Why There is No Single Healthy Microbiome

microbiome-detailsThe human microbiome is getting more and more attention, and it’s definitely no longer just scientists and folks in the ancestral health community who are interested in the trillions of critters that live in and on the human body. As with everything related to health and fitness, there are a couple of questions that people find especially intriguing… What is optimal? How does the healthiest possible microbiome look like, and how do I get it? This quest for the perfect microbiome has not only led many people to tweak their diet and lifestyle in an attempt to be the best possible host, but also to the rapid growth of what is now a billion dollar market of probiotics, prebiotics, and other products that are specifically designed to modulate the microbial communities in and on the human body. However, while we do know that certain types of bacteria, such as lactobacillus and bifidobacteria, are considered beneficial to human health, the question as to what exactly characterizes a healthy microbiome is still largely unanswered.

Lately, some researchers have investigated the questions above by studying hunter-gatherers (e.g., the Hadza) and rural communities (e.g., children from Burkina Faso, Africa) in an attempt to establish how the “default”/natural state of the human microbiome looks like (1,2). However, while this approach certainly provides a lot of clues as to how the westernized microbiome differs from the ancestral microbiome, these studies have, just like the studies on industralized populations, shown a great deal of variability between healthy people. Why? The human microbiota is a dynamic community of several different ecosystems that respond to changes in environment and lifestyle (3,4,5,6). These changes are partly seen as shifts in the community structure, but we also know that microbes swap genes between them through horizontal gene transfer, meaning that new species with a slightly different genetic material are created. This conclusion from a recent scientific report clearly illustrates the idea behind the dynamic and adaptable microbiome:

A new look at the Human Microbiome Project shows wide variation in the types of bacteria found in healthy people. Based on their findings, there is no single healthy microbiome. Rather each person harbors a unique and varied collection of bacteria that’s the result of life history as well their interactions with the environment, diet and medication use (7).

Our body the ecosystem

To better be able to understand how the human microbiome adapts and responds to various types of stimuli, let’s compare the human gut ecosystem to the ecosystem(s) of plants and animals that live in a rainforest. I want to make it perfectly clear that this is not a perfect analogy, partly because microorganisms are able to propagate through others means than traditional reproduction, and the processes that go on in and on the human body are therefore slightly more complicated than the ones happening to plants and animals in a rainforest. However, it does provide a good example that is easy to understand.

When you’re consuming new types of microorganisms (e.g., a soil-based probiotic), this process is in many ways the same thing that goes on when new species of plants and animals are introduced into a rainforest. To take this analogy further, imagine that the environmental conditions in the rainforest change (e.g., temperature, food availability). This event will select for those organisms which have the highest reproductive success in the new habitat, an idea we can use to understand what happens to the gut microbiome when we alter the conditions in the gut in some way. E.g., when someone who’s eating a completely carnivorous diet one day suddenly starts consuming a herbivorous diet, this event will select for organisms which have traits that confer a reproductive advantage in the new environment.

This is where the problem with the typical western lifestyle lies; we’re not using these selective pressures to our advantage. Instead of eating high-quality whole food, we’re eating refined, sugar-laden junk food that promotes an environment where proinflammatory bacteria can thrive in the mouth and small intestine (8). Instead of introducing beneficial bacteria that suppress the growth of pathogenic microbes and protect us from invaders, we use broad-spectrum antibiotics that carpet-bomb the microbiome and promote an environment where opportunistic microbes are allowed to overgrow (6,9). Instead of eating fermentable substrates that induce the growth of beneficial bacteria in the colon and lower the pH so harmful bacteria can’t thrive, we eat a refined diet that is primarily absorbed in the small intestine (10). And the list goes on…

So, in many ways, the changes that occur in and on your body are similar to those that have shaped the global ecosystem and human species. When environmental conditions change, those who were best able to adapt to the new conditions survive and pass their DNA along.

So, you can already see why there is no such thing as one single healthy microbiome.

When it comes to the gut microbiome, it’s essential to have a microbial community that is in sync with the diet you’re eating

The dynamic nature of the human microbiome is especially apparent when it comes to the gut ecosystem, a community that is shaped by the food we eat, drugs we take, air we breathe, etc. This means that a person eating a high-fiber vegetarian diet will have a very different combination of microbes in the gut compared to someone eating a carnivorous diet. And this is the way it should be. One of the most important keys to good health is to have a gut microbiome that is in sync with the diet you’re eating. The vegetarian eating massive amounts of plant food should have a gut community dominated by bacteria that are capable of degrading polysaccharides in his/her diet, and someone who eats a diet largely based on animal source food should have a gut community that is thoroughly adapted to that type of diet. Just imagine the difference between a native Eskimo eating a high-fat, low carbohydrate diet made up primarily of seafood and land mammals and a Kitavan Islander eating a high-carbohydrate diet composed of fruits, tubers, vegetables, and some fish.

