber intake among our African Paleolithic ancestors. However, by looking at contemporary hunter-gatherers who live in a part of the world where the human species is thought to have originated, we get a window – albeit imperfect – into how the diet of some of our early ancestors may have looked like.

The Hadza, an indigenous ethnic group in north-central Tanzania, living around Lake Eyasi in the central Rift Valley, are one such group. These people consume a lot of fiber-rich Underground Storage Organs (USOs), a fallback food that may have been an important part of the diet for many hunter-gatherer tribes throughout hominin evolution (10, 11).

It’s likely that your intake of fermentable fiber is lower than optimal

Uncultivated vegetables and fruits are a lot more fibrous than commercial ones (7), and since a well-balanced diet shouldn’t just include plants, but also healthy fats and animal products, contemporary whole foods diets often end up having a lower fiber content than traditional human diets.

It can be difficult to get “enough” dietary fiber through a contemporary Paleo Diet – or most other modern diets for that matter. That’s not a flaw of the actual Paleo Diet itself, as true Paleolithic diets tend to be quite fibrous. It’s rather the result of a transition from eating wild plants to eating cultivated plants, as well as a reflection of some of the problems associated with modern food production.

Loren Cordain estimates in a scientific paper that a contemporary Paleolithic Diet contains approximately 42.5 g of plant fiber (12), which is a lot more than the average intake in contemporary industrialized nations, but still lower than the actual intake among hunter-gatherers. Also, it’s important to note that the example diet that was used to estimate this intake level is probably higher in fibrous plant foods than the diet of many contemporary Paleo dieters. This is especially true for those who swear by a low-carbohydrate approach and/or choose to eat a lot of butter, dark chocolate, coconut oil, and other high-fat, calorie-dense foods at the expense of plant foods.

Just because most hunter-gatherers and traditional people ate a fiber-rich diet doesn’t in itself lead to the conclusion that we should strive to eat a lot of fiber every day. However, if there’s one thing the data consistently show, it’s that an evolutionary perspective on nutrition gives us many hints as to how we should eat to achieve great health. The statement that most of us are getting less than optimal levels of fiber through our diet is also supported by a pile of research papers, which especially highlights the benefits of eating enough MACs (2, 3, 4).

Are you missing the microbes you need to break down the fiber you’re eating?

There’s no doubt that the health benefits of consuming “a lot” of fermentable fibers (from whole, real food) are many. However, we have to keep in mind that not everyone will react the same way to consumption of these compounds. Just like people who lack the genetic capability to produce the enzyme lactase aren’t able to break down lactose found in cow’s milk (unless they harbor lactase producing gut bacteria), those who harbour a “simplified” gut microbiota that don’t produce the necessary enzymes to break down the fermentable substrates that are consumed, won’t experience the aforementioned benefits, but rather gastrointestinal distress.

In the modern, industrialized world, antibiotics have long been given out for even the smallest sniffle, a lot of people eat highly refined western diets, and we’ve disconnected ourselves from the natural environment. It’s therefore no doubt that gut dysbiosis is a widespread problem, a statement that is supported by studies which show that non-westernized people harbour a much greater diversity of gut microbes than westerners, and by the fact that chronic diseases that are known to be triggered or exacerbated by microbial imbalances in the gut have skyrocketed in prevalence lately (13, 14, 15).

Getting more prebiotic fibers into our diet is one way to turn this around, but enhancing ecosystem diversity, such as through traditionally fermented vegetables, high-quality probiotics, “dirty” vegetables, and/or microbiota transplants are also important, especially for those with a gut microbiota that doesn’t live up to its reputation.

How to become a more gracious host

So, how can we get more fiber through our diet and take better care of our “friendly” gut bugs? The natural answer is of course to eat more vegetables, fruits, and other plant foods, with an emphasis on those that are high in resistant starch, inulin-type fructans, and other MACs. Onions, leeks, slightly green bananas, and root vegetables are some examples of foods that are especially good sources of prebiotic fiber. Preparation (e.g., heating) and processing techniques affect the fiber content of food, so this is something that should be considered.

Fruits and particularly vegetables are superior to whole grains, as they are more fibrous on a calorie-by-calorie basis, lower in antinutrients, more nutrient-dense, less insulinogenic, and higher in fermentable fibers (7).

While it’s a good thing to include several types of fiber-rich plants in your diet, as opposed to just a few species, you should make sure that your diet stays fairly similar from day-to-day, because if you’re jumping from diet to diet or constantly changing what types of foods you eat, your gut microbiome will never have time to adapt to your diet

I want to end by saying that although eating plenty of fiber-rich plant foods is important for a well-functioning and healthy body, it’s obviously not the only thing to consider in the context of designing a healthy diet. Fiber is just one of the many components of the food we eat.

A well-balanced, nutrient-dense diet doesn’t just contain fibrous plant foods, but also high-quality meats and healthy fats, among other things. Also, perhaps needless to say, it should be low in refined grains, refined vegetable oils, added salt, and other nutrient-poor foods that have entered into the human diet recently.

