Do you experience gastrointestinal issues, sugar cravings, fatigue, low libido, and/or other chronic health problems despite eating a very healthy diet? The reason is probably that you harbour a gut microbiota that is mismatched with the diet you’re eating. You can eat as much fiber-rich vegetables, grass-fed meat, fatty fish high in omega-3, and extra virgin coconut oil as you want, it’s not going to make you healthy if you don’t possess a diverse, resilient microbiota that is adapted to break down the indigestible (to the human host) compounds you get through your diet.
A healthy diet is just one part of the equation, the part everyone focuses on. The gut microbiota is the other part of the equation, the part everyone forgets.
Dr. Art Ayers, a former Harvard professor with a Ph.D. in Molecular, Cellular and Developmental Biology and one of my heroes in the world of health and medicine, has made the point above repeatedly on his blog. (I highly recommend that you read his articles if you want to learn more about the true causes and cures of chronic disease).
He makes the case that a healthy gut microbiota is a diverse community of microbes that is matched to the diet the person consumes. In other words, a healthy microbiota for a Hadza hunter-gatherer who consumes a fiber-rich diet will look very different from that of a Inuit eating an animal-based diet.
The important thing isn’t that you possess a specific set of beneficial microbial species, but that you harbour microbes that carry genes that code for enzymes that can break down the food you’re eating. It’s the genes that matter.
A healthy gut microbiota is an essential part of a well-functioning digestive system
At this point, you might be a little confused, so let me try to explain how I look at these concepts…
The human body was shaped over millions of years of evolution. We carry with us two major sets of genetic information: Our human genome, which we inherit from mum and dad, and the human microbiome, which is the collective genomes of all the microorganisms that live “in” and on our bodies. Compared to the human genome, the human microbiome is highly malleable, in the sense that what we eat, the types of drugs we take, how we exercise, and the type of environment we live in can have a profound impact on the composition of the microbiota (1, 2, 3).
The microbes that inhabit our body carry out essential functions that we haven’t evolved the genetic capability to perform ourselves. We have essentially outsourced certain parts of our immune function, metabolism, and digestion to these tiny critters. This is particularly important to keep in mind in the discussion of diet and gut microbiota adaptation.
The human body, excluding its associated microorganisms, possesses the genetic capability to break down mono- and disaccharides, starch, fats, and protein (of the major nutrients we get from our diet). Some exceptions do exist; for example, about 70% of the world’s population loses the ability to produce the enzyme lactase after infancy, and they therefore can’t break down the disaccharide lactose.
Non-starch polysaccharides, as well as certain other nutrients we get from our diet, are broken down by gut bacteria. That is, if we harbor microorganisms that are able to degrade these compounds. A lot of people don’t get the “promised” health benefits from eating a nutrient-dense, whole foods diet because they harbor a gut microbiome that is poorly matched with the diet they’re eating. In other words, you can eat as many prebiotic fibers as you want, but if you don’t possess a microbiota that is adapted to break down these substrates, you’re not going to experience the many positive effects associated with fiber consumption, but rather gastrointestinal distress and a leaky gut.
If nutrients pass into the colon that the microbiota is incapable of breaking down into end-products such as butyrate and acetate, food intolerance, gastrointestinal distress, and inflammation occur.
Why you shouldn’t follow the low FODMAP diet or other similar diets
A lot of people with a degraded gut microbiota experience health improvements when they adopt a low FODMAP diet, specific carbohydrate diet, or other similar diet, because these types of diets exclude certain indigestible (to the human host) carbohydrates that we depend on our gut bugs to break down.
The problem is that these types of diets only mask the problem, they do nothing to correct the underlying issue. Actually, they may exacerbate the underlying problem, due to the fact that many fermentable fibers are excluded from these diets; fibers that beneficial microbes in the colon depend on for growth and reproduction.
In other words, the long-term solution isn’t to adhere to a diet that restricts certain forms of carbohydrates, but rather to recruit new bacteria that are capable of breaking down the nutrients we get from our food that the human host is incapable of digesting without the help of the microbiome.
The microbiota plays a more important role in our digestion than previously thought
We now know that it’s not just the non-starch complex carbohydrates we get from our diet that are broken down by gut bacteria. For example: Some gut bacteria are able to degrade gluten, phytic acid, and lactose, meaning that if we have these gut bugs in our GI tract, many of the adverse effects associated with the consumption of these compounds could potentially be avoided (4, 5, 6, 7)
As for lactose, several studies have shown that consumption of yoghurt, kefir, and certain probiotics improves symptoms of lactose intolerance (5, 8, 9) This makes sense, because when we consume these products, we’re also eating bacteria that are able to break down lactose. These bugs can potentially colonize our gut or transfer genetic material to bacteria living in gut biofilms, meaning that we essentially add genes to our microbiome that are needed to break down lactose.
The human body is an environment for the microbiota. The microbes that live in our gut reside there because we we provide them with a habitat they can live in. If you suddenly shift your diet, your gut microbiota also changes, because different microorganisms specialize in degrading different nutrients. If you change what you eat repeatedly – e.g., jump from diet to diet every other week or consume different foods every day – the gut microbiome never gets a chance to properly adapt to the diet you’re eating. In other words, too much dietary variation is unhealthy.
If you experience gastrointestinal issues, sugar cravings, fatigue, low libido, and/or other chronic health problems despite eating a very healthy diet (e.g., a fiber-rich Paleo-style diet), the solution most likely isn’t to remove certain foods from your diet, try a new dietary pattern, or otherwise change what you eat. Rather, you have to acquire the bacteria that are missing from your gut and work on improving the health of your gut microbiota. Unfortunately, at the moment, you can’t simply go into the drug store and buy a pill that contains the microbes you need. However, as you know if you’ve been reading this blog, there are several other sources of bacteria out there, such as homemade fermented vegetables, raw, minimally cleaned plants from the garden or farmer’s market, healthy people and pets, and high-quality probiotic supplements.
P.S. If you want to read more about how to achieve a healthier gut microbiota, I recommend reading my previous articles on the topic and/or checking out some of the posts over at Cooling Inflammation (e.g., this one and this one).
Now I want to hear from you: Have you consumed a healthy diet for quite some time, but still feel sick, tired, and/or fatigued? After reading this post, do you suspect that your gut bugs may be to blame?