Problems arise when there’s a mismatch between the diet we’re eating and the gut microbiome’s food degrading capabilities, which can occur from antibiotic use, excessive hygiene, and other factors associated with the modern western lifestyle. This type of perturbation can harm the overall community structure by allowing some types of opportunistic microbes to overgrow and/or wiping out key species.

In my recent article titled “The Unexpected Flaw of the Paleo Diet Phioloshophy” I talked about the role certain microorganisms play in the breakdown of gluten peptides, lactose, phytic acid, and other food ingredients that are often hard for the human host to digest. Essentially, different microbes and their DNA/enzymes are capable of degrading different types of compounds found in food. For example, someone eating a lot of gluten-containing grains “should have” bacteria in the upper GI tract that are capable of breaking down gluten peptides. However, as the western lifestyle is a master manipulator of the microbiome, this is not always the case, and consequently we see a rapid rise in gluten-related disorders (not the only reason).

Frequent dietary shifts can also provoke a diet-microbiome mismatch if the gut microbiome doesn’t have time to adapt. Yes, in terms of our microbial inhabitants, too much dietary variety doesn’t seem to be a good thing.  To bring this idea into a real life example, let’s consider the process that goes on when you introduce a new food into your diet. For simplicity’s sake, let’s say that food is a legume that contains plenty of indigestible (to the human host) carbohydrates. Initially, consumption of this legume typically leads to some type of gastrointestinal discomfort, such as bloating and/or flatulence. However, if you continue eating this food on a regular basis, the gut microbiota adapts, as it will provided it’s a relatively stable community, GI symptoms disappear, and we’ve reached a new equilibrium.

So, very frequent dietary shifts can lead to a gut microbiome that never manages to adapt. This is especially true for the western gut, which generally contains a less diverse community of microbes.

Most of the reasearch on the human microbiome has focused on the microbial communities in the gut. However, this adaptive response to changes in the environment also occurs everywhere else we harbor microorganisms. More and more research is coming out on the microbiome of the skin, vagina, lungs, and several other body site, and it will be very interesting to learn more about these ecosystems.

The simplified western microbiome

This dynamic nature of the gut microbiome is also one of the keys to understanding the increased microbial diversity in the hunter-gatherer microbiome compared to the westernized microbiome. While hunter-gatherers often (not always) eat a wide range of plant species on a regular basis, the typical diet of someone in the western world is largely made up of refined grains, dairy products, and vegetable oils. Not only does this type of diet promote a “simplified” gut microbiome, but these foods are primarily absorbed in the small intestine and therefore never each the microbial reactor in the colon.

Besides these major differences, we also have to remember that plants (and to a certain extent other foods) eaten in its natural, raw form come with a wide spectrum of microorganisms clinging to the leaves and roots. It’s therefore no doubt that hunter-gatherers and many rural populations ingest plenty of soil-based organisms from the food they eat. One might expect that this type of behaviour would lead to frequent infections from foodborne pathogens, but this is not what’s being reported in the literature. One the contrary, the dirtiness of the ancestral lifestyle seems to be one of the key reasons hunter-gatherers have such robust and diverse microbiomes. However, given that our environment and food production techniques in the modern world are very different from that of ancestral humans, this doesn’t suggest that we should abandon all food hygiene practises.


The second genome adapts to changes in environment and lifestyle, and this dynamic nature of the microbial communities explains why there doesn’t exist such a thing as a single “perfect” microbiome. The perfect microbiome for you is a microbiome that is perfectly adapted to your environment/lifestyle. When it comes to the gut microbiome, the most important thing is to have a diet and bacterial community that are in sync. However, this definitely doesn’t mean that all diets/lifestyles are the same. We want to live in a way that promotes a diverse and robust microbiome where “beneficial bacteria” dominate.


  1. Hi Eirik

    What would you do to have a good microbiome in an industrialized city?
    Do you recommend a supplement of fructooligosaccharides? Which one?

  2. Fantastic as always Eric. I learn so much reading your stuff. Your taking me to school!

  3. Also check out this TRX workouts http://www.99suspensiontraining.com

  4. Hi Eirik,

    Good job

    Thank you very much.


  1. […] Why There is No Single Healthy Microbiome – Erik Garnas – Organic Fitness […]

  2. […] about, the gut microbiota – the collection of microorganisms that live in the gut – adapts to changes in environment and lifestyle. For example, if you change from a low-carb diet rich in animal source food to a high-carbohydrate […]

  3. […] host is only able to break down some of the food ingredients we eat (e.g., starch, simple sugars), the gut microbiome can adapt to break down a wide range of food ingredients. It therefore doesn’t come as a surprise that lack of microbial diversity (“western […]

  4. […] about, the gut microbiota – the collection of microorganisms that live in the gut – adapts to changes in environment and lifestyle. For example, if you change from a low-carb diet rich in animal source food to a high-carbohydrate […]

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