Picture: Creative Commons picture by Skånska Matupplevelser. Some rights reserved.
Note: A previous version of this article of mine appeared in Paleo Magazine, the first, and only print magazine dedicated to the Paleo lifestyle and ancestral health. You can subscribe to Paleo Magazine here!


  1. Thanks for a good article, Eirik. I’ve always eaten a lot of vegetables because I like them and probably because I grew up eating them. I think people who don’t like vegetables don’t feed them to their children, and then those children often grow up disliking them too. I don’t eat nearly as much fruit. For whatever reason I just don’t find most fruit all that appealing. Even on a Paleo-type diet, most of us tend to eat what appeals to us and we skip that which doesn’t. As you say, this could be detrimental to the gut microbiome.

    • I eat mostly veggies too. Unfortunately, a lot of the fruit you’ll find at the typical grocery store is markedly higher in sugar and lower in fiber than uncultivated varieties. There are some exceptions though, which is why I tend to include fruit when I talk about good sources of prebiotics.

  2. This article was an interesting an eye-opener. Thank you!
    BTW, generally speaking veggies /whole-food/Paleo lifestyle are lower in calories than the SAD therefore the benefits of eating an apple (or two) a day are far greater than not eating fruit; I also find them easier to digest than potatoes/bananas, either because of starch content or the water content – I’m not sure which – but I know that glucose can really rock those workouts and improve digestion 🙂

    • Glad you enjoyed it 🙂

      I didn’t mean to say that fruit shouldn’t be a part of a healthy diet. I eat some fruit pretty much every day myself. All I’m saying is that a Pink Lady apple or two a day won’t get you very far in terms of boosting your prebiotic intake.

      • Oh, right, sorry; I didn’t mean to imply my apple comment came from the article; I mentioned the apple because of the other comment about the article and your reply about fruit. Also I was wondering ( and should have asked) if you think the easy digestibility of an apple versus potato/banana is due to the water content or the starch… but I guess that probably is a very individualized situation.

        • No problem.

          Hmm, not quite sure what you mean by “easy digestibility”?

          • well, apples have fiber as do potatoes/bananas; however potatoes and bananas both are higher in starch and (I believe) a lower water content than apples (which I believe doesn’t have starch); however all 3 have fiber and glucose. This leads me to the question of digestion — personally I have no problems digesting apples, and I’ve been known to eat 2 in a row. However I have to limit the sweet potatoes I eat (to like one a week) and I avoid bananas altogether. I’m curious of your thoughts about that — if it’s the water content of apples that make digesting them easier and do they contain starch.

          • That’s weird, as ripe bananas and cooked potatoes are not foods that are prone to cause digestive issues in people. Are you sure it’s these foods that trigger the problem? It may be that you’re reacting to the resistant starch (RS), but if you’re eating ripe bananas and tender potatoes, the RS content is so small that I think it’s unlikely that it should be an issue.

          • Well I guess I’m not sure of anything anymore. Weird for sure, but at least you’ve put it into perspective for me so thank you for that! 🙂

  3. Eirik, I’ve known healthy people who would get sick if they ate a banana, including my former husband. I don’t eat bananas very often either because they’ve upset my stomach in the past. I seem to have outgrown that in recent years but still don’t consume them often. Weird, yes, but it happens. Read up on banana allergies.

  4. Simone Einstoss says:

    The article is very informative, and provides an option to what the doctor suggested to me: avoid wheat, milk, and eggs, because they are causing your intestinal inflammation.

    A detail: I am vegetarian and I normally eat oats, salads, wholemeal rice, and the occasional industrial biscuits.

    I never ate much milk and egg products, so it surprised me the doctor told me to avoid these.

    Would you say that perhaps eating more “old style wholemeal bread” (not baked) could be good to developing bacteria able to deal with wheat, for instance? If yes, what could I do to get bacteria to digest yoghurt and cheese (things I like)?

    Many thanks for your help.


    • Hi Simone!

      Welcome to the blog.

      It seems like your diet is very different from the one I recommend. Here’s a summary of my dietary recommendations:

      Would you say that perhaps eating more “old style wholemeal bread” (not baked) could be good to developing bacteria able to deal with wheat, for instance?

      This is an interesting question. Recent studies show that some gut microbes are able to degrade gluten, phytic acid, and other potentially problematic compounds found in wheat and some other cereal grains. However, it’s too early to tell how one can go about acquiring these gut bugs and to which extent these bacteria can mitigate the adverse effects associated with the consumption of wheat. My general recommendation is to reduce or eliminate your consumption of wheat and other cereal grains.

      If yes, what could I do to get bacteria to digest yoghurt and cheese (things I like)?

      Yoghurt and cheese mostly contain fat and protein (little carbohydrate), which are primarily digested – by enzymes that you, the human host, produce – and absorbed in the small intestine. The gut microbiome is primarily involved in the digestion of carbohydrates.

      Let me know if you have any further questions.

  5. The advocates of low carb diets use the Inuit example, but it’s not proper since the low carb western diet is far from being the same than Inuit, cause they eat rotten meat and other fermented stuff together with some plants as well, that though they almost don’t count to the caloric intake, they feed the microbiome.
    In our society we hardly eat rotten seal meat and blubber…